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  1. Article ; Online: Structure specific neuro-toxicity of α-synuclein oligomer.

    Mondal, Animesh / Dolui, Sandip / Dhabal, Sukhamoy / Kundu, Shubham / Das, Lopamudra / Bhattacharjee, Ashish / Maiti, Nakul C

    International journal of biological macromolecules

    2023  Volume 253, Issue Pt 1, Page(s) 126683

    Abstract: Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein ... ...

    Abstract Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.
    MeSH term(s) Humans ; alpha-Synuclein/chemistry ; Parkinson Disease/metabolism ; Protein Conformation ; Neurons/metabolism ; Protein Conformation, beta-Strand ; Amyloid/chemistry ; Amyloidogenic Proteins
    Chemical Substances alpha-Synuclein ; Amyloid ; Amyloidogenic Proteins
    Language English
    Publishing date 2023-09-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.126683
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Coomassie brilliant blue G-250 acts as a potential chemical chaperone to stabilize therapeutic insulin.

    Pariary, Ranit / Dolui, Sandip / Shome, Gourav / Mohid, Sk Abdul / Saha, Achintya / Ratha, Bhisma N / Harikishore, Amaravadhi / Jana, Kuladip / Mandal, Atin K / Bhunia, Anirban / Maiti, Nakul C

    Chemical communications (Cambridge, England)

    2023  Volume 59, Issue 52, Page(s) 8095–8098

    Abstract: Our studies show Coomassie Brilliant Blue G-250 as a promising chemical chaperone that stabilises the α-helical native human insulin conformers, disrupting their aggregation. Furthermore, it also increases the insulin secretion. This multipolar effect ... ...

    Abstract Our studies show Coomassie Brilliant Blue G-250 as a promising chemical chaperone that stabilises the α-helical native human insulin conformers, disrupting their aggregation. Furthermore, it also increases the insulin secretion. This multipolar effect coupled with its non-toxic nature could be useful for developing highly bioactive, targeted and biostable therapeutic insulin.
    MeSH term(s) Humans ; Rosaniline Dyes ; Molecular Chaperones ; Insulins
    Chemical Substances coomassie Brilliant Blue (M1ZRX790SI) ; Rosaniline Dyes ; Molecular Chaperones ; Insulins
    Language English
    Publishing date 2023-06-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc01791e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Single point mutations at the S129 residue of α-synuclein and their effect on structure, aggregation, and neurotoxicity.

    Pandit, Esha / Das, Lopamudra / Das, Anoy Kumar / Dolui, Sandip / Saha, Saumen / Pal, Uttam / Mondal, Animesh / Chowdhury, Joydeep / Biswas, Subhas C / Maiti, Nakul C

    Frontiers in chemistry

    2023  Volume 11, Page(s) 1145877

    Abstract: Parkinson's disease is an age-related neurological disorder, and the pathology of the disease is linked to different types of aggregates of α-synuclein or alpha-synuclein (aS), which is an intrinsically disordered protein. The C-terminal domain (residues ...

    Abstract Parkinson's disease is an age-related neurological disorder, and the pathology of the disease is linked to different types of aggregates of α-synuclein or alpha-synuclein (aS), which is an intrinsically disordered protein. The C-terminal domain (residues 96-140) of the protein is highly fluctuating and possesses random/disordered coil conformation. Thus, the region plays a significant role in the protein's solubility and stability by an interaction with other parts of the protein. In the current investigation, we examined the structure and aggregation behavior of two artificial single point mutations at a C-terminal residue at position 129 that represent a serine residue in the wild-type human aS (wt aS). Circular Dichroism (CD) and Raman spectroscopy were performed to analyse the secondary structure of the mutated proteins and compare it to the wt aS. Thioflavin T assay and atomic force microscopy imaging helped in understanding the aggregation kinetics and type of aggregates formed. Finally, the cytotoxicity assay gave an idea about the toxicity of the aggregates formed at different stages of incubation due to mutations. Compared to wt aS, the mutants S129A and S129W imparted structural stability and showed enhanced propensity toward the α-helical secondary structure. CD analysis showed proclivity of the mutant proteins toward α-helical conformation. The enhancement of α-helical propensity lengthened the lag phase of fibril formation. The growth rate of β-sheet-rich fibrillation was also reduced. Cytotoxicity tests on SH-SY5Y neuronal cell lines established that the S129A and S129W mutants and their aggregates were potentially less toxic than wt aS. The average survivability rate was ∼40% for cells treated with oligomers (presumably formed after 24 h of incubation of the freshly prepared monomeric protein solution) produced from wt aS and ∼80% for cells treated with oligomers obtained from mutant proteins. The relative structural stability with α-helical propensity of the mutants could be a plausible reason for their slow rate of oligomerization and fibrillation, and this was also the possible reason for reduced toxicity to neuronal cells.
    Language English
    Publishing date 2023-05-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2023.1145877
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Impact of porous nanomaterials on inhibiting protein aggregation behaviour.

    Bardhan, Munmun / Dolui, Sandip / Chaudhuri, Siddhi / Paul, Uttam / Bhattacharjee, Gaurav / Ghosal, Manorama / Maiti, Nakul C / Mukhopadhyay, Debashis / Senapati, Dulal

    RSC advances

    2021  Volume 11, Issue 6, Page(s) 3354–3362

    Abstract: Aggregation of intrinsically disordered as well as the ordered proteins under certain premises or physiological conditions leads to pathological disorder. Here we have presented a detailed investigation on the effect of a porous metallic (Au) and a non- ... ...

    Abstract Aggregation of intrinsically disordered as well as the ordered proteins under certain premises or physiological conditions leads to pathological disorder. Here we have presented a detailed investigation on the effect of a porous metallic (Au) and a non-metallic (Si) nanomaterial on the formation of ordered (fiber-like/amyloid) and disordered (amorphous) aggregates of proteins. Porous nanogold (PNG) was found to reduce the amyloid aggregation of insulin but does not have much impact on the lag phase in the aggregation kinetics, whereas porous nano-silica (PNS) was found both to decrease the amount of aggregation as well as prolong the lag phase of amyloid fiber formation from insulin. On the other hand, both the porous nanoparticles are found to decrease the extent of amorphous aggregation (with slight improvement for PNS) of pathogenic huntingtin (Htt) protein in Huntington's disease cell model. This is a noted direct observation in controlling and understanding protein aggregation diseases which may help us to formulate nanotherapeutic drugs for future clinical applications.
    Language English
    Publishing date 2021-01-15
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d0ra10927d
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  5. Article ; Online: Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease.

    Uday, R V Sriram / Misra, Rajdip / Harika, Annaram / Dolui, Sandip / Saha, Achintya / Pal, Uttam / Ravichandiran, V / Maiti, Nakul C

    PloS one

    2021  Volume 16, Issue 9, Page(s) e0257206

    Abstract: Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established ... ...

    Abstract Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.
    MeSH term(s) Amino Acid Sequence ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Imidazoles/chemistry ; Imidazoles/pharmacology ; Indoles/chemistry ; Indoles/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Oximes/chemistry ; Oximes/pharmacology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protein Structure, Secondary ; Purines/chemistry ; Purines/pharmacology ; Quinazolinones/chemistry ; Quinazolinones/pharmacology ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/chemistry
    Chemical Substances Antiviral Agents ; Imidazoles ; Indoles ; Oximes ; Protease Inhibitors ; Purines ; Quinazolinones ; Viral Nonstructural Proteins ; nintedanib (G6HRD2P839) ; dabrafenib (QGP4HA4G1B) ; idelalisib (YG57I8T5M0)
    Language English
    Publishing date 2021-09-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0257206
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Envisaging the Structural Elevation in the Early Event of Oligomerization of Disordered Amyloid β Peptide.

    Roy, Anupam / Chandra, Kousik / Dolui, Sandip / Maiti, Nakul C

    ACS omega

    2017  Volume 2, Issue 8, Page(s) 4316–4327

    Abstract: In Alzheimer's disease (AD), amyloid β (Aβ) protein plays a detrimental role in neuronal injury and death. Recent in vitro and in vivo studies suggest that soluble oligomers of the Aβ peptide are neurotoxic. Structural properties of the oligomeric ... ...

    Abstract In Alzheimer's disease (AD), amyloid β (Aβ) protein plays a detrimental role in neuronal injury and death. Recent in vitro and in vivo studies suggest that soluble oligomers of the Aβ peptide are neurotoxic. Structural properties of the oligomeric assembly, however, are largely unknown. Our present investigation established that the 40-residue-long Aβ peptide (Aβ40) became more helical, ordered, and compact in the oligomeric state, and both the helical and β-sheet components were found to increase significantly in the early event of oligomerization. The band-selective two-dimensional NMR analysis suggested that majority of the residues from sequence 12 to 22 gained a higher-ordered secondary structure in the oligomeric condition. The presence of a significant amount of helical conformation was confirmed by Raman bands at 1650 and 1336 cm
    Language English
    Publishing date 2017-08-08
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.7b00522
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Envisaging the Structural Elevation in the Early Event of Oligomerization of Disordered Amyloid β Peptide

    Anupam Roy / Kousik Chandra / Sandip Dolui / Nakul C. Maiti

    ACS Omega, Vol 2, Iss 8, Pp 4316-

    2017  Volume 4327

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease.

    R V Sriram Uday / Rajdip Misra / Annaram Harika / Sandip Dolui / Achintya Saha / Uttam Pal / V Ravichandiran / Nakul C Maiti

    PLoS ONE, Vol 16, Iss 9, p e

    2021  Volume 0257206

    Abstract: Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established ... ...

    Abstract Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.
    Keywords Medicine ; R ; Science ; Q
    Subject code 540
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Structural Insight of Amyloidogenic Intermediates of Human Insulin.

    Dolui, Sandip / Roy, Anupam / Pal, Uttam / Saha, Achintya / Maiti, Nakul C

    ACS omega

    2018  Volume 3, Issue 2, Page(s) 2452–2462

    Abstract: Engaging Raman spectroscopy as a primary tool, we investigated the early events of insulin fibrilization and determined the structural content present in oligomer and protofibrils that are formed as intermediates in the fibril formation pathway. Insulin ... ...

    Abstract Engaging Raman spectroscopy as a primary tool, we investigated the early events of insulin fibrilization and determined the structural content present in oligomer and protofibrils that are formed as intermediates in the fibril formation pathway. Insulin oligomer, as obtained upon incubation of zinc-free insulin at 60 °C, was mostly spherical in shape, with a diameter of 3-5 nm. Longer incubation produced "necklace"-like beaded protofibrillar assembly species. These intermediates eventually transformed into 5-8 nm thick fibers with smooth surface texture. A broad amide I band in the Raman spectrum of insulin monomer appeared at 1659 cm
    Language English
    Publishing date 2018-02-27
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN 2470-1343
    DOI 10.1021/acsomega.7b01776
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Structural Insight of Amyloidogenic Intermediates of Human Insulin

    Sandip Dolui / Anupam Roy / Uttam Pal / Achintya Saha / Nakul C. Maiti

    ACS Omega, Vol 3, Iss 2, Pp 2452-

    2018  Volume 2462

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2018-02-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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