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  1. Article ; Online: Molecular docking, simulations of animal peptides against the envelope protein of Dengue virus.

    Guntamadugu, Reena / Ramakrishnan, Ranjani / Darala, Gowtham / Kothandan, Sangeetha

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–15

    Abstract: Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus ( ... ...

    Abstract Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus (HIV), influenza virus and hepatitis C virus. So far, no peptide drug has been approved for antiviral treatment against Dengue virus, and many are under clinical trials. Therefore, developing a reasonable peptide against the Dengue virus Envelope protein structure will be a successful strategy for treating Dengue. Hence, we investigated protein-protein docking interactions between 215 peptides retrieved from the AVP database against the envelope protein using Cluspro and HADDOCK followed by the evaluation of their allegenicity, toxicity and physicochemical characteristics investigation. Further validation of the protein-peptide complexes was performed with Molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann surface area (MMPBSA) analysis on the hit inhibitors. This study revealed that Indolicidin (-75.026 ± 1.54 KJ/mol) and Human Neutrophil peptide-1 (-71.6551 ± 2.112 KJ/mol) shows higher negative ΔG binding implicating their relative stabilization in the protein-peptide interactions during 100 ns of dynamic simulations. Also, both the peptides exhibited desirable physicochemical properties and were nonallergenic. Hence, we further aim to test these peptides by
    Language English
    Publishing date 2023-11-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2275183
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: In silico

    Farhana, Aisha / Kothandan, Sangeetha / Alsrhani, Abdullah / Mok, Pooi Ling / Subbiah, Suresh Kumar / Khan, Yusuf Saleem

    Contrast media & molecular imaging

    2022  Volume 2022, Page(s) 4202623

    Abstract: S100A4 protein overexpression has been reported in different types of cancer and plays a key role by interacting with the tumor suppressor protein Tp53. Single nucleotide polymorphisms (SNP) in S100A4 could directly influence the biomolecular interaction ...

    Abstract S100A4 protein overexpression has been reported in different types of cancer and plays a key role by interacting with the tumor suppressor protein Tp53. Single nucleotide polymorphisms (SNP) in S100A4 could directly influence the biomolecular interaction with the tumor suppressor protein Tp53 due to their aberrant conformations. Hence, the study was designed to predict the deleterious SNP and its effect on the S100A4 protein structure and function. Twenty-one SNP data sets were screened for nonsynonymous mutations and subsequently subjected to deleterious mutation prediction using different computational tools. The screened deleterious mutations were analyzed for their changes in functionality and their interaction with the tumor suppressor protein Tp53 by protein-protein docking analysis. The structural effects were studied using the 3DMissense mutation tool to estimate the solvation energy and torsion angle of the screened mutations on the predicted structures. In our study, 21 deleterious nonsynonymous mutations were screened, including F72V, E74G, L5P, D25E, N65S, A28V, A8D, S20L, L58P, and K26N were found to be remarkably conserved by exhibiting the interaction either with the EF-hand 1 or EF-hand 2 domain. The solvation and torsion values significantly deviated for the mutant-type structures with S20L, N65S, and F72L mutations and showed a marked reduction in their binding affinity with the Tp53 protein. Hence, these deleterious mutations might serve as prospective targets for diagnosing and developing personalized treatments for cancer and other related diseases.
    MeSH term(s) Humans ; Mutation/genetics ; Neoplasms ; Polymorphism, Single Nucleotide/genetics ; S100 Calcium-Binding Protein A4/genetics
    Chemical Substances S100 Calcium-Binding Protein A4 ; S100A4 protein, human (142662-27-9)
    Language English
    Publishing date 2022-07-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2232678-9
    ISSN 1555-4317 ; 1555-4309
    ISSN (online) 1555-4317
    ISSN 1555-4309
    DOI 10.1155/2022/4202623
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6273: Show issues Location:
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  3. Article: Exosomes and Cancer Stem Cells in Cancer Immunity: Current Reports and Future Directions.

    Lee, Na-Kyeong / Kothandan, Vinoth Kumar / Kothandan, Sangeetha / Byun, Youngro / Hwang, Seung-Rim

    Vaccines

    2021  Volume 9, Issue 5

    Abstract: Cancer stem cells (CSCs), which have the capacity to self-renew and differentiate into various types of cells, are notorious for their roles in tumor initiation, metastasis, and therapy resistance. Thus, underlying mechanisms for their survival provide ... ...

    Abstract Cancer stem cells (CSCs), which have the capacity to self-renew and differentiate into various types of cells, are notorious for their roles in tumor initiation, metastasis, and therapy resistance. Thus, underlying mechanisms for their survival provide key insights into developing effective therapeutic strategies. A more recent focus has been on exosomes that play a role in transmitting information between CSCs and non-CSCs, resulting in activating CSCs for cancer progression and modulating their surrounding microenvironment. The field of CSC-derived exosomes (CSCEXs) for different types of cancer is still under exploration. A deeper understanding and further investigation into CSCEXs' roles in tumorigenicity and the identification of novel exosomal components are necessary for engineering exosomes for the treatment of cancer. Here, we review the features of CSCEXs, including surface markers, cargo, and biological or physiological functions. Further, reports on the immunomodulatory effects of CSCEXs are summarized, and exosome engineering for CSC-targeting is also discussed.
    Language English
    Publishing date 2021-05-01
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9050441
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in the

    Farhana, Aisha / Koh, Avin Ee-Hwan / Kothandan, Sangeetha / Alsrhani, Abdullah / Mok, Pooi Ling / Subbiah, Suresh Kumar

    International journal of molecular sciences

    2021  Volume 22, Issue 22

    Abstract: Cancer cells are able to proliferate in an unregulated manner. There are several mechanisms involved that propel such neoplastic transformations. One of these processes involves bypassing cell death through changes in gene expression and, consequently, ... ...

    Abstract Cancer cells are able to proliferate in an unregulated manner. There are several mechanisms involved that propel such neoplastic transformations. One of these processes involves bypassing cell death through changes in gene expression and, consequently, cell growth. This involves a complex epigenetic interaction within the cell, which drives it towards oncogenic transformations. These epigenetic events augment cellular growth by potentially altering chromatin structures and influencing key gene expressions. Therapeutic mechanisms have been developed to combat this by taking advantage of the underlying oncogenic mechanisms through chemical modulation. Camptothecin (CPT) is an example of this type of drug. It is a selective topoisomerase I inhibitor that is effective against many cancers, such as colorectal cancer. Previously, we successfully formulated a magnetic nanocarrier-conjugated CPT with β-cyclodextrin and iron NPs (Fe
    MeSH term(s) Camptothecin/chemistry ; Camptothecin/pharmacology ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/metabolism ; Genes, Neoplasm ; HT29 Cells ; Histones/genetics ; Histones/metabolism ; Humans ; Nanocapsules/chemistry ; Nanocapsules/therapeutic use ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Wnt Signaling Pathway/drug effects
    Chemical Substances Histones ; Nanocapsules ; Neoplasm Proteins ; Camptothecin (XT3Z54Z28A)
    Language English
    Publishing date 2021-11-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222212286
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Computational screening of dual inhibitors from FDA approved antiviral drugs on SARS-CoV-2 spike protein and the main protease using molecular docking approach.

    Sabarimurugan, Shanthi / Purushothaman, Indu / Swaminathan, Rajarajan / Dharmarajan, Arun / Warrier, Sudha / Kothandan, Sangeetha

    Acta virologica

    2021  Volume 65, Issue 2, Page(s) 160–172

    Abstract: The deadly disease-causing novel coronavirus has recently swept across the world and endangered many human lives. Although, various research on therapeutic measures to solve this pandemic crisis has been published; no favourable results have been ... ...

    Abstract The deadly disease-causing novel coronavirus has recently swept across the world and endangered many human lives. Although, various research on therapeutic measures to solve this pandemic crisis has been published; no favourable results have been achieved. We propose the use of potential FDA-approved dual inhibitors which can inhibit two targets (either on entry-level or the main protease) for the effective treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We screened 12 FDA-approved antiviral inhibitors listed in Drug bank and analysed the ADMET properties of each drug of interest to study the bioavailability, safety and toxicity. Two potential targets, the spike protein and the main protease of SARS-CoV-2 obtained from PDB have been used for molecular docking. All the selected drugs were docked with both targets and demonstrated strong hydrogen bond (HB) interactions in multiple active sites. Amongst these, the range of binding energy was from 3-7 kcal/mol for spike protein and 2-8 kcal/mol for the main protease. Upon comparison of all the processed drugs ganciclovir and zanamivir displayed significant binding energy with HB interactions with both, spike (-9.2 and -9 kcal/mol respectively) and the main protease (-9 kcal/mol). Ribavirin and tenofovir showed significant binding energy above -8 kcal/mol with seven HB interactions with the main protease and also spike protein. The novel findings regarding the antiviral properties of these dual inhibitors using a computational approach will be a good starting point for the efficacy determination of these drugs for pre-clinical and clinical studies aimed at developing active antivirals to target SARS-CoV-2. Keywords: SARS-CoV-2; FDA-approved drugs; viral inhibitors; in-silico analysis; molecular docking.
    MeSH term(s) Antiviral Agents/pharmacology ; COVID-19 ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Antiviral Agents ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptide Hydrolases (EC 3.4.-)
    Language English
    Publishing date 2021-06-15
    Publishing country Slovakia
    Document type Journal Article
    ZDB-ID 210452-0
    ISSN 1336-2305 ; 0001-723X
    ISSN (online) 1336-2305
    ISSN 0001-723X
    DOI 10.4149/av_2021_208
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 336: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article: Crosstalk between Stress Granules, Exosomes, Tumour Antigens, and Immune Cells: Significance for Cancer Immunity.

    Kothandan, Vinoth Kumar / Kothandan, Sangeetha / Kim, Do Hee / Byun, Youngro / Lee, Yong-Kyu / Park, In-Kyu / Hwang, Seung Rim

    Vaccines

    2020  Volume 8, Issue 2

    Abstract: RNA granules and exosomes produced by tumour cells under various stresses in the microenvironment act as critical determinants of cell survival by promoting angiogenesis, cancer metastasis, chemoresistance, and immunosuppression. Meanwhile, developmental ...

    Abstract RNA granules and exosomes produced by tumour cells under various stresses in the microenvironment act as critical determinants of cell survival by promoting angiogenesis, cancer metastasis, chemoresistance, and immunosuppression. Meanwhile, developmental cancer/testis (CT) antigens that are normally sequestered in male germ cells of the testes, but which are overexpressed in malignant tumour cells, can function as tumour antigens triggering immune responses. As CT antigens are potential vaccine candidates for use in cancer immunotherapy, they could be targeted together with crosstalk between stress granules, exosomes, and immune cells for a synergistic effect. In this review, we describe the effects of exosomes and exosomal components presented to the recipient cells under different types of stresses on immune cells and cancer progression. Furthermore, we discuss their significance for cancer immunity, as well as the outlook for their future application.
    Language English
    Publishing date 2020-04-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines8020172
    Database MEDical Literature Analysis and Retrieval System OnLINE

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