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  1. Article ; Online: An overview on monkeypox virus: Pathogenesis, transmission, host interaction and therapeutics.

    Rampogu, Shailima / Kim, Yongseong / Kim, Seon-Won / Lee, Keun Woo

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1076251

    Abstract: ... ...

    Abstract Orthopoxvirus
    MeSH term(s) Animals ; Humans ; Monkeypox virus ; Mpox (monkeypox)/epidemiology ; Zoonoses ; Africa ; Host Microbial Interactions
    Language English
    Publishing date 2023-02-10
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1076251
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Curcumin Chalcone Derivatives Database (CCDD): a Python framework for natural compound derivatives database.

    Rampogu, Shailima / Balasubramaniyam, Thananjeyan / Lee, Joon-Hwa

    PeerJ

    2023  Volume 11, Page(s) e15885

    Abstract: We built the Curcumin Chalcone Derivatives Database (CCDD) to enable the effective virtual screening of highly potent curcumin and its analogs. The two-dimensional (2D) structures were drawn using the ChemBioOffice package and converted to 3D structures ... ...

    Abstract We built the Curcumin Chalcone Derivatives Database (CCDD) to enable the effective virtual screening of highly potent curcumin and its analogs. The two-dimensional (2D) structures were drawn using the ChemBioOffice package and converted to 3D structures using Discovery Studio Visualizer V 2021 (DS). The database was built using different Python modules. For the 3D structures, different Python packages were used to obtain the data frame of compounds. This framework is also used to visualize the compounds. The webserver enables the users to screen the compounds according to Lipinski's rule of five. The structures can be downloaded in .sdf and .mol format. The data frame (df) can be downloaded in .csv format. Our webserver can help computational drug discovery researchers find new therapeutics and build new webservers. The CCDD is freely available at: https://srampogu-ccdd-ccdd-8uldk8.streamlit.app/.
    MeSH term(s) Chalcones ; Curcumin ; Chalcone ; Databases, Factual ; Drug Discovery
    Chemical Substances Chalcones ; Curcumin (IT942ZTH98) ; Chalcone (5S5A2Q39HX)
    Language English
    Publishing date 2023-08-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.15885
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Explicit molecular dynamics simulation studies to discover novel natural compound analogues as

    Rampogu, Shailima / Shaik, Baji / Kim, Ju Hyun / Jung, Tae Sung / Ha, Min Woo / Lee, Keun Woo

    Heliyon

    2023  Volume 9, Issue 2, Page(s) e13324

    Abstract: Tuberculosis (TB) in one of the dreadful diseases present globally. This is caused ... ...

    Abstract Tuberculosis (TB) in one of the dreadful diseases present globally. This is caused by
    Language English
    Publishing date 2023-01-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e13324
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  4. Article: Pharmacophore Modelling-Based Drug Repurposing Approaches for SARS-CoV-2 Therapeutics.

    Rampogu, Shailima / Lee, Keun Woo

    Frontiers in chemistry

    2021  Volume 9, Page(s) 636362

    Abstract: The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to ... ...

    Abstract The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to repurpose the approved drugs. In this pursuit, an exhaustive computational method has been used on the DrugBank compounds targeting nsp16/nsp10 complex (PDB code: 6W4H). A structure-based pharmacophore model was generated, and the selected model was escalated to screen DrugBank database, resulting in three compounds. These compounds were subjected to molecular docking studies at the protein-binding pocket employing the CDOCKER module available with the Discovery Studio v18. In order to discover potential candidate compounds, the co-crystallized compound S-adenosyl methionine (SAM) was used as the reference compound. Additionally, the compounds remdesivir and hydroxycholoroquine were employed for comparative docking. The results have shown that the three compounds have demonstrated a higher dock score than the reference compounds and were upgraded to molecular dynamics simulation (MDS) studies. The MDS results demonstrated that the three compounds, framycetin, kanamycin, and tobramycin, are promising candidate compounds. They have represented a stable binding mode at the targets binding pocket with an average protein backbone root mean square deviation below 0.3 nm. Additionally, they have prompted the hydrogen bonds during the entire simulations, inferring that the compounds have occupied the active site firmly. Taken together, our findings propose framycetin, kanamycin, and tobramycin as potent putative inhibitors for COVID-19 therapeutics.
    Language English
    Publishing date 2021-05-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711776-5
    ISSN 2296-2646
    ISSN 2296-2646
    DOI 10.3389/fchem.2021.636362
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  5. Article ; Online: Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors.

    Rampogu, Shailima / Jung, Tae Sung / Ha, Min Woo / Lee, Keun Woo

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 10583

    Abstract: Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and ...

    Abstract Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.
    MeSH term(s) Humans ; SARS-CoV-2 ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; COVID-19 ; Drug Repositioning ; Pandemics
    Chemical Substances Poly(ADP-ribose) Polymerase Inhibitors
    Language English
    Publishing date 2023-06-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-36342-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Pharmacophore Modelling-Based Drug Repurposing Approaches for SARS-CoV-2 Therapeutics

    Shailima Rampogu / Keun Woo Lee

    Frontiers in Chemistry, Vol

    2021  Volume 9

    Abstract: The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to ... ...

    Abstract The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating effect globally with no effective treatment. The swift strategy to find effective treatment against coronavirus disease 2019 (COVID-19) is to repurpose the approved drugs. In this pursuit, an exhaustive computational method has been used on the DrugBank compounds targeting nsp16/nsp10 complex (PDB code: 6W4H). A structure-based pharmacophore model was generated, and the selected model was escalated to screen DrugBank database, resulting in three compounds. These compounds were subjected to molecular docking studies at the protein-binding pocket employing the CDOCKER module available with the Discovery Studio v18. In order to discover potential candidate compounds, the co-crystallized compound S-adenosyl methionine (SAM) was used as the reference compound. Additionally, the compounds remdesivir and hydroxycholoroquine were employed for comparative docking. The results have shown that the three compounds have demonstrated a higher dock score than the reference compounds and were upgraded to molecular dynamics simulation (MDS) studies. The MDS results demonstrated that the three compounds, framycetin, kanamycin, and tobramycin, are promising candidate compounds. They have represented a stable binding mode at the targets binding pocket with an average protein backbone root mean square deviation below 0.3 nm. Additionally, they have prompted the hydrogen bonds during the entire simulations, inferring that the compounds have occupied the active site firmly. Taken together, our findings propose framycetin, kanamycin, and tobramycin as potent putative inhibitors for COVID-19 therapeutics.
    Keywords SARS-CoV-2 ; novel coronavirus ; COVID-19 ; drug repurposing ; pharmacophore modelling ; Chemistry ; QD1-999
    Subject code 540
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Role of quassinoids as potential antimalarial agents: An in silico approach.

    Rampogu, Shailima

    Ancient science of life

    2016  Volume 35, Issue 2, Page(s) 85–89

    Abstract: Background: Malaria is an infection caused by mosquitoes in human beings which can be dangerous if untreated. A well known plant product, quassinoids are known to have antimalarial activity. These bioactive phytochemicals belong to the triterpene family. ...

    Abstract Background: Malaria is an infection caused by mosquitoes in human beings which can be dangerous if untreated. A well known plant product, quassinoids are known to have antimalarial activity. These bioactive phytochemicals belong to the triterpene family. Quassinoids are used in the present study to act against malarial dihydrofolate reductase (Pf-DHFR), a potential antimalarial target. Nevertheless, viṣama jvara (~malaria) has been treated with the bark of Cinchona since a long time.
    Aim: The aim of the present experiment is to perform the protein-ligand docking for Pf- DHFR and Quassinoids and study their binding affinities.
    Setting and design: The software used for the present study is the discovery studio (Accelrys 2.1), Protein Data Bank (PDB), and Chemsketch.
    Materials and methods: The protein for the present study was imported from protein data bank with the PDB Id, 4dpd and was prepared for docking. The ligands used for the study are the quassinoids. They were drawn using chemsketch and the 3D structures were generated. The docking was done subsequently.
    Statistical analysis used: Molecular modeling technique was used for the protein-ligand docking analysis.
    Results: The docking results showed that the Quassinoids Model_1 showed the highest dock score of 40.728.
    Conclusion: The present study proves the promising potential of quassinoids as novel drugs against malaria. The dock results conclude that the quassinoids can be adopted as an alternative drug against malaria.
    Language English
    Publishing date 2016-02-10
    Publishing country India
    Document type Journal Article
    ZDB-ID 2660395-0
    ISSN 2249-9547 ; 0257-7941
    ISSN (online) 2249-9547
    ISSN 0257-7941
    DOI 10.4103/0257-7941.171676
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  8. Article ; Online: Phytotherapeutic applications of alkaloids in treating breast cancer.

    Rampogu, Shailima / Balasubramaniyam, Thananjeyan / Lee, Joon-Hwa

    Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie

    2022  Volume 155, Page(s) 113760

    Abstract: Breast cancer is one of the major causes of mortality in women worldwide. The current treatments available are radiation therapy (RT), surgery, endocrine (hormone) therapy (ET), chemotherapy (CT), and targeted therapy. These treatments are associated ... ...

    Abstract Breast cancer is one of the major causes of mortality in women worldwide. The current treatments available are radiation therapy (RT), surgery, endocrine (hormone) therapy (ET), chemotherapy (CT), and targeted therapy. These treatments are associated with certain side effects that demand the use of natural compounds due to their lower to negligible side effects. One such category of natural compounds is alkaloids. Alkaloids are a group of natural compounds that have gained widespread attention due to their use as potential therapeutics. Alkaloids exert anti-inflammatory and antiviral properties along with antimicrobial activities. In the current review, 12 alkaloids are reviewed in detail for their potential in treating breast cancer. These alkaloids have been shown to induce apoptosis, decrease tumor volume, inhibit cell proliferation and migration, and induce autophagy and they can also be used as a component of combination therapy. This review provides comprehensive information on the in vitro and in vivo therapeutic abilities of alkaloids to counteract breast cancer.
    MeSH term(s) Female ; Humans ; Breast Neoplasms/drug therapy ; Breast Neoplasms/pathology ; Alkaloids/pharmacology ; Alkaloids/therapeutic use ; Anti-Inflammatory Agents/therapeutic use ; Antiviral Agents/therapeutic use ; Anti-Infective Agents/therapeutic use ; Hormones
    Chemical Substances Alkaloids ; Anti-Inflammatory Agents ; Antiviral Agents ; Anti-Infective Agents ; Hormones
    Language English
    Publishing date 2022-09-29
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 392415-4
    ISSN 1950-6007 ; 0753-3322 ; 0300-0893
    ISSN (online) 1950-6007
    ISSN 0753-3322 ; 0300-0893
    DOI 10.1016/j.biopha.2022.113760
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole.

    Rampogu, Shailima / Shaik, Mohammed Rafi / Khan, Merajuddin / Khan, Mujeeb / Oh, Tae Hwan / Shaik, Baji

    Database : the journal of biological databases and curation

    2023  Volume 2023

    Abstract: The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from ... ...

    Abstract The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from the literature. The two-dimensional (2D) structures were drawn using ChemDraw, and the .sdf file was created employing Discovery Studio Visualizer v2017. These compounds were read on the R-shiny app using ChemmineR, and the dataframe consisting of a total of 1146 compounds was generated and manipulated employing the dplyr package. The web server is provided with JSME 2D sketcher. The descriptors of the compounds are obtained using propOB with a filter. The users can download the filtered data in the .csv and .sdf formats, and the entire dataset of a compound can be downloaded in .sdf format. This web server facilitates the researchers to screen plausible inhibitors for different diseases. Additionally, the method used in building the web server can be adapted for developing other small-molecule databases (web servers) in RStudio. Database URL: https://srampogu.shinyapps.io/CBPDdb_Revised/.
    MeSH term(s) Benzothiazoles ; Coumarins ; Databases, Factual ; Pyrazoles
    Chemical Substances Benzothiazoles ; Coumarins ; Pyrazoles
    Language English
    Publishing date 2023-09-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2496706-3
    ISSN 1758-0463 ; 1758-0463
    ISSN (online) 1758-0463
    ISSN 1758-0463
    DOI 10.1093/database/baad062
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A review on Millepachine and its derivatives as potential multitarget anticancer agents.

    Rampogu, Shailima / Badvel, Pallavi / Hoon Jo, Byung / Kim, Yongseong / Kim, Seon-Won / Lee, Keun Woo

    Biochemical and biophysical research communications

    2023  Volume 681, Page(s) 249–270

    Abstract: Chalcones have a long history of being used for many medical purposes. These are the most prestigious scaffolds in medicine. The potential of Millepachine and its derivatives to treat various malignancies has been demonstrated in this review. The ... ...

    Abstract Chalcones have a long history of being used for many medical purposes. These are the most prestigious scaffolds in medicine. The potential of Millepachine and its derivatives to treat various malignancies has been demonstrated in this review. The anticancer effects of Millepachine and its derivatives on ovarian cancer, hepatocellular carcinoma, breast, liver, colon, cervical, prostate, stomach, and gliomas are highlighted in the current review. Several genes that are crucial in reducing the severity of the disease have been altered by these substances. They mainly work by preventing tubulin polymerizing. They also exhibit apoptosis and cell cycle arrest at the G2/M phase. Additionally, these compounds inhibit invasion and migration and have antiproliferative effects. Preclinical studies have shown that Millepachine and its derivatives offer exceptional potential for treating a number of cancers. These results need to be confirmed in clinical research in order to develop viable cancer therapies.
    MeSH term(s) Male ; Humans ; Chalcones/pharmacology ; Chalcones/therapeutic use ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Carcinoma, Hepatocellular ; Apoptosis ; Liver Neoplasms ; Tubulin/metabolism ; Cell Proliferation ; Cell Line, Tumor ; Structure-Activity Relationship ; Tubulin Modulators/pharmacology ; Drug Screening Assays, Antitumor
    Chemical Substances millepachine ; Chalcones ; Antineoplastic Agents ; Tubulin ; Tubulin Modulators
    Language English
    Publishing date 2023-09-19
    Publishing country United States
    Document type Review ; Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2023.09.044
    Database MEDical Literature Analysis and Retrieval System OnLINE

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