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Gokara M, Yusuf Zamal M, Lavudiya VS, Subramanyam R. Deciphering the binding mechanism of gingerol molecules with plasma proteins: implications for drug delivery and therapeutic potential. J Biomol Struct Dyn 2024:1-18. [PMID: 38305837 DOI: 10.1080/07391102.2024.2310795] [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: 07/30/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
Ginger is a highly valued herb, renowned globally for its rich content of phenolic compounds. It has been traditionally used to treat various health conditions such as cardiovascular diseases, digestive issues, migraines, Alzheimer's disease, tumor reduction and chronic inflammation. Despite its potential medicinal applications, the therapeutic effectiveness of ginger is hindered by its limited availability and low plasma concentration levels. In this study, we explored the interaction of ginger's primary phenolic compounds, specifically 6-gingerol (6 G), 8-gingerol (8 G) and 10-gingerol (10 G), with plasma proteins which are human serum albumin (HSA) and α-1-acid glycoprotein (AGP). These two plasma proteins significantly influence drug distribution and disposition as they are key binding sites for most drugs. Fluorescence emission spectra indicated strong binding of 6, 8 and 10 G with HSA, with binding constants of 2.03 ± 0.01 × 104 M-1, 4.20 ± 0.01 × 104 M-1 and 6.03 ± 0.01 × 106 M-1, respectively. However, the binding of gingerols with AGP was found to be negligible. Molecular displacement by site-specific probes and molecular docking analyses revealed that gingerols bind at the IIA domain, with stability provided by hydrogen bonds, van der Waals forces, conventional hydrogen bonds, carbon-hydrogen bonds, alkyl and Pi-alkyl interactions. Further, the partial unfolding of the protein was observed upon binding the gingerol compound with HSA. In addition, molecular dynamic simulations demonstrated that gingerols remained stable in the subdomain IIA over 100 ns. This stability, coupled with Molecular Mechanics Generalized Born Surface Area indicating free energies of -43.765, -57.504 and -66.69 kcal/mol for 6, 8 and 10 G, respectively, reinforces the robust binding potential of these compounds. Circular dichroism studies suggested that the interaction of gingerols leads to the minimal transformation of HSA secondary structure, with the pattern being 10 G > 8 G > 6 G, a finding further substantiated by root mean square deviation and root mean square fluctuation fluctuations. These results propose that HSA has a stronger affinity to gingerols than AGP, which could have significant implications on the therapeutic circulating levels of gingerols.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahesh Gokara
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Mohammad Yusuf Zamal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vijay Srinivas Lavudiya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Vesović M, Jelić R, Nikolić M, Nedeljković N, Živanović A, Bukonjić A, Mrkalić E, Radić G, Ratković Z, Kljun J, Tomović D. Investigation of the interaction between S-isoalkyl derivatives of the thiosalicylic acid and human serum albumin. J Biomol Struct Dyn 2024:1-14. [PMID: 38192057 DOI: 10.1080/07391102.2024.2301745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
S-isoalkyl derivatives of thiosalicylic acid (isopropyl-(L1), isobutyl-(L2) and isoamyl-(L3)) were selected in order to investigate the binding interaction with the human serum albumin (HSA) using different spectroscopic methods and molecular docking simulation. Association constants and number of binding sites were used to analyze the quenching mechanism. The experimental results showed that the fluorescence quenching of HSA by L1, L2 and L3 occurs because of static quenching and that binding processes were spontaneous, with the leading forces in bonding by hydrogen bonding, hydrophobic interactions, and electrostatic interactions. Fluorescence spectroscopy, UV-Vis spectroscopy and synchronous fluorescence spectroscopy showed that ligands (L1, L2 and L3) can bind to HSA and that the binding of ligands induced some microenvironmental and conformational changes in HSA. The calculated distance between the donor and the acceptor according to fiFörster's theory confirms the energy transfer efficiency between the acceptor and HSA. Results of site marker competitive experiments showed that the tested compounds bind to HSA in domain IIA (Site I). Molecular dynamics and docking calculations demonstrated that L3 binds to the Sudlow site I of HSA with lower values of binding energies compared to L1 and L2, indicating the formation of the most stable ligand-HSA complex. Understanding the binding mechanisms of S-isoalkyl derivatives of the thiosalicylic acid to HSA may provide valuable data for the future studies of their biological activity and application as potential antitumor drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Marina Vesović
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Ratomir Jelić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Miloš Nikolić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Nikola Nedeljković
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Ana Živanović
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Andriana Bukonjić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Emina Mrkalić
- University of Kragujevac, Institute for Information Technologies, Department of Science, Jovana Cvijića bb, Kragujevac, Serbia
| | - Gordana Radić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
| | - Zoran Ratković
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, Kragujevac, Serbia
| | - Jakob Kljun
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana, Slovenia
| | - Dušan Tomović
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac, Serbia
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Yelamanda Rao K, Jeelan Basha S, Monika K, Naidu Gajula N, Sivakumar I, Kumar S, Vadde R, Aramati BMR, Subramanyam R, Damu AG. Development of quinazolinone and vanillin acrylamide hybrids as multi-target directed ligands against Alzheimer's disease and mechanistic insights into their binding with acetylcholinesterase. J Biomol Struct Dyn 2023; 41:11148-11165. [PMID: 37098803 DOI: 10.1080/07391102.2023.2203255] [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: 07/29/2022] [Accepted: 12/13/2022] [Indexed: 04/27/2023]
Abstract
In view of Multi-Target Directed Ligand (MTDL) approach in treating Alzheimer's Disease (AD), a series of novel quinazolinone and vanillin cyanoacetamide based acrylamide derivatives (9a-z) were designed, synthesized, and assessed for their activity against a panel of selected AD targets including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), amyloid β protein (Aβ), and also 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and neuroprotective activities. Five of the target analogs 9e, 9h, 9 l, 9t and 9z showed elevated AChE inhibitory activity with IC50 values of 1.058 ± 0.06, 1.362 ± 0.09, 1.434 ± 0.10, 1.015 ± 0.10, 1.035 ± 0.02 µM respectively, high inhibition selectivity against AChE over BChE and good DPPH radical scavenging activity. Enzyme kinetic studies of the potent hybrids in the series disclosed their mixed inhibition approach. Active analogs were found to be non-toxic on SK-N-SH cell lines and have excellent neuroprotective effects against H2O2-induced cell death. Strong modulating affinities on Aβ aggregation process were observed for most active compounds since; they irretrievably interrupted the morphology of Aβ42 fibrils, increased the aggregates and declined the Aβ-induced toxicity in neurons. From the fluorescence emission studies, the binding constants (K) were determined as 2.5 ± 0.021x103, 2.7 ± 0.015x103, 3.7 ± 0.020x103, 2.4 ± 0.013x104, and 5.0 ± 0.033x103 M-1 and binding free energies as -5.82 ± 0.033, -6.07 ± 0.042, -6.26 ± 0.015, -7.71 ± 0.024, and -6.29 ± 0.026 kcal M-1 for complexes of AChE-9e, 9h, 9 l, 9t and 9z, respectively. Moreover, the CD analysis inferred the limited modifications in the AChE secondary structure when it binds to 9e, 9h, 9 l, 9t and 9z. On the basis of docking studies against AChE, the most active congeners were well oriented in the enzyme's active site by interacting with both catalytic active site (CAS) and peripheral anionic site (PAS). In summary, these quinazolinone and vanillin acrylamide hybrid analogs can be used as promising molecular template to further explore their in vivo efficiency in the development of lead compound to treat AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kandrakonda Yelamanda Rao
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Shaik Jeelan Basha
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Kallubai Monika
- Department of Biochemistry, Rayalaseema University, Kurnool, Andhra Pradesh, India
| | - Navya Naidu Gajula
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Irla Sivakumar
- Soft Condensed Matter, Raman Research Institute, Sadashivanagar, Bangalore, India
| | - Sandeep Kumar
- Soft Condensed Matter, Raman Research Institute, Sadashivanagar, Bangalore, India
- Department of Chemistry, Nitte Meenakshi Institute of Technology, Yelahanka, Bangalore, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Amooru Gangaiah Damu
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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Zhao T, Yang B, Ji S, Luo J, Liu Y, Zhong Y, Lu B. Effects of the structure and interaction force of phytosterol/whey protein isolate self-assembly complex on phytosterol digestion properties. Food Chem 2023; 403:134311. [DOI: 10.1016/j.foodchem.2022.134311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/30/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022]
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Yelamanda Rao K, Jeelan Basha S, Monika K, Sreelakshmi M, Sivakumar I, Mallikarjuna G, Yadav RM, Kumar S, Subramanyam R, Damu AG. Synthesis and anti-Alzheimer potential of novel α-amino phosphonate derivatives and probing their molecular interaction mechanism with acetylcholinesterase. Eur J Med Chem 2023; 253:115288. [PMID: 37031527 DOI: 10.1016/j.ejmech.2023.115288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Abstract
Pleiotropic interference may be a prerequisite for the efficient limitation of the progression of multi-factorial diseases such as Alzheimer's disease (AD). Concept of designing the single chemical entity acting on two or more targets of interest has potential advantage in AD therapy. In line with this, rational design and synthesis of frame work of hybrids bearing 2,3-disubstituted quinazolinone, vanillin and α-amino phosphonate scaffolds (5a─v) were carried out. A congeneric set of twenty-two synthetic derivatives (5a─v) were evaluated for their cholinesterase inhibitory, antioxidant, DNA nicking, DNA protection, neuroprotective and Aβ aggregation modulatory activities. Amongst tested activities, the most significant and worth mentioning is that the analogues 5m, 5p and 5u were found to be the most potent, selective, and mixed type inhibitors of EeAChE with IC50 values of 0.296 ± 0.030, 0.289 ± 0.027, and 0.306 ± 0.028 μM, respectively. Further, the biophysical approaches indicated that the compounds 5m, 5p, and 5u have a strong binding affinity towards AChE. Kinetic and Molecular docking studies have revealed that the most active congeners were well oriented in the AChE active site by interacting with both catalytic active site (CAS) and peripheral anionic site (PAS). A few parameters derived from molecular dynamics (MD) simulation trajectories emphasized the stability of AChE-5p and 5m complexes throughout the 100 ns simulations, and the local conformational changes of the residues of AChE validate the stability of AChE-5p and 5m complexes. Further, these derivatives significantly impacted ABTS radical scavenging capacities and maximal DNA protection activity. Importantly, Thioflavin T (ThT) assay and FE-SEM study demonstrated compounds 5m, 5p and 5u as effective Aβ1-42 fibril modulators at molecular level by the formation of micro size co-assembled mature structures, thus efficiently abolishing the cytotoxicity of Aβ1-42. Finally, these active compounds are determined to be non-toxic and highly neuroprotective against H2O2-induced cell death in SK-N-SH cell lines. Furthermore, in silico ADMET prediction studies have revealed that the targeted analogues satisfied most of the characteristics of CNS acting drugs. These multi-functional efficacies indicated worthiness of these α-amino phosphonate derivatives being chosen for further pharmacokinetics, toxicity, and behavioral research to test their potential for AD treatment.
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Bhardwaj BK, Venkatesh T, Suresh PS. Study on the interaction of the bromodomain inhibitor JQ1 with human serum albumin by spectroscopic and molecular docking studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Ahmad F, Lakshmi PTV, Arunachalam A. An in silico comparative study of curcumin and 2-deoxyuridine nucleoside derivatives: Reveals the role of angiogenin in ER stress-induced apoptosis signaling. Chem Biol Drug Des 2022; 101:1048-1081. [PMID: 36412086 DOI: 10.1111/cbdd.14184] [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: 10/31/2021] [Revised: 09/06/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Angiogenin (ANG) protein plays a crucial role in angiogenesis, neovascularization, and cancer metastasis in NSCLC (non-small cell lung cancer) via non-coding tiRNA. It protects the cell under ER (endoplasmic reticulum) stress-induced apoptosis through the translational reprogramming process. Although B82 (Curcumin derivatives) induces ER stress-induced apoptosis, its mechanism of action was not studied. Therefore, it was hypothesized that the ribonucleolytic activity of ANG may be regulated by B82, resulting in modulated ER stress signaling for apoptosis. Hence, we designed and proposed a synthesis scheme for RNA-based anti-angiogenic derivatives of 2-deoxyuridine nucleoside forming peptide bond with amino acids like serine (Ser-3) and para-hydroxy-phenyl glycine (Normtyr-1) and compared B82 with them to know the binding affinity with ANG, anti-angiogenic potential, and its probable mechanism of anti-RNase activity through MD simulation study. Therefore, using Gromos96 43a1 and 43a2 force fields, MD simulation was performed to investigate binding affinity, ligand-induced molecular surface area change, conformational change, and dynamics of catalytic site residues to predict ligand binding to ANG in this study. The obtained binding free energy (∆Gbind ) result showed the total average ∆Gbind as -113.480 ± 1.682 (Normtyr-1) > -53.038 ± 33.069 (B82) > -27.909 ± 16.438 (Ser-3) kJ/mole specify role of B82 in regulating ER stress signaling induced apoptosis through ANG ribonucleolytic activity inhibition, suitability of 43a2 force fields and methodology in ligand screening. It shows the crucial role of Leu115 and His13 residue involvement in total ∆Gbind contribution. Hence, based on the MD result, novel conformation of catalytic residues, and ∆Gbind , a promising combination candidate could be proposed for metastatic NSCLC therapy.
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Affiliation(s)
- Faizan Ahmad
- Department of Bioinformatics, Pondicherry University, Pondicherry, India
| | | | - Annamalai Arunachalam
- PG and Research Department of Botany Arignar Anna Government Arts College Villupuram Tamil Nadu India
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Yue Y, Wang Y, Tu Q, Xu Y, Zhang Y, Tang Q, Liu J. A comprehensive insight into the effects of punicalagin on pepsin: Multispectroscopy and simulations methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Deep Fusion of Intelligent Meridian Sensing Technology and Huoluo Xiaoling Pills in the Treatment of Knee Osteoarthritis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8043674. [PMID: 36119920 PMCID: PMC9473892 DOI: 10.1155/2022/8043674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022]
Abstract
Based on the deep fusion of intelligent meridian sensing technology and Huoluo Xiaoling Pill (HXP) in the treatment of knee osteoarthritis (KOA), firstly, the effective components and targets of Salvia miltiorrhiza, Angelica sinensis, frankincense, and myrrh were obtained by using TCMSP, SwissADME, and Swisstarget databases. Similarly, relevant targets of KOA were collected through GeneCards, OMIM, TTD, PharmGKB, and DrugBank databases. Next, the potential targets of ZXP in the treatment of KOA were obtained by intersection of drug and disease targets. Finally, Cytoscape 3.7.1 software was used to construct a “disease-drug-component-target” network, and Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Gnomes (KEGG) signaling pathway enrichment analysis were performed on the core targets through Metascape website. A total of 99 active components and 203 corresponding potential therapeutic targets were obtained from the components of HXP. And KOA has 2543 potential therapeutic targets, of which 120 cross targets correspond to 120 active compounds in HXP. Then, topology analysis displayed that the six targets form the core PPI network. In addition, GO and KEGG enrichment analyses showed that these core targets were mainly enriched in inflammatory response, apoptosis, oxidation reaction, and other related pathways.
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Synthesis, characterization and investigating the binding mechanism of novel coumarin derivatives with human serum albumin: Spectroscopic and computational approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132366] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gan C, Liu Q, Zhang Y, Shi T, He WS, Jia C. A novel phytosterols delivery system based on sodium caseinate-pectin soluble complexes: Improving stability and bioaccessibility. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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S. A, V. S, R. S, V. S. Structural exploration of interactions of (+) catechin and (−) epicatechin with bovine serum albumin: Insights from molecular dynamics and spectroscopic methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Yeggoni DP, Rachamallu A, Subramanyam R. Comparative binding studies of bacosine with human serum albumin and α-1-acid glycoprotein biophysical evaluation and computational approach. J Pharm Biomed Anal 2021; 209:114478. [PMID: 34894460 DOI: 10.1016/j.jpba.2021.114478] [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] [Received: 06/17/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 01/25/2023]
Abstract
Bacosine (BAC) is a natural product isolated from a herb and used in the Ayurvedic system of medicine. It is reported to have a wide array of biological activities, which has generated interest in its therapeutic potential. To better understand how BAC may operate as a potential anti-cancer therapeutic, we examined its anti-cancer properties in the human breast cancer cell line, MCF-7. In order to get an idea of how it may behave in vivo, we also evaluated its interaction with human serum albumin (HSA) and α-1-acid glycoprotein (AGP) using fluorescence spectroscopy and in silico molecular modelling. Based on our in vitro studies, we found that BAC inhibited MCF-7 cell growth in a dose-dependent manner with an IC50 value of 9 µM. In addition, the intrinsic fluorescence of HSA and AGP was quenched by BAC, consistent with a static quenching mechanism. Fluorescence emission spectroscopy revealed a binding of 2.97 ± 0.01 × 104 M-1 for HSA-BAC which corresponded to a free energy change of - 6.07 kcal/mol at 25 °C. In addition, we found that BAC had a binding constant of 1.8 ± 0.02 × 103 M-1 to AGP which corresponded to a change in free energy - 4.42 kcal/mol at 25 °C. We also identified the site of BAC binding to the HSA protein using the site-specific marker, phenylbutazone, along with molecular docking studies. Circular dichroism spectra revealed partial changes in the secondary structure of HSA in the presence of BAC suggesting direct interactions. Molecular dynamics simulations demonstrated that the HSA-BAC complex reaches an equilibration state at around 4 ns, suggesting that the HSA-BAC complex is quite stable. Our results provide evidence that serum proteins can act as a carrier protein for BAC, potentially impacting its development as an anti-cancer agent.
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Affiliation(s)
- Daniel Pushparaju Yeggoni
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Aparna Rachamallu
- National Institute of Animal Biotechnology, Q City Road, Gachibowli, Hyderabad, Telangana 500032, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Shaik JB, Kandrakonda YR, Kallubai M, Gajula NN, Dubey S, Aramati BMR, Subramanyam R, Amooru GD. Deciphering the AChE-binding mechanism with multifunctional tricyclic coumarin anti-Alzheimer's agents using biophysical and bioinformatics approaches and evaluation of their modulating effect on Amyloidogenic peptide assembly. Int J Biol Macromol 2021; 193:1409-1420. [PMID: 34740688 DOI: 10.1016/j.ijbiomac.2021.10.204] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
Investigating the drug-AChE binding mechanism is vital in understanding its cogent use in medical practice against Alzheimer's disease (AD). The production and accumulation of oligomers of β-amyloid is a central event in the neuropathology of AD. Beside the inhibition of assembly process, modulation of the aggregation process of these proteins towards minimally toxic pathways may be a possible therapeutic strategy for AD. Hence, the present study aims to examine the effect of multifunctional fused tricyclic 7-hydroxy 4-methyl coumarin analogs (HMC1-5) on the self-induced aggregation of β-amyloid using Thioflavin T (ThT) assay, scanning electron microscopic study, AlamarBlue and immune blotting assays and also the binding mechanism with AChE by fluorescence emission, conformational, molecular docking and molecular dynamic simulation studies under physiological pH 7.4. The ThT assay, FE-SEM study, cell line and western blots establish that the HMC1-5 molecules could irreversibly disrupt preformed Aβ42 fibrils, accelerate the aggregates into micro size co-assembled structures, and effectively eliminate the cytotoxicity of Aβ1-42. Fluorescence emission studies indicating a strong binding affinity between HMC1-5 and AChE with the binding constants of 1.04 × 105, 3.57 × 104, 1.97 × 104, 3.07 × 104 and 2.95 × 104 M-1, respectively and binding sites number found to be 1. CD studies disclosed a partial unfolding in the secondary structure of AChE upon binding with HMC1-5. Docking analysis inferred that the HMC1-5 were bound through hydrophobic and hydrophilic interactions to the AChE active site. Molecular dynamics simulations emphasized the stability of AChE-HMC1-5 complexes throughout the 100 ns simulations, and the local conformational changes of the residues of AChE validate the stability of complexes. These results provide new and unique complementary approach for modulating the biological effects of the Aβ aggregates by coumarin analogs and new insights for further in vivo investigations as novel anti AD agents.
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Affiliation(s)
- Jeelan Basha Shaik
- Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | | | - Monika Kallubai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Navya Naidu Gajula
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Shreya Dubey
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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Chemometrics in investigation of small molecule-biomacromolecule interactions: A review. Int J Biol Macromol 2021; 181:478-493. [PMID: 33798569 DOI: 10.1016/j.ijbiomac.2021.03.184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/27/2021] [Indexed: 01/24/2023]
Abstract
Chemometrics is chemical discipline in which mathematical and statistical methods are coupled with chemical data to extract useful information which cannot be extracted by the use of conventional methods. When experimental techniques are assisted by chemometric methods, very interesting studies will be performed which enable us to obtain valuable information about the system under our study. Chemico-biological interactions are very useful studies which are performed to obtain information about binding of small molecules with biological macromolecules. Recently, these studies have been assisted by chemometric methods to perform advanced studies which can help us to have a deep insight to them. Literature survey showed us that multivariate analysis of the chemico-biological interactions is becoming popular and nowadays, chemometricians are using multivariate chemometric methods for resolving chemico-biological interactions. This article focuses on the works published in the literature to provide a background for those who are interested to work in this field and finally, the results will be discussed and concluded.
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Mrkalić E, Jelić R, Stojanović S, Sovrlić M. Interaction between olanzapine and human serum albumin and effect of metal ions, caffeine and flavonoids on the binding: A spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119295. [PMID: 33338934 DOI: 10.1016/j.saa.2020.119295] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/03/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
In this study, the binding of olanzapine (OLZ) to human serum albumin (HSA) and the influence of metal ions (Ca2+, Mg2+, Cu2+, Zn2+, Fe3+), caffeine (CAF) and flavonoids (diosmin (DIO), catechin (CAT), quercetin (QUE)), on their affinity, was investigated by fluorescence spectroscopy and UV-vis absorption spectroscopy. Fluorescence experiments suggest that OLZ quench the fluorescence of HSA through the mixed quenching mechanism and non-radiation energy transferring as a result of the HSA-OLZ complex formation. OLZ spontaneously bind in the site I on HSA, and according to thermodynamic parameters, the reaction was spontaneous and mainly driven by hydrogen bonds and van der Waals interactions. The presence of Mn+ ions, CAF, DIO and CAT decreased binding affinity between OLZ and HSA which indicates that they could compete against OLZ in the site I. Contrary, in the presence of QUE the binding affinity of the HSA-OLZ system enhanced, which may be explained by conformational changes in HSA (non-competitive interference).
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Affiliation(s)
- Emina Mrkalić
- University of Kragujevac, Institute for Information Technologies, Department of Science, Jovana Cvijića bb, Kragujevac 34000, Serbia
| | - Ratomir Jelić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac 34000, Serbia.
| | - Stefan Stojanović
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac 34000, Serbia
| | - Miroslav Sovrlić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, Kragujevac 34000, Serbia
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Jahanban-Esfahlan A, Roufegarinejad L, Tabibiazar M, Lorenzo J, Amarowicz R. Exploring the Interactions Between Caffeic Acid and Human Serum Albumin Using Spectroscopic and Molecular Docking Techniques. POL J FOOD NUTR SCI 2021. [DOI: 10.31883/pjfns/133203] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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18
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Dubey S, Kallubai M, Subramanyam R. Improving the inhibition of β-amyloid aggregation by withanolide and withanoside derivatives. Int J Biol Macromol 2021; 173:56-65. [PMID: 33465364 DOI: 10.1016/j.ijbiomac.2021.01.094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/11/2020] [Accepted: 01/14/2021] [Indexed: 12/01/2022]
Abstract
Here, we have studied the ameliorative effects of Withania somnifera derivatives (Withanolide A, Withanolide B, Withanoside IV, and Withanoside V) on the fibril formation of amyloid-β 42 for Alzheimer's disease. We analyzed reduction in the aggregation of β amyloid protein with these Ashwagandha derivatives by Thioflavin T assay in the oligomeric and fibrillar state. We have tested the cytotoxic activity of these compounds against human SK-N-SH cell line for 48 h, and the IC 50 value found to be 28.61 ± 2.91, 14.84 ± 1.45, 18.76 ± 0.76 and 30.14 ± 2.59 μM, respectively. After the treatment of the cells with half the concentration of IC 50 value, there was a remarkable decrease in the number of apoptotic cells stained by TUNEL assay indicating the DNA damage and also observed significant decrease of reactive oxygen species. Also, the binding and molecular stability of these derivatives with amyloid β was also studied using bioinformatics tools where these molecules were interacted at LVFFA region which is inhibition site of amyloid-β1 42. These studies revealed that the Withanolides and Withanosides interact with the hydrophobic core of amyloid-β 1-42 in the oligomeric stage, preventing further interaction with the monomers and diminishing aggregation.
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Affiliation(s)
- Shreya Dubey
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana 500046, India
| | - Monika Kallubai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana 500046, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana 500046, India.
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Kheirdoosh F, Kashanian S, Khodaei MM, Sariaslani M, Falsafi M, Moghadam NH, Salehzadeh S, Pazhavand M, Kashanian M. Spectroscopic studies on the interaction of aspartame with human serum albumin. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:300-316. [PMID: 33455539 DOI: 10.1080/15257770.2021.1872792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this work the binding of artificial sweetener aspartame with human serum albumin (HSA) was studied at physiological pH. Binding studies of aspartame (APM) with HSA are useful to understand APM -HSA interaction, mechanism and providing guidance for the application and design of new and more efficient artificial sweeteners. The interaction was investigated by spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD) techniques. The results indicated that the binding of APM to HSA caused fluorescence quenching of HSA through static quenching mechanism with binding constant 1.42 × 10+4 M-1 at 298 K and the number of binding sites is approximately one. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be -41.20 kJ mol-1 and -58.19 J mol-1 K-1, respectively, according to van't Hoff equation, which indicated that reaction is enthalpically driven. Quenching of the fluorescence of HSA was found to be a static quenching process. The binding constants and number of binding sites were obtained at three different temperatures (298, 308 and 318 K). Combining above results and those of spectrofluorometric competition experiment and circular dichroism (CD), indicated that APM binds to HSA via Sudlow's site I. Furthermore, the study of molecular docking on HSA binding also indicated that APM can strongly bind to the site I (subdomain IIA) of HSA mainly by hydrophobic interaction and hydrogen bond interactions exist between APM and HSA.
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Affiliation(s)
- Fahimeh Kheirdoosh
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Soheila Kashanian
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Nano drug delivery research center, Kermanshah University of medical sciences, Kermanshah, Iran
| | - Mohammad Mehdi Khodaei
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Mahya Sariaslani
- School of Paramedical, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Monireh Falsafi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | | | | | - Mahsa Pazhavand
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Mahdi Kashanian
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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20
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Ortiz‐Escarza JM, Medina ME, Trigos A. On the peroxyl radical scavenging ability of β‐sitosterol in lipid media: A theoretical study. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Manuel E. Medina
- Centro de Investigación en Micología Aplicada Universidad Veracruzana Xalapa Mexico
| | - Angel Trigos
- Centro de Investigación en Micología Aplicada Universidad Veracruzana Xalapa Mexico
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21
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Ganorkar K, Mukherjee S, Singh P, Ghosh SK. Stabilization of a potential anticancer thiosemicarbazone derivative in Sudlow site I of human serum albumin: In vitro spectroscopy coupled with molecular dynamics simulation. Biophys Chem 2020; 269:106509. [PMID: 33302053 DOI: 10.1016/j.bpc.2020.106509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022]
Abstract
Human Serum Albumin (HSA) is the most important protein in human blood plasma and can acts as a major transporting agent for various drug molecules with flexible binding interaction. To elucidate the interaction of a newly designed potential anticancer thiosemicarbazone based luminophore (E)-1-(4-(diethylamino)-2-hydroxybenzylidene)-4,4-dimethyl-thiosemicarbazide (DAHTS) with HSA under physiological condition, in vitro optical spectroscopic experiments viz UV-Vis absorption, steady state fluorescence, fluroscence anisotropy, time resolved fluorscence (TRF) and cicular dichroism (CD) spectroscopy have been scrutinised. The experimental findings have been corroborated with in silico molecular docking analysis and Molecular Dynamics (MD) simulation. The spectroscopic results demonstrated that the conventionally anion-favouring Sudlow site I of HSA copiously adapt neutral DAHTS molecule with moderate binding affinity. The mean fluorescence lifetime of the sole tryptophan (Trp-214) present in the macromolecule experiences an appreciable diminution with an increase in concentration of the synthesized molecule. DAHTS localize itself close to Trp-214 within subdomain IIA (Sudlow site I) and surrounded by multiple hydrophobic amino acid residues (Val-235, Val-231, Ala-229, Phe-228, Val-325, Phe-326, Leu-327, Met-329, Phe-330, Leu-331, Tyr-332, Leu-346, Leu-347, Val-482, Leu-349, Ala-350, Ala-210, Trp-214, Ala- 213 and Val-216) in HSA. The distinct fluorescence lifetime, diverse pathways and changing rate of population indicates that the rotamerisation of Trp-214 residue is controlled by the guest molecule. Sudlow site I of HSA behaves flexibly and induces an allosteric modulation in the macromolecule resulting a minor deformation in the protein secondary structure as observed in CD (observed 11% change of α-helix content) as well as in MD simulation. The integrated multi-spectroscopic research described herein provides several important information about the binding interaction of a thiosemicarbazone Schiff base with HSA, which can be very significant for thiosemicarbazone based drug designing for academia as well as industry.
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Affiliation(s)
- Kapil Ganorkar
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Soham Mukherjee
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850, USA
| | - Piyush Singh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India
| | - Sujit Kumar Ghosh
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, Maharashtra 440010, India.
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22
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Liang Z, Sun Y, Zeng H, Sun K, Yang R, Li Z, Zhang K, Chen X, Qu L. Simultaneous Detection of Human Serum Albumin and Sulfur Dioxide in Living Cells Based on a Catalyzed Michael Addition Reaction. Anal Chem 2020; 92:16130-16137. [DOI: 10.1021/acs.analchem.0c03806] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zengqiang Liang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yuanqiang Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Huajin Zeng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kai Sun
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Ran Yang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xiaolan Chen
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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23
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Nayarisseri A, Khandelwal R, Madhavi M, Selvaraj C, Panwar U, Sharma K, Hussain T, Singh SK. Shape-based Machine Learning Models for the Potential Novel COVID-19 Protease Inhibitors Assisted by Molecular Dynamics Simulation. Curr Top Med Chem 2020; 20:2146-2167. [PMID: 32621718 DOI: 10.2174/1568026620666200704135327] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/20/2020] [Accepted: 04/25/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The vast geographical expansion of novel coronavirus and an increasing number of COVID-19 affected cases have overwhelmed health and public health services. Artificial Intelligence (AI) and Machine Learning (ML) algorithms have extended their major role in tracking disease patterns, and in identifying possible treatments. OBJECTIVE This study aims to identify potential COVID-19 protease inhibitors through shape-based Machine Learning assisted by Molecular Docking and Molecular Dynamics simulations. METHODS 31 Repurposed compounds have been selected targeting the main coronavirus protease (6LU7) and a machine learning approach was employed to generate shape-based molecules starting from the 3D shape to the pharmacophoric features of their seed compound. Ligand-Receptor Docking was performed with Optimized Potential for Liquid Simulations (OPLS) algorithms to identify highaffinity compounds from the list of selected candidates for 6LU7, which were subjected to Molecular Dynamic Simulations followed by ADMET studies and other analyses. RESULTS Shape-based Machine learning reported remdesivir, valrubicin, aprepitant, and fulvestrant as the best therapeutic agents with the highest affinity for the target protein. Among the best shape-based compounds, a novel compound identified was not indexed in any chemical databases (PubChem, Zinc, or ChEMBL). Hence, the novel compound was named 'nCorv-EMBS'. Further, toxicity analysis showed nCorv-EMBS to be suitable for further consideration as the main protease inhibitor in COVID-19. CONCLUSION Effective ACE-II, GAK, AAK1, and protease 3C blockers can serve as a novel therapeutic approach to block the binding and attachment of the main COVID-19 protease (PDB ID: 6LU7) to the host cell and thus inhibit the infection at AT2 receptors in the lung. The novel compound nCorv- EMBS herein proposed stands as a promising inhibitor to be evaluated further for COVID-19 treatment.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India,Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd., Mahalakshmi Nagar, Indore-452010, Madhya
Pradesh, India,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia,Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad-500001, Telangana State, India
| | - Chandrabose Selvaraj
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore-452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia,Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King
Saud University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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24
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Fabrication and characterization of water-soluble phytosterol ester nanodispersion by emulsification-evaporation combined ultrasonic method. J FOOD ENG 2020. [DOI: 10.1016/j.jfoodeng.2019.109895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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25
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Stojanović SD, Nićiforović JM, Živanović SM, Odović JV, Jelić RM. Spectroscopic studies on the drug–drug interaction: the influence of fluoroquinolones on the affinity of tigecycline to human serum albumin and identification of the binding site. MONATSHEFTE FUR CHEMIE 2020. [DOI: 10.1007/s00706-020-02627-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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26
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Luo M, Sui Y, Tian R, Lu N. Formation of a bovine serum albumin diligand complex with rutin for the suppression of heme toxicity. Biophys Chem 2020; 258:106327. [DOI: 10.1016/j.bpc.2020.106327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 12/13/2022]
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27
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Wang Y, Liu T, Ma F, Lu X, Mao H, Zhou W, Yang L, Li P, Zhan Y. A Network Pharmacology-Based Strategy for Unveiling the Mechanisms of Tripterygium Wilfordii Hook F against Diabetic Kidney Disease. J Diabetes Res 2020; 2020:2421631. [PMID: 33274236 PMCID: PMC7695487 DOI: 10.1155/2020/2421631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/01/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Diabetic kidney disease (DKD) poses a major public-health burden globally. Tripterygium wilfordii Hook F (TwHF) is a widely employed herbal medicine in decreasing albuminuria among diabetic patients. However, a holistic network pharmacology strategy to investigate the active components and therapeutic mechanism underlying DKD is still unavailable. METHODS We collected TwHF ingredients and their targets by traditional Chinese Medicine databases (TCMSP). Then, we obtained DKD targets from GeneCards and OMIM and collected and analyzed TwHF-DKD common targets using the STRING database. Protein-protein interaction (PPI) network was established by Cytoscape and analyzed by MCODE plugin to get clusters. In addition, the cytoHubba software was used to identify hub genes. Finally, all the targets of clusters were subjected for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses via DAVID. RESULTS A total of 51 active ingredients in TwHF were identified and hit by 88 potential targets related to DKD. Compounds correspond to more targets include kaempferol, beta-sitosterol, stigmasterol, and Triptoditerpenic acid B, which appeared to be high-potential compounds. Genes with higher degree including VEGFA, PTGS2, JUN, MAPK8, and HSP90AA1 are hub genes of TwHF against DKD, which are involved in inflammation, insulin resistance, and lipid homeostasis. Kaempferol and VEGFA were represented as the uppermost active ingredient and core gene of TwHF in treating DKD, respectively. DAVID results indicated that TwHF may play a role in treating DKD through AGE-RAGE signaling pathway, IL-17 signaling pathway, TNF signaling pathway, insulin resistance, and calcium signaling pathway (P < 0.05). CONCLUSION Kaempferol and VEGFA were represented as the uppermost active ingredient and core gene of TwHF in treating DKD, respectively. The key mechanisms of TwHF against DKD might be involved in the reduction of renal inflammation by downregulating VEGFA.
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Affiliation(s)
- Yuyang Wang
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Tongtong Liu
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
| | - Fang Ma
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
| | - Xiaoguang Lu
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
| | - Huimin Mao
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
| | - Weie Zhou
- Beijing Key Laboratory for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing 100029, China
| | - Liping Yang
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
| | - Ping Li
- Beijing Key Laboratory for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yongli Zhan
- Department of Nephrology, Guang'anmen Hospital of China Academy of Traditional Chinese Medical Sciences, Beijing 100053, China
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28
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Chadha N, Singh D, Milton MD, Mishra G, Daniel J, Mishra AK, Tiwari AK. Computational prediction of interaction and pharmacokinetics profile study for polyamino-polycarboxylic ligands on binding with human serum albumin. NEW J CHEM 2020. [DOI: 10.1039/c9nj05594k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human serum albumin (HSA) is one of the most abundant plasma proteins available in blood and responsible for transport of fatty acids, drugs and metabolites at its binding sites which are very important for the assessment of pharmacokinetics profile of the polyamino-polycarboxylic ligands.
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Affiliation(s)
- Nidhi Chadha
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
- Department of Chemistry
| | - Dushyant Singh
- Department of Chemistry
- Christ Church P. G. College
- C S J M University
- Kanpur
- India
| | | | - Gauri Mishra
- Department of Zoology
- Swami Shraddhanand College
- University of Delhi
- Delhi 110036
- India
| | - Joseph Daniel
- Department of Chemistry
- Christ Church P. G. College
- C S J M University
- Kanpur
- India
| | - Anil K. Mishra
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
| | - Anjani K. Tiwari
- Division of Cyclotron and Radiopharmaceutical Sciences
- Institute of Nuclear Medicine and Allied Sciences
- Delhi 110054
- India
- Department of Chemistry
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29
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Ansari A, Ali A, Asif M. Steroidal thiazolidinone derivatives: Design, synthesis and their molecular interaction with human serum albumin. Steroids 2019; 148:99-113. [PMID: 31082411 DOI: 10.1016/j.steroids.2019.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
A series of steroidal thiazolidinone derivatives have been synthesized through one-pot multicomponent reaction involving steroidal ketone, thiosemicarbazide/methyl-thiosemicarbazide and DMAD in presence of AlCl3 as a Lewis acid catalyst. Among all the synthesized steroidal thiazolidinone derivatives, compound 7-9 (ST 7-9) were investigated for their in vitro molecular interaction with human serum albumin. Intrinsic fluorescence spectroscopy, constant wavelength synchronous fluorescence spectroscopy, circular dichroism and UV-visible absorption techniques have been exploited to characterize the binding phenomena in phosphate buffer solution at pH 7.4. The experimental results indicated that ST 7-9 bind to HSA and the intrinsic fluorescence of HSA was quenched through static quenching mechanism. The binding parameters were calculated and the binding constants obtained were 1.44 × 105 M-1 for ST 7, 0.84 × 105 M-1 for ST 8 and 1.06 × 105 M-1 for ST 9. Circular dichroism analysis confirms that the presence of ST 7-9, altered the secondary structure of HSA due to partial unfolding of the polypeptide chain. Furthermore, hemolytic activity assay demonstrated that the synthesized steroidal thiazolidinone derivatives have good compatibility towards human red blood cells. Finally, molecular docking studies revealed that the steroidal thiazolidinones can bind in the hydrophobic cavity of HSA, by hydrophobic and hydrogen bonding interaction. These results provided valuable information about the binding mechanism of ST 7-9 with HSA and play a pivotal role in the development of steroidal heterocycle inspired compounds.
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Affiliation(s)
- Anam Ansari
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Abad Ali
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Organometallic Synthesis and Catalysis Group, Chemical Engineering Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411 008, Maharashtra, India
| | - Mohd Asif
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
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30
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Sasmal M, Islam ASM, Bhowmick R, Maiti D, Dutta A, Ali M. Site-Selective Interaction of Human Serum Albumin with 4-Chloro-7-nitro-1,2,3-benzoxadiazole Modified Olanzapine Derivative and Effect of β-Cyclodextrin on Binding: In the Light of Spectroscopy and Molecular Docking. ACS APPLIED BIO MATERIALS 2019; 2:3551-3561. [DOI: 10.1021/acsabm.9b00429] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mihir Sasmal
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Abu Saleh Musha Islam
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Rahul Bhowmick
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Debjani Maiti
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Ananya Dutta
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
| | - Mahammad Ali
- Department of Chemistry, Jadavpur University, 188, Raja S. C. Mullick Road, Kolkata 700 032, India
- Vice-Chancellor, Aliah University, ll-A/27, Action Area II, Newtown, Kolkata, West Bengal 700160, India
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31
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Synthesis and biological evaluation of flavone-8-acrylamide derivatives as potential multi-target-directed anti Alzheimer agents and investigation of binding mechanism with acetylcholinesterase. Bioorg Chem 2019; 88:102960. [DOI: 10.1016/j.bioorg.2019.102960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/18/2019] [Accepted: 04/28/2019] [Indexed: 01/10/2023]
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Dubey S, Madana SK, Kallubai M, Sarkar A, Subramanyam R. Unraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach. J Biomol Struct Dyn 2019; 38:1927-1937. [PMID: 31099311 DOI: 10.1080/07391102.2019.1620127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Most of the drugs binding to human serum albumin (HSA) are transported to various parts of the body. Here, we have studied the molecular interaction between HSA and synthesized uridine derivatives, 1-[(3R, 4S, 5 R)-2-methyl-3, 4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dion.)(C-MU); [(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxy-4-methyl-tetrahydrofuran-2-yl] methyl methyl phosphochloridate (CM-MU) and [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-2-methyl-3,4-dihydroxyoxolan-2-yl] methyl dihydrogen phosphate (P-MU). Cytotoxic studies of these synthesized compounds with mouse macrophages (RAW 246.7) and HeLa cells (human cervical cancer cells) and binding mechanism of these uridine derivatives with HSA were performed. Subsequently, fluorescence quenching was observed upon titration of uridine derivatives with HSA via static mode of quenching, and the binding constants (K2-C-MU = 4 ± 0.03 × 104M-1, K5-CM-MU = 1.95 ± 0.03 × 104 M-1 and K5-P-MU =1.56 ± 0.03 × 104 M-1) were found to be in sync with the computational results. Further, molecular displacement and molecular docking data revealed that all the derivatives are binding in the subdomain IIA and IIB regions of HSA. The protein secondary structure of complexes was determined by circular dichroism, indicating partial unfolding of the protein upon addition of the uridine derivatives. Furthermore, atomic force microscopy data reveal the change in topology upon binding of 2-C-MU, 5-CM-MU and 5-P-MU with HSA, indicating change in the microenvironment around tryptophan region. Additionally, cytotoxicity studies on HeLa and Raw Cell lines suggested that these molecules have significant anti-proliferative and anti-inflammatory properties. Hence, the study may be of help for development of new drugs based on uridine derivatives which may be helpful for combating various potential diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shreya Dubey
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Suneel Kumar Madana
- Department of Chemistry, Periyar Maniammai Institute of Science & Technology, Thanjavur, India
| | - Monika Kallubai
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Arijit Sarkar
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Rajagopal Subramanyam
- Department of Plant Science, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
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33
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Nagati V, Nakkka S, Yeggoni DP, Subramanyam R. Forskolin-loaded human serum albumin nanoparticles and its biological importance. J Biomol Struct Dyn 2019; 38:1539-1550. [PMID: 31057091 DOI: 10.1080/07391102.2019.1614481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, forskolin-loaded human serum albumin nanoparticles (FR-HSANPs) were successfully prepared by incorporation and affinity-binding methods. FR-HSANPs were characterized by transmission electron microscope that most of them are circular in shape and size is around 340 nm. The drug loading was more than 88% and further sustained release profiles were observed as it is 77.5% in 24 h time. Additionally, the cytotoxicity results with HepG2 cells indicated that FR-HSANPs showed significantly higher cytotoxicity and lower cell viability as compared to free forskolin (FR). Furthermore, to understand the binding mechanism of human serum albumin (HSA) with forskolin resulted from fluorescence quenching as a static mechanism and the binding constant is 6.26 ± 0.1 × 104 M-1, indicating a strong binding affinity. Further, association and dissociation kinetics of forskolin-HSA was calculated from surface plasmon resonance spectroscopy and the binding constant found to be Kforskolin = 3.4 ± 0.24 × 104 M-1 and also fast dissociation was observed. Further, we used circular dichroism and molecular dynamics simulations to elucidate the possible structural changes including local conformational changes and rigidity of the residues of both HSA and HSA-forskolin complexes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veerababu Nagati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sailaja Nakkka
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Jaunet-Lahary T, Vercauteren DP, Fleury F, Laurent AD. Computational simulations determining disulfonic stilbene derivative bioavailability within human serum albumin. Phys Chem Chem Phys 2019; 20:18020-18030. [PMID: 29931001 DOI: 10.1039/c8cp00704g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Disulfonic stilbene (DS) derivatives are a member of the large family of compounds widely employed in medicine and biology as modulators for membrane transporters or inhibitors of a protein involved in DNA repair. They constitute interesting compounds that have not yet been investigated within the bioavailability framework. No crystallographic structures exist involving such compounds embedded in the most common drug carrier, human serum albumin (HSA). The present work studies, for the first time, the physico-chemical features driving the inclusion of three DS derivatives (amino, nitro and acetamido, named DADS, DNDS and DATDS, respectively) within the four common HSA binding sites using combined molecular docking and molecular dynamics simulations. A careful analysis of each ligand within each of the studied binding sites is carried out, highlighting specific interactions and key residues playing a role in stabilizing the ligand within each pocket. The comparison between DADS, DNDS and DATDS reveals that depending on the binding site, the conclusions are rather different. For instance, the IB binding site shows a specificity to DADS compounds while IIIA is the most favorable site for DNDS and DATDS.
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Affiliation(s)
- Titouan Jaunet-Lahary
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
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Dietary Sargassum fusiforme improves memory and reduces amyloid plaque load in an Alzheimer's disease mouse model. Sci Rep 2019; 9:4908. [PMID: 30894635 PMCID: PMC6426980 DOI: 10.1038/s41598-019-41399-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 03/05/2019] [Indexed: 12/12/2022] Open
Abstract
Activation of liver X receptors (LXRs) by synthetic agonists was found to improve cognition in Alzheimer's disease (AD) mice. However, these LXR agonists induce hypertriglyceridemia and hepatic steatosis, hampering their use in the clinic. We hypothesized that phytosterols as LXR agonists enhance cognition in AD without affecting plasma and hepatic triglycerides. Phytosterols previously reported to activate LXRs were tested in a luciferase-based LXR reporter assay. Using this assay, we found that phytosterols commonly present in a Western type diet in physiological concentrations do not activate LXRs. However, a lipid extract of the 24(S)-Saringosterol-containing seaweed Sargassum fusiforme did potently activate LXRβ. Dietary supplementation of crude Sargassum fusiforme or a Sargassum fusiforme-derived lipid extract to AD mice significantly improved short-term memory and reduced hippocampal Aβ plaque load by 81%. Notably, none of the side effects typically induced by full synthetic LXR agonists were observed. In contrast, administration of the synthetic LXRα activator, AZ876, did not improve cognition and resulted in the accumulation of lipid droplets in the liver. Administration of Sargassum fusiforme-derived 24(S)-Saringosterol to cultured neurons reduced the secretion of Aβ42. Moreover, conditioned medium from 24(S)-Saringosterol-treated astrocytes added to microglia increased phagocytosis of Aβ. Our data show that Sargassum fusiforme improves cognition and alleviates AD pathology. This may be explained at least partly by 24(S)-Saringosterol-mediated LXRβ activation.
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Maurya N, Maurya JK, Singh UK, Dohare R, Zafaryab M, Moshahid Alam Rizvi M, Kumari M, Patel R. In Vitro Cytotoxicity and Interaction of Noscapine with Human Serum Albumin: Effect on Structure and Esterase Activity of HSA. Mol Pharm 2019; 16:952-966. [DOI: 10.1021/acs.molpharmaceut.8b00864] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Jitendra Kumar Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Upendra Kumar Singh
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Ravins Dohare
- Nonlinear Dynamic Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Md Zafaryab
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - M. Moshahid Alam Rizvi
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Meena Kumari
- Biophysical Chemistry Laboratory, Department of Chemistry, IIT Delhi, Hauzkhas, New Delhi 110016, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
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37
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ud din Parray M, Maurya N, Ahmad Wani F, Borse MS, Arfin N, Ahmad Malik M, Patel R. Comparative effect of cationic gemini surfactant and its monomeric counterpart on the conformational stability of phospholipase A2. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.07.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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38
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Nagati V, Kallubai M, Chinthapalli DK, Subramanyam R. Exploration of binding studies of β-oxalyldiamino propionic acid (β-ODAP), a non-protein amino acid with human serum albumin-biophysical and computational approach. J Biomol Struct Dyn 2018; 37:3914-3922. [DOI: 10.1080/07391102.2018.1528181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Veerababu Nagati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Monika Kallubai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Dubey S, Kallubai M, Sarkar A, Subramanyam R. Elucidating the active interaction mechanism of phytochemicals withanolide and withanoside derivatives with human serum albumin. PLoS One 2018; 13:e0200053. [PMID: 30403672 PMCID: PMC6221254 DOI: 10.1371/journal.pone.0200053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
Withania somnifera (Ashwagandha) is an efficient medicinal plant known in Ayurveda and Chinese medicine since ancient times, whose extracts are consumed orally as food supplement or as a health tonic owing to its several restorative properties for various CNS disorders, inflammation, tumour, stress, rheumatism etc. In this study, we have analyzed the binding interaction of four derivatives of Withania somnifera (Withanolide A, Withanolide B, Withanoside IV and Withanoside V) with HSA because of their important pharmacological properties. To unravel the binding between derivatives of Withania somnifera and HSA, fluorescence spectroscopy was used. Binding studies were further studied by molecular docking and dynamics and results confirmed greater stability upon binding of derivatives with HSA. Circular dichroism data illustrated change in the secondary structure of protein upon interaction with these derivatives, particularly the helical structure was increased and β-sheets and random coils were decreased. Furthermore, morphological and topological changes were observed using AFM and TEM upon binding of ligands with HSA indicating that HSA-withnoside/withanolide complexes were formed. All the results cumulatively demonstrate strong binding of withanosides and withanolides derivatives with serum albumin, which should further be explored to study the pharmacokinetics and pharmacodynamics of these derivatives.
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Affiliation(s)
- Shreya Dubey
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Monika Kallubai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Arijit Sarkar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Telangana, India
- * E-mail:
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40
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In vitro binding interaction of atorvastatin with calf thymus DNA: multispectroscopic, gel electrophoresis and molecular docking studies. J Pharm Biomed Anal 2018; 161:101-109. [DOI: 10.1016/j.jpba.2018.08.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
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41
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Chaubey B, Pal S. Binding Interaction of Organofluorine–Serum Albumin: A Comparative Ligand-Detected 19F NMR Analysis. J Phys Chem B 2018; 122:9409-9418. [DOI: 10.1021/acs.jpcb.8b06583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bhawna Chaubey
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
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42
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Gan R, Zhao L, Sun Q, Tang P, Zhang S, Yang H, He J, Li H. Binding behavior of trelagliptin and human serum albumin: Molecular docking, dynamical simulation, and multi-spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:187-195. [PMID: 29787915 DOI: 10.1016/j.saa.2018.05.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/11/2018] [Accepted: 05/13/2018] [Indexed: 06/08/2023]
Abstract
This study aims to investigate the interaction mechanism of a hypoglycemic agent, trelagliptin (TLP), and human serum albumin (HSA) through computer simulation and assisted spectroscopy methods. Computer simulation including molecular docking and molecular dynamics analysis was conducted under physiological conditions. Molecular docking results indicate that TLP bound to HSA at site I, and the binding behavior was mainly governed by hydrophobic force. Competitive experiments further verified the theoretical conclusion from molecular docking. Molecular dynamics simulation revealed that TLP indeed stably bound to site I of HSA in the hydrophobic subdomain IIA. Moreover, TLP presented a certain effect on the structural compactness of HSA. In molecular dynamics simulation, hydrogen bonds appeared, which suggested the reliability and stability of the combination. The binding energy of the stable phase is around -250 kJ/mol. Fluorescence quenching studies and time-resolved fluorescence analysis indicated that the evident fluorescence quenching phenomenon of HSA could be due to TLP binding initiated by static quenching mechanism. The binding constants (Ka) of the complex were found to be around 104 via fluorescence data, and the calculated thermodynamic parameters indicated that hydrophobic force played major role in the binding of TLP to HSA. Synchronous fluorescence and three-dimensional fluorescence results demonstrated that TLP slightly disturbed the microenvironment of amino residues. Circular dichroism spectra showed that TLP affected the secondary structure of HSA. The theoretical and experimental results showed excellent agreement.
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Affiliation(s)
- Ruixue Gan
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Ludan Zhao
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Qiaomei Sun
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Peixiao Tang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China.
| | - Shuangshuang Zhang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Hongqin Yang
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Jiawei He
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China
| | - Hui Li
- College of Chemical Engineering, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu 610065, China.
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43
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Lu N, Sui Y, Zeng L, Tian R, Peng YY. Generation of a Diligand Complex of Bovine Serum Albumin with Quercetin and Carbon Nanotubes for the Protection of Bioactive Quercetin and Reduction of Cytotoxicity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8355-8362. [PMID: 30016096 DOI: 10.1021/acs.jafc.8b02327] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The interactions between proteins and bioactive ligands (such as flavonoids and nanomaterials) are vital to the design of effective protein carriers for the protection of bioactive molecules and reduction of the cytotoxicity of nanotubes. Bovine serum albumin (BSA) can bind various bioactive components and subsequently form protein-ligand complexes. Herein, the binding of BSA to quercetin and single-walled carbon nanotubes (SWCNTs) was investigated by using experimental and molecular-docking methods. The fluorescence intensity of BSA was decreased by both quercetin and SWCNTs in static quenching mode (i.e., compound formation), which was authenticated by Stern-Volmer calculations. Although quercetin showed a higher affinity for BSA than SWCNTs, the binding of both components to BSA was located in site I (subdomain IIA). BSA-diligand complexes were successfully generated when SWCNTs and quercetin, in that sequence, were added. The cytotoxicity of SWCNTs and the formation of reactive oxygen species in endothelial cells were decreased with the BSA-diligand complexes relative to those of SWCNTs or BSA-SWCNT corona, whereas the stability problems of quercetin were ameliorated in the BSA-diligand complex relative to in the free flavonoid. The BSA-diligand complex showed a better inhibitive effect on the cytotoxicity of SWCNTs than the BSA-SWCNT complex, and thus the coexistence of quercetin played a crucial role. These data demonstrate the advantages and possibility of designing BSA carriers for the protection of bioactive ligands and reduction of the cytotoxicity of nanotubes in functional-food and biomedical applications.
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Affiliation(s)
- Naihao Lu
- Key Laboratory of Green Chemistry, Jiangxi Province; Key Laboratory of Functional Small Organic Molecule, Ministry of Education; and College of Chemistry and Chemical Engineering , Jiangxi Normal University , Nanchang 330022 , China
| | - Yinhua Sui
- Key Laboratory of Green Chemistry, Jiangxi Province; Key Laboratory of Functional Small Organic Molecule, Ministry of Education; and College of Chemistry and Chemical Engineering , Jiangxi Normal University , Nanchang 330022 , China
| | - Lizeng Zeng
- Key Laboratory of Green Chemistry, Jiangxi Province; Key Laboratory of Functional Small Organic Molecule, Ministry of Education; and College of Chemistry and Chemical Engineering , Jiangxi Normal University , Nanchang 330022 , China
| | - Rong Tian
- Key Laboratory of Green Chemistry, Jiangxi Province; Key Laboratory of Functional Small Organic Molecule, Ministry of Education; and College of Chemistry and Chemical Engineering , Jiangxi Normal University , Nanchang 330022 , China
| | - Yi-Yuan Peng
- Key Laboratory of Green Chemistry, Jiangxi Province; Key Laboratory of Functional Small Organic Molecule, Ministry of Education; and College of Chemistry and Chemical Engineering , Jiangxi Normal University , Nanchang 330022 , China
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44
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Effect of cationic gemini surfactant and its monomeric counterpart on the conformational stability and esterase activity of human serum albumin. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.03.070] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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45
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Basha SJ, Mohan P, Yeggoni DP, Babu ZR, Kumar PB, Rao AD, Subramanyam R, Damu AG. New Flavone-Cyanoacetamide Hybrids with a Combination of Cholinergic, Antioxidant, Modulation of β-Amyloid Aggregation, and Neuroprotection Properties as Innovative Multifunctional Therapeutic Candidates for Alzheimer’s Disease and Unraveling Their Mechanism of Action with Acetylcholinesterase. Mol Pharm 2018; 15:2206-2223. [DOI: 10.1021/acs.molpharmaceut.8b00041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shaik Jeelan Basha
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Penumala Mohan
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Daniel Pushparaju Yeggoni
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Zinka Raveendra Babu
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Palaka Bhagath Kumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry Central University, Puducherry 605014, India
| | - Ampasala Dinakara Rao
- Centre for Bioinformatics, School of Life Sciences, Pondicherry Central University, Puducherry 605014, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Amooru Gangaiah Damu
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
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46
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Jelic RM, Stojanovic SD, Beric JD, Odovic J. The Effect of Tigecycline on the Binding of Fluoroquinolones to Human Serum Albumin. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2018. [DOI: 10.1515/sjecr-2017-0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
The co-administration of several drugs in multidrug therapy may alter the binding of each drug to human serum albumin (HSA) and, thus, their pharmacology effect. Therefore, in this study, the interaction mechanism between HSA and two fluoroquinolones (FQs), sparfloxacin (SPF) and levofloxacin (LVF), was investigated using fluorescence and absorption methods in the absence and presence of the competing drugtigecycline (TGC). The the UV-Vis and fluorescence spectroscopy results showed that the fluorescence quenching of HSA was a result of the formation of the HSA-SPF and HSA-LVF complexes. The fluorescence quenching of HSA-TGC revealed that tigecycline can regulate the binding sites, binding mode and binding affinity of fluoroquinolones. The binding constants (KA) and binding sites (n) of the interaction systems were calculated. The results confirmed that the KA values of the HSA-FQ system decreased in the presence of TGC, indicating that TGC can affect the binding ability of FQ for HSA. This interaction may increase the free plasma concentration of unbound FQ and enhance their pharmacology effect.
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Affiliation(s)
| | | | - Jelena D. Beric
- Faculty of Medical Science , University of Kragujevac , Serbia
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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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48
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Voltammetric behavior of Mammeisin (MA) at a glassy carbon electrode and its interaction with Bovine Serum Albumin (BSA). Bioelectrochemistry 2018; 119:20-25. [DOI: 10.1016/j.bioelechem.2017.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 11/23/2022]
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49
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Nerusu A, Reddy PS, Ramachary DB, Subramanyam R. Unraveling the Stability of Plasma Proteins upon Interaction of Synthesized Androstenedione and Its Derivatives-A Biophysical and Computational Approach. ACS OMEGA 2017; 2:6514-6524. [PMID: 30023521 PMCID: PMC6045264 DOI: 10.1021/acsomega.7b00577] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/20/2017] [Indexed: 06/08/2023]
Abstract
4-Androstene-3-17-dione (4A), also known as androstenedione, is the key intermediate of steroid metabolism. 5β-Androstane-3-17-dione (5A) and (+)-6-methyl-5β-androstane-3-17-dione (6M) are the steroid derivatives of androstenedione. The interactions of androstenedione and its derivatives with plasma proteins are important in understanding the distribution and bioavailability of these molecules. In our present study, we have studied the binding affinity of androstenedione and its derivatives with plasma proteins such as human serum albumin (HSA) and α1-acid glycoprotein (AGP). Our results showed that the 4A, 5A, and 6M steroid molecules can form stable complexes with HSA and AGP. The affinity of the studied steroid molecules with HSA is high compared to that with AGP, and the binding constants obtained for 4A, 5A, and 6M with HSA are 5.3 ± 2 × 104, 5.3 ± 1 × 104, and 9.5 ± 0.2 × 104 M-1, respectively. Further, binding sites of these steroid molecules in HSA are identified using molecular displacement and docking studies: it is found that 4A and 5A bind to domain III while 6M binds to domain II of HSA. Furthermore, the circular dichroism data revealed that there is a partial unfolding of the protein while interacting with androstenedione and its derivatives. Also, molecular dynamics simulations were carried out for HSA-androstenedione and its derivative complexes to understand their stability; hence, these results yielded that HSA-androstenedione and its derivative complexes were stabilized after 15 ns and maintained their stable structures.
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Affiliation(s)
- Aparna Nerusu
- Department
of Plant Science, School of Life Sciences,
University of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
| | - P. Srinivasa Reddy
- Catalysis
Laboratory, School of Chemistry, University
of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
| | - Dhevalapally B. Ramachary
- Catalysis
Laboratory, School of Chemistry, University
of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
| | - Rajagopal Subramanyam
- Department
of Plant Science, School of Life Sciences,
University of Hyderabad, Gachibowli, Hyderabad, Telangana 500046, India
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50
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Patel BK, Dasmandal S, Mahapatra A. Unraveling the binding of phenolphthalein with serum protein and releasing by β-cyclodextrin. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.09.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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