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Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024. [PMID: 39003571 DOI: 10.1111/febs.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
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Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
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2
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Pineda-Alemán R, Cabarcas-Herrera C, Alviz-Amador A, Galindo-Murillo R, Pérez-Gonzalez H, Rodríguez-Cavallo E, Méndez-Cuadro D. Molecular dynamics of structural effects of reactive carbonyl species derivate of lipid peroxidation on bovine serum albumin. Biochim Biophys Acta Gen Subj 2024; 1868:130613. [PMID: 38593934 DOI: 10.1016/j.bbagen.2024.130613] [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: 07/03/2023] [Revised: 03/09/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Serum albumin is the most abundant protein in the Mammalia blood plasma at where plays a decisive role in the transport wide variety of hydrophobic ligands. BSA undergoes oxidative modifications like the carbonylation by the reactive carbonyl species (RCSs) 4-hydroxy-2-nonenal (HNE), 4 hydroxy-2-hexenal (HHE), malondialdehyde (MDA) and 4-oxo-2-nonenal (ONE), among others. The structural and functional changes induced by protein carbonylation have been associated with the advancement of neurodegenerative, cardiovascular, metabolic and cancer diseases. METHODS To elucidate structural effects of protein carbonylation with RCSs on BSA, parameters for six new non-standard amino acids were designated and molecular dynamics simulations of its mono‑carbonylated-BSA systems were conducted in the AMBER force field. Trajectories were evaluated by RMSD, RMSF, PCA, RoG and SASA analysis. RESULTS An increase in the conformational instability for all proteins modified with local changes were observed, without significant changes on the BSA global three-dimensional folding. A more relaxed compaction level and major solvent accessible surface area for modified systems was found. Four regions of high molecular fluctuation were identified in all modified systems, being the subdomains IA and IIIB those with the most remarkable local conformational changes. Regarding essential modes of domain movements, it was evidenced that the most representatives were those related to IA subdomain, while IIIB subdomain presented discrete changes. CONCLUSIONS RCSs induces local structural changes on mono‑carbonylated BSA. Also, this study extends our knowledge on how carbonylation by RCSs induce structural effects on proteins.
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Affiliation(s)
- Rafael Pineda-Alemán
- Analytical Chemistry and Biomedicine Group, Medicine Faculty, University of Cartagena, Cartagena, Colombia
| | - Camila Cabarcas-Herrera
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Antistio Alviz-Amador
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | | | - Humberto Pérez-Gonzalez
- Department of Mathematics, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Erika Rodríguez-Cavallo
- Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia
| | - Darío Méndez-Cuadro
- Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia.
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3
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Bargakshatriya R, Pramanik SK. Stimuli-Responsive Prodrug Chemistries for Cancer Therapy. Chembiochem 2023; 24:e202300155. [PMID: 37341379 DOI: 10.1002/cbic.202300155] [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: 02/24/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 06/22/2023]
Abstract
Prodrugs are pharmacologically inactive, chemically modified derivatives of active drugs, which, following in vivo administration, are converted to the parent drugs through chemical or enzymatic cleavage. The prodrug approach holds tremendous potential to create the enhanced version of an existing pharmacological agent and leverage those improvements to augment the drug molecules' bioavailability, targeting ability, therapeutic efficacy, safety, and marketability. Especially in cancer therapy, prodrug application has received substantial attention. A prodrug can effectively broaden the therapeutic window of its parent drug by enhancing its release at targeted tumor sites while reducing its access to healthy cells. The spatiotemporally controlled release can be achieved by manipulating the chemical, physical, or biological stimuli present at the targeted tumor site. The critical strategy comprises drug-carrier linkages that respond to physiological or biochemical stimuli in the tumor milieu to yield the active drug form. This review will focus on the recent advancements in the development of various fluorophore-drug conjugates that are widely used for real-time monitoring of drug delivery. The use of different stimuli-cleavable linkers and the mechanisms of linker cleavage will be discussed. Finally, the review will conclude with a critical discussion of the prospects and challenges that might impede the future development of such prodrugs.
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Affiliation(s)
- Rupa Bargakshatriya
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sumit Kumar Pramanik
- CSIR-Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Pramanik SK, Sanphui P, Das AK, Banerji B, Biswas SC. Small-Molecule Cdc25A Inhibitors Protect Neuronal Cells from Death Evoked by NGF Deprivation and 6-Hydroxydopamine. ACS Chem Neurosci 2023; 14:1226-1237. [PMID: 36942687 DOI: 10.1021/acschemneuro.2c00474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative diseases that are presently incurable. There have been reports of aberrant activation of cell cycle pathways in neurodegenerative diseases. Previously, we have found that Cdc25A is activated in models of neurodegenerative diseases, including AD and PD. In the present study, we have synthesized a small library of molecules targeting Cdc25A and tested their neuroprotective potential in cellular models of neurodegeneration. The Buchwald reaction and amide coupling were crucial steps in synthesizing the Cdc25A-targeting molecules. Several of these small-molecule inhibitors significantly prevented neuronal cell death induced by nerve growth factor (NGF) deprivation as well as 6-hydroxydopamine (6-OHDA) treatment. Lack of NGF signaling leads to neuron death during development and has been associated with AD pathogenesis. The NGF receptor TrkA has been reported to be downregulated at the early stages of AD, and its reduction is linked to cognitive failure. 6-OHDA, a PD mimic, is a highly oxidizable dopamine analogue that can be taken up by the dopamine transporters in catecholaminergic neurons and can induce cell death by reactive oxygen species (ROS) generation. Some of our newly synthesized molecules inhibit Cdc25A phosphatase activity, block loss of mitochondrial activity, and inhibit caspase-3 activation caused by NGF deprivation and 6-OHDA. Hence, it may be proposed that Cdc25A inhibition could be a therapeutic possibility for neurodegenerative diseases and these Cdc25A inhibitors could be effective treatments for AD and PD.
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Rudra DS, Pal U, Chowdhury N, Maiti NC, Bagchi A, Swarnakar S. Omeprazole prevents stress induced gastric ulcer by direct inhibition of MMP-2/TIMP-3 interactions. Free Radic Biol Med 2022; 181:221-234. [PMID: 35150824 DOI: 10.1016/j.freeradbiomed.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/30/2022]
Abstract
The healing of damaged tissues in gastric tract starts with the extracellular matrix (ECM) remodeling by the action of matrix metalloproteinases (MMPs). Particularly, MMP-2 (gelatinase-A) maintains ECM structure and function by degrading type IV collagen, the major component of basement membranes and by clearing denatured collagen. The proteolytic activities of MMPs are critically balanced by endogenous tissue inhibitors of metalloproteinases (TIMPs) and disruption of this balance results in several diseases. The well-known drug omeprazole is a proton pump inhibitor used for curing gastric ulcer. However, the action of omeprazole in ECM remodeling on gastroprotection has never been explored. Herein, using rat model of gastric ulcer, we report that restraint cold stress caused increase apoptosis to surface epithelia of gastric tissues along with TIMP-3 upregulation and inhibition of MMP-2 activity thereon. In contrast, omeprazole treatment suppressed TIMP-3 while increasing MMP-2 activity and thereby, restoring MMP-2/TIMP-3 balance. Additionally, nanomolar binding constant (Kd = 318 nM) of omeprazole with purified MMP-2 indicates a direct effect of omeprazole in restoring MMP-2 activity. Further in silico simulations revealed a plausible mechanism of action of omeprazole for TIMP-3 deactivation. Altogether, omeprazole restores MMP-2 activity and reduces apoptosis while preventing acute stress-induced gastric ulcer that occurs via suppression of nuclear factor kappa B (NF-κB) activity and peroxisome proliferator-activated receptor gamma activity (PPAR-γ). This represents an unprecedented correlation between physical docking of drug molecule to a protease and the severity of organ injury and provides a novel therapeutic approach to prevent stress induced tissue damage.
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Affiliation(s)
- Deep Sankar Rudra
- Infectious Diseases & Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Uttam Pal
- Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Nilkanta Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, 741235, West Bengal, India.
| | - Nakul Chandra Maiti
- Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia, 741235, West Bengal, India.
| | - Snehasikta Swarnakar
- Infectious Diseases & Immunology, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India.
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Biswas P, Pal U, Adhikari A, Mondal S, Ghosh R, Mukherjee D, Saha‐Dasgupta T, Choudhury SS, Das R, Pal SK. Essential Loop Dynamics Modulates Catalytic Activity in α‐Chymotrypsin. ChemistrySelect 2022. [DOI: 10.1002/slct.202104262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pritam Biswas
- Department of Microbiology St. Xavier's College, 30, Mother Teresa Sarani Kolkata 700016 India
| | - Uttam Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Aniruddha Adhikari
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Susmita Mondal
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Ria Ghosh
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Dipanjan Mukherjee
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Tanusri Saha‐Dasgupta
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | | | - Ranjan Das
- Department of Chemistry West Bengal state University, Barasat Kolkata 700126 India
| | - Samir Kumar Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
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Li Y, Li N, Chen F, Yang X, Lei Y, Liu Y, Tuo X. Evaluation of binding properties of human serum albumin and mono-benzyl phthalate (MBZP): Multi-spectroscopic analysis and computer simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Sharma M, Pal U, Kumari M, Bagchi D, Rani S, Mukherjee D, Bera A, Pal SK, Saha Dasgupta T, Mozumdar S. Effect of solvent on the photophysical properties of isoxazole derivative of curcumin: A combined spectroscopic and theoretical study. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Mondal P, Sengupta P, Pal U, Saha S, Bose A. Biophysical and theoretical studies of the interaction between a bioactive compound 3,5-dimethoxy-4-hydroxycinnamic acid with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 245:118936. [PMID: 32977108 DOI: 10.1016/j.saa.2020.118936] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/12/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
3,5-Dimethoxy-4-hydroxycinnamic acid commonly known as Sinapic acid is a well-known derivative of hydroxycinnamic acids, is commonly present in human diet. Due to its wide variety of pharmacological activities like antioxidant, antimicrobial, anti-inflammatory, anticancer, and anti-anxiety, it has attracted much attention for the researchers. In our previous published work we have already analyzed the interaction between sinapic acid (SA) with a model transport protein. In this work our aim is to demonstrate a detailed investigation of the binding interaction between sinapic acid with another carrier of genetic information in a living cell, the DNA. Here we have used calf thymus DNA (ct-DNA) as a model. The binding characteristic of SA with ct-DNA was investigated by different spectroscopic and theoretical tools. The spectroscopic investigation revealed that quenching of intrinsic fluorescence of SA by ct-DNA occurs through dynamic quenching mechanism. The thermodynamic parameters established the involvement of hydrogen bonding and weak van der Waals forces in the interaction. Further, the circular dichroism, competitive binding experiment with ethidium bromide and potassium iodide quenching experiment suggested that SA possibly binds to the groove position of the ct-DNA. Finally, molecular docking analysis established the SA binds to minor groove position of ct-DNA in G-C rich region through hydrogen bonding interaction. Additionally, gel electrophoresis analysis has been performed to determine the protective efficacy of SA against UVB induced DNA damage and 50 μM of SA was found to protect the DNA from UVB induced damage. We hope that our study could provide the validation of SA on behalf of therapeutics and development of next generation therapeutic drug as well as designing new efficient drug molecule and methodology for the interaction study of the drug with DNA.
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Affiliation(s)
- Prasenjit Mondal
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, West Bengal, India
| | - Priti Sengupta
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, West Bengal, India
| | - Uttam Pal
- Technical Research Centre, S.N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata, India
| | - Sutapa Saha
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, India
| | - Adity Bose
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, West Bengal, India.
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10
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In silico validation of potent phytochemical orientin as inhibitor of SARS-CoV-2 spike and host cell receptor GRP78 binding. Heliyon 2021; 7:e05923. [PMID: 33458435 PMCID: PMC7799170 DOI: 10.1016/j.heliyon.2021.e05923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/06/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
The present wellbeing worry to the whole world is the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also called COVID-19. This global health crisis first appeared in Wuhan, China around December 2019 and due to its extremely contagious nature it had spread to almost 187 countries. Still now no effective method of treatment or vaccine is developed for controlling the disease. Therefore, the sole obliging strategy is to take precautionary measures by repurposing drugs from the pre-existing library of therapeutically potent molecules. In this situation of pandemic this repurposing technique may save the labour-intensive and tiresome process of new drug development. Orientin is a natural flavonoid with several beneficial effects. This phytochemical can be isolated from different plants like tulsi or holy basil, black bamboo, passion flowers etc. It's antiviral, anti-inflammation, vasodilatation, cardioprotective, radioprotective, neuroprotective, anticarcinogenic and antinociceptive effects are already established. In this research, it is intriguing to find out whether this molecule can interfere the interaction of SARS-CoV-2 spike glycoprotein and their host receptor GRP78. Our in silico docking and molecular dynamics simulation results indicate the binding of Orientin in the overlapping residues of GRP78 binding region of SARS-CoV-2 spike model and SARS-CoV-2 spike model binding region of GRP78 substrate-binding domain. Therefore, the results included in this research work provide a strong possibility of using Orientin as a promising precautionary or therapeutic measure for COVID-19.
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Kang J, Kang AM. Comment on "Physicochemical stimuli as tuning parameters to modulate the structure and stability of nanostructured lipid carriers and release kinetics of encapsulated antileprosy drugs" by R. Kanwar, M. Gradzielski, S. Prevost, G. Kaur, M. S. Appavou and S. K. Mehta, J. Mater. Chem. B, 2019, 7, 6539. J Mater Chem B 2020; 8:10205-10208. [PMID: 33125021 DOI: 10.1039/d0tb01160f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a recent article [R. Kanwar et al., J. Mater. Chem. B, 2019, 7(42), 6539-6555], the authors characterized the interactions between drug-loaded nanostructured lipid carriers and bovine serum albumin using thermodynamics. They found that the interactions are spontaneous and driven by entropy. In this present paper, we report our analysis of these results in terms of equilibrium thermodynamics to show that the binding reactions exhibit enthalpy-entropy compensation. Our findings may prove useful for designing nanostructured lipid carriers.
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Affiliation(s)
- Jonghoon Kang
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA.
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12
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Rani S, Bagchi D, Pal U, Kumari M, Sharma M, Bera A, Shabir J, Pal SK, Saha-Dasgupta T, Mozumdar S. The Role of Imidazolium-Based Surface-Active Ionic Liquid to Restrain the Excited-State Intramolecular H-Atom Transfer Dynamics of Medicinal Pigment Curcumin: A Theoretical and Experimental Approach. ACS OMEGA 2020; 5:25582-25592. [PMID: 33073084 PMCID: PMC7557247 DOI: 10.1021/acsomega.0c02438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/18/2020] [Indexed: 05/06/2023]
Abstract
The naturally occurring polyphenolic compound curcumin has shown various medicinal and therapeutic effects. However, there are various challenges associated with curcumin, which limits its biomedical applications, such as its high degradation rate and low aqueous solubility at neutral and alkaline pH. In the present study, efforts have been directed towards trying to resolve such issues by encapsulating curcumin inside the micelles formed by imidazolium-based surface-active ionic liquid (SAIL). The shape and size of the micelles formed by the SAIL have been characterized by using DLS analysis as well as TEM measurements. The photo-physics of curcumin in the presence of ionic liquid (IL) and also with the addition of salt (NaCl) has been explored by using different optical spectroscopic tools. The time-dependent absorption studies have shown that there is relatively higher suppression in the degradation rate of curcumin after encapsulation by the imidazolium-based SAIL in an aqueous medium. The TCSPC studies have revealed that there is deactivation in the nonradiative intramolecular hydrogen transfer process of curcumin in the presence of IL micelles as well as with the addition of salt. Furthermore, the time-dependent fluorescence anisotropy measurement has been carried out to figure out the location of curcumin inside the micellar system. In order to correlate all experimental findings, density functional theory (DFT) and classical molecular dynamics (MD) simulations at neutral pH media have been performed. It has been found that the van der Waals force of interactions plays a major role in the stabilization of curcumin in the micelles rather than the coulombic forces. It also has been observed that the van der Waals interactions remain unaffected in the presence of salt. However, as revealed by the MD simulation results, the micelles are found to be more compact in size after the addition of salt. The RMSD results show that the micelles formed by the SAIL achieve greater stability after a particular time constraint. Our results have divulged that the SAIL could act as a promising drug delivery system.
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Affiliation(s)
- Swati Rani
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Damayanti Bagchi
- Department
of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, West Bengal 700106, India
| | - Uttam Pal
- Technical
Research Centre, S. N. Bose National Centre
for Basic Sciences, Block
JD, Sector III, Salt Lake, Kolkata, West Bengal 700106, India
| | - Mamta Kumari
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Manisha Sharma
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Arpan Bera
- Department
of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, West Bengal 700106, India
| | - Javaid Shabir
- Department
of Chemistry, University of Delhi, Delhi 110007, India
| | - Samir Kumar Pal
- Department
of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, West Bengal 700106, India
| | - Tanusri Saha-Dasgupta
- Department
of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata, West Bengal 700106, India
| | - Subho Mozumdar
- Department
of Chemistry, University of Delhi, Delhi 110007, India
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Biswas P, Adhikari A, Pal U, Singh P, Das M, Saha-Dasgupta T, Choudhury SS, Das R, Pal SK. Flexibility modulates the catalytic activity of a thermostable enzyme: key information from optical spectroscopy and molecular dynamics simulation. SOFT MATTER 2020; 16:3050-3062. [PMID: 32133476 DOI: 10.1039/c9sm02479d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Enzymes are dynamical macromolecules and their conformation can be altered via local fluctuations of side chains, large scale loop and even domain motions which are intimately linked to their function. Herein, we have addressed the role of dynamic flexibility in the catalytic activity of a thermostable enzyme almond beta-glucosidase (BGL). Optical spectroscopy and classical molecular dynamics (MD) simulation were employed to study the thermal stability, catalytic activity and dynamical flexibility of the enzyme. An enzyme assay reveals high thermal stability and optimum catalytic activity at 333 K. Polarization-gated fluorescence anisotropy measurements employing 8-anilino-1-napthelenesulfonic acid (ANS) have indicated increasing flexibility of the enzyme with an increase in temperature. A study of the atomic 3D structure of the enzyme shows the presence of four loop regions (LRs) strategically placed over the catalytic barrel as a lid. MD simulations have indicated that the flexibility of BGL increases concurrently with temperature through different fluctuating characteristics of the enzyme's LRs. Principal Component Analysis (PCA) and the Steered Molecular Dynamics (SMD) simulation manifest the gatekeeper role of the four LRs through their dynamic fluctuations surrounding the active site which controls the catalytic activity of BGL.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata 700016, India.
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Multi-spectroscopic and computational evaluation on the binding of sinapic acid and its Cu(II) complex with bovine serum albumin. Food Chem 2019; 301:125254. [DOI: 10.1016/j.foodchem.2019.125254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 11/20/2022]
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15
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Ghosh R, Bharathkar SK, Kishore N. Anticancer altretamine recognition by bovine serum albumin and its role as inhibitor of fibril formation: Biophysical insights. Int J Biol Macromol 2019; 138:359-369. [DOI: 10.1016/j.ijbiomac.2019.07.093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 01/15/2023]
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16
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Maity A, Pal U, Chakraborty B, Sengupta C, Sau A, Chakraborty S, Basu S. Preferential photochemical interaction of Ru (III) doped carbon nano dots with bovine serum albumin over human serum albumin. Int J Biol Macromol 2019; 137:483-494. [DOI: 10.1016/j.ijbiomac.2019.06.126] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 12/11/2022]
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17
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Bose A, Sengupta P, Pal U, Senapati S, Ahsan M, Roy S, Das U, Sen K. Encapsulation of Thymol in cyclodextrin nano-cavities: A multi spectroscopic and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 208:339-348. [PMID: 30343222 DOI: 10.1016/j.saa.2018.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Cyclodextrins have a wide range of applications in different areas of drug delivery and pharmaceutical industry due to their complexation ability and other versatile characteristics. Here we have studied the binding interactions of a small biologically important phenolic molecule, Thymol (Th), with both α and β cyclodextrins (CDs), which are well known drug delivery vehicles. Extent of encapsulation has been determined using several spectroscopic techniques. In fluorescence experiments, significant increase in fluorescence intensities have been discerned for both the CDs but there had been a much early saturation for αCD. Anisotropy experiments have been performed too and very surprisingly no appreciable increase in anisotropy value was observed in either case. Isothermal titration calorimetry (ITC) data, however, show signature of binding of Th with the βCD. These intriguing results were explained with the help of molecular docking and dynamics simulation studies. The docking calculations have shown that Th goes inside both α and βCD. In keeping with the final NMR data and molecular dynamics we have ultimately concluded that solvated Th molecules are the main participants in the interaction with CDs which is responsible for these intriguing behaviors. Finally we have also performed an antioxidant assay to reveal the practical application of such encapsulation. It has been found that on encapsulation there is an enhancement of the antioxidant behavior of Th. Then we have also performed an antibacterial assay to show the unchanged antibacterial properties of Th on encapsulation. Hence it can be deduced that Th can be safely delivered through CDs in living system without hampering its beneficial properties.
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Affiliation(s)
- Adity Bose
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India.
| | - Priti Sengupta
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, West Bengal, India
| | - Uttam Pal
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Block AF, Saltlake, Kolkata 700064, West Bengal, India
| | - Sanjib Senapati
- Department of Biotechnology, Indian Institute of Technology, Madras, IIT P.O., Chennai 600 036, India
| | - Mohd Ahsan
- Department of Biotechnology, Indian Institute of Technology, Madras, IIT P.O., Chennai 600 036, India
| | - Santanu Roy
- Department of Microbiology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata 700131, India
| | - Upasana Das
- Department of Microbiology, Acharya Prafulla Chandra College, New Barrackpore, Kolkata 700131, India
| | - Kamalika Sen
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700 009, India
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18
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Sau A, Sanyal S, Bera K, Sen S, Mitra AK, Pal U, Chakraborty PK, Ganguly S, Satpati B, Das C, Basu S. DNA Damage and Apoptosis Induction in Cancer Cells by Chemically Engineered Thiolated Riboflavin Gold Nanoassembly. ACS APPLIED MATERIALS & INTERFACES 2018; 10:4582-4589. [PMID: 29338178 DOI: 10.1021/acsami.7b18837] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Herein we have engineered a smart nuclear targeting thiol-modified riboflavin-gold nano assembly, RfS@AuNPs, which accumulates selectively in the nucleus without any nuclear-targeting peptides (NLS/RGD) and shows photophysically in vitro DNA intercalation. A theoretical model using Molecular Dynamics has been developed to probe the mechanism of formation and stability as well as dynamics of the RfS@AuNPs in aqueous solution and within the DNA microenvironment. The RfS@AuNPs facilitate the binucleated cell formation that is reflected in the significant increase of DNA damage marker, γ-H2AX as well as the arrest of most of the HeLa cells at the pre-G1 phase indicating cell death. Moreover, a significant upregulation of apoptotic markers confirms that the cell death occurs through the apoptotic pathway. Analyses of the microarray gene expression of RfS@AuNPs treated HeLa cells show significant alterations in vital biological processes necessary for cell survival. Taken together, our study reports a unique nuclear targeting mechanism through targeting the riboflavin receptors, which are upregulated in cancer cells and induce apoptosis in the targeted cells.
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Affiliation(s)
| | | | | | | | - Amrit Krishna Mitra
- Department of Chemistry, Government General Degree College, Singur, Hooghly, West Bengal 712409, India
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19
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Kennedy AE, Vohra R, Scott JA, Ross GM. Effects of serum albumin on SPR-measured affinity of small molecule inhibitors binding to nerve growth factor. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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20
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Yadav DK, Bharitkar YP, Hazra A, Pal U, Verma S, Jana S, Singh UP, Maiti NC, Mondal NB, Swarnakar S. Tamarixetin 3-O-β-d-Glucopyranoside from Azadirachta indica Leaves: Gastroprotective Role through Inhibition of Matrix Metalloproteinase-9 Activity in Mice. JOURNAL OF NATURAL PRODUCTS 2017; 80:1347-1353. [PMID: 28493718 DOI: 10.1021/acs.jnatprod.6b00957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Neem (Azadirachta indica) is a well-known medicinal and insecticidal plant. Although previous studies have reported the antiulcer activity of neem leaf extract, the lead compound is still unidentified. The present study reports tamarixetin 3-O-β-d-glucopyranoside (1) from a methanol extract of neem leaves and its gastroprotective activity in an animal model. Compound 1 showed significant protection against indomethacin-induced gastric ulceration in mice in a dose-dependent manner. Moreover, ex vivo and circular dichroism studies confirmed that 1 inhibited the enzyme matrix metalloproteinase-9 (MMP-9) activity with an IC50 value of ca. 50 μM. Molecular docking and dynamics showed the binding of 1 into the pocket of the active site of MMP-9, forming a coordination complex with the catalytic zinc, thus leading to inhibition of MMP-9 activity.
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Affiliation(s)
| | - Yogesh P Bharitkar
- Department of Natural Products, National Institute of Pharmaceutical Education and Research , Kolkata 700032, WB, India
| | - Abhijit Hazra
- Department of Natural Products, National Institute of Pharmaceutical Education and Research , Kolkata 700032, WB, India
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Zhuang X, Zhao B, Liu S, Song F, Cui F, Liu Z, Li Y. Noncovalent Interactions between Superoxide Dismutase and Flavonoids Studied by Native Mass Spectrometry Combined with Molecular Simulations. Anal Chem 2016; 88:11720-11726. [PMID: 27760293 DOI: 10.1021/acs.analchem.6b03359] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in the etiology of amyotrophic lateral sclerosis (ALS). The use of small molecules may stabilize the spatial structure of SOD1 dimer, thus, preventing its dissociation and aggregation. In this study, "native" mass spectrometry (MS) was used to study the noncovalent interactions between SOD1 and flavonoid compounds. MS experiments were performed on a quadruple time-of-flight (Q-ToF) mass spectrometer with an electrospray ionization (ESI) source and T-wave ion mobility. ESI-MS was used to detect the SOD1-flavonoid complexes and compare their relative binding strengths. The complement of ion mobility separation allowed comparison in the binding affinities between flavonoid isomers and provided information on the conformational changes. Molecular docking together with molecular dynamics simulations and MM/PBSA methods were applied to gain insights into the binding modes and free energies of SOD1-flavonoid complexes at the molecule level. Among all the flavonoids investigated, flavonoid glycosides preferentially bind to SOD1 than their aglycone counterparts. Naringin, one of the compounds that has the strongest binding affinity to SOD1, was subjected to further characterization. Experiment results show that the binding of naringin can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results suggest that naringin could reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This developed analytical strategy could also be applied to study the interactions between SOD1 and other drug-like molecules, which may have the effect to reduce the aggregation.
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Affiliation(s)
- Xiaoyu Zhuang
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Bing Zhao
- University of the Chinese Academy of Sciences, Beijing 100039, China
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