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  1. Article ; Online: A fragment-based structural analysis of MMP-2 inhibitors in search of meaningful structural fragments.

    Banerjee, Suvankar / Amin, Sk Abdul / Jha, Tarun

    Computers in biology and medicine

    2022  Volume 144, Page(s) 105360

    Abstract: The matrix metalloproteinase family of ... ...

    Abstract The matrix metalloproteinase family of Zn
    MeSH term(s) Antineoplastic Agents/pharmacology ; Catalytic Domain ; Humans ; Matrix Metalloproteinase 2/chemistry ; Matrix Metalloproteinase Inhibitors/chemistry ; Matrix Metalloproteinase Inhibitors/pharmacology ; Neoplasms
    Chemical Substances Antineoplastic Agents ; Matrix Metalloproteinase Inhibitors ; Matrix Metalloproteinase 2 (EC 3.4.24.24)
    Language English
    Publishing date 2022-03-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2022.105360
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 653: Show issues Location:
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  2. Article ; Online: Advances in structure-activity relationships of HDAC inhibitors as HIV latency-reversing agents.

    Khatun, Samima / Amin, Sk Abdul / Choudhury, Debasmita / Chowdhury, Boby / Jha, Tarun / Gayen, Shovanlal

    Expert opinion on drug discovery

    2024  Volume 19, Issue 3, Page(s) 353–368

    Abstract: Introduction: HIV-infected cells may rebound due to the existence of the silent HIV-infected memory CD4+ T cells (HIV latency). This HIV latency makes the disease almost incurable. In latency, the integrated proviral DNA of HIV is transcriptionally ... ...

    Abstract Introduction: HIV-infected cells may rebound due to the existence of the silent HIV-infected memory CD4+ T cells (HIV latency). This HIV latency makes the disease almost incurable. In latency, the integrated proviral DNA of HIV is transcriptionally silenced partly due to the activity of histone deacetylases (HDACs). Hence, inhibition of HDAC is considered a prime target for HIV latency reversal.
    Areas covered: A brief biology and function of HDACs have been discussed to identify key points to design HDAC inhibitors (HDACis). This article summarizes recent achievements in the development of HDACis to achieve HIV latency reversal. Structure-activity relationships (SARs) of some series of compounds were also explored.
    Expert opinion: Depletion of the HIV reservoir is the only way to end this deadly epidemic. HDACis are latency-reversing agents (LRA) that can be used to 'shock' the latently infected CD4+ T cells to induce them to produce viral proteins. It is interesting to note that HDAC3, which is extensively expressed in resting T cells, is specifically preferred by benzamide-containing HDACis for inhibition. Thus, the benzamide class of compounds should be explored. Nevertheless, more data on selective HDAC inhibition is needed for further development of HDACis in HIV latency reversal.
    MeSH term(s) Humans ; Histone Deacetylase Inhibitors/pharmacology ; Virus Latency ; Histone Deacetylases/metabolism ; Benzamides ; HIV Infections/drug therapy ; Structure-Activity Relationship
    Chemical Substances Histone Deacetylase Inhibitors ; Histone Deacetylases (EC 3.5.1.98) ; Benzamides
    Language English
    Publishing date 2024-01-23
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2259618-5
    ISSN 1746-045X ; 1746-0441
    ISSN (online) 1746-045X
    ISSN 1746-0441
    DOI 10.1080/17460441.2024.2305730
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives.

    Khatun, Samima / Bhagat, Rinki Prasad / Amin, Sk Abdul / Jha, Tarun / Gayen, Shovanlal

    Computers in biology and medicine

    2024  Volume 175, Page(s) 108468

    Abstract: Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the ... ...

    Abstract Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2024.108468
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  4. Article ; Online: Fight against novel coronavirus: A perspective of medicinal chemists.

    Amin, Sk Abdul / Jha, Tarun

    European journal of medicinal chemistry

    2020  Volume 201, Page(s) 112559

    Abstract: The ongoing novel coronavirus disease (COVID-19) pandemic makes us painfully perceive that our bullet shells are blank so far for fighting against severe human coronavirus (HCoV). In spite of vast research work, it is crystal clear that the evident does ... ...

    Abstract The ongoing novel coronavirus disease (COVID-19) pandemic makes us painfully perceive that our bullet shells are blank so far for fighting against severe human coronavirus (HCoV). In spite of vast research work, it is crystal clear that the evident does not warrant the commercial blossoming of anti-HCoV drugs. In this circumstance, drug repurposing and/or screening of databases are the only fastest option. This study is an initiative to recapitulate the medicinal chemistry of severe acute respiratory syndrome (SARS)-CoV-2 (SARS-CoV-2). The aim is to present an exquisite delineation of the current research from the perspective of a medicinal chemist to allow the rapid development of anti-SARS-CoV-2 agents.
    MeSH term(s) Antiviral Agents/therapeutic use ; Betacoronavirus/drug effects ; COVID-19 ; Coronavirus Infections/drug therapy ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Drug Discovery ; Drug Repositioning ; Humans ; Pandemics ; Pharmaceutical Preparations/administration & dosage ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; SARS-CoV-2 ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Pharmaceutical Preparations
    Keywords covid19
    Language English
    Publishing date 2020-06-12
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2020.112559
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Exploring molecular fingerprints of different drugs having bile interaction: a stepping stone towards better drug delivery.

    Sardar, Sourav / Bhattacharya, Arijit / Amin, Sk Abdul / Jha, Tarun / Gayen, Shovanlal

    Molecular diversity

    2023  

    Abstract: Bile acids are amphiphilic substances produced naturally in humans. In the context of drug delivery and dosage form design, it is critical to understand whether a drug interacts with bile inside the gastrointestinal (GI) tract or not. This study focuses ... ...

    Abstract Bile acids are amphiphilic substances produced naturally in humans. In the context of drug delivery and dosage form design, it is critical to understand whether a drug interacts with bile inside the gastrointestinal (GI) tract or not. This study focuses on the identification of structural fingerprints/features important for bile interaction. Molecular modelling methods such as Bayesian classification and recursive partitioning (RP) studies are executed to find important fingerprints/features for the bile interaction. For the Bayesian classification study, the ROC score of 0.837 and 0.950 are found for the training set and the test set compounds, respectively. The fluorine-containing aliphatic/aromatic group, the branched chain of the alkyl group containing hydroxyl moiety and the phenothiazine ring etc. are identified as good fingerprints having a positive contribution towards bile interactions, whereas, the bad fingerprints such as free carboxylate group, purine, and pyrimidine ring etc. have a negative contribution towards bile interactions. The best tree (tree ID: 1) from the RP study classifies the bile interacting or non-interacting compounds with a ROC score of 0.941 for the training and 0.875 for the test set. Additionally, SARpy and QSAR-Co analyses are also been performed to classify compounds as bile interacting/non-interacting. Moreover, forty-six recently FDA-approved drugs have been screened by the developed SARpy and QSAR-Co models to assess their bile interaction properties. Overall, this attempt may facilitate the researchers to identify bile interacting/non-interacting molecules in a faster way and help in the design of formulations and target-specific drug development.
    Language English
    Publishing date 2023-06-27
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-023-10670-2
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    Zs.A 4946: Show issues Location:
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  6. Article ; Online: Are inhibitors of histone deacetylase 8 (HDAC8) effective in hematological cancers especially acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL)?

    Amin, Sk Abdul / Khatun, Samima / Gayen, Shovanlal / Das, Sanjib / Jha, Tarun

    European journal of medicinal chemistry

    2023  Volume 258, Page(s) 115594

    Abstract: Histone deacetylase 8 (HDAC8) aberrantly deacetylates histone and non-histone proteins. These include structural maintenance of chromosome 3 (SMC3) cohesin protein, retinoic acid induced 1 (RAI1), p53, etc and thus, regulating diverse processes such as ... ...

    Abstract Histone deacetylase 8 (HDAC8) aberrantly deacetylates histone and non-histone proteins. These include structural maintenance of chromosome 3 (SMC3) cohesin protein, retinoic acid induced 1 (RAI1), p53, etc and thus, regulating diverse processes such as leukemic stem cell (LSC) transformation and maintenance. HDAC8, one of the crucial HDACs, affects the gene silencing process in solid and hematological cancer progressions especially on acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). A specific HDAC8 inhibitor PCI-34051 showed promising results against both T-cell lymphoma and AML. Here, we summarize the role of HDAC8 in hematological malignancies, especially in AML and ALL. This article also introduces the structure/function of HDAC8 and a special attention has been paid to address the HDAC8 enzyme selectivity issue in hematological cancer especially against AML and ALL.
    MeSH term(s) Humans ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylase Inhibitors/therapeutic use ; Histone Deacetylase Inhibitors/chemistry ; Percutaneous Coronary Intervention ; Histone Deacetylases/metabolism ; Leukemia, Myeloid, Acute/pathology ; Hematologic Neoplasms ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; Repressor Proteins
    Chemical Substances Histone Deacetylase Inhibitors ; Histone Deacetylases (EC 3.5.1.98) ; HDAC8 protein, human (EC 3.5.1.98) ; Repressor Proteins
    Language English
    Publishing date 2023-06-25
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2023.115594
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Exploring structural requirements of HDAC10 inhibitors through comparative machine learning approaches.

    Bhattacharya, Arijit / Amin, Sk Abdul / Kumar, Prabhat / Jha, Tarun / Gayen, Shovanlal

    Journal of molecular graphics & modelling

    2023  Volume 123, Page(s) 108510

    Abstract: Histone deacetylase (HDAC) inhibitors are in the limelight of anticancer drug development and research. HDAC10 is one of the class-IIb HDACs, responsible for cancer progression. The search for potent and effective HDAC10 selective inhibitors is going on. ...

    Abstract Histone deacetylase (HDAC) inhibitors are in the limelight of anticancer drug development and research. HDAC10 is one of the class-IIb HDACs, responsible for cancer progression. The search for potent and effective HDAC10 selective inhibitors is going on. However, the absence of human HDAC10 crystal/NMR structure hampers the structure-based drug design of HDAC10 inhibitors. Different ligand-based modeling techniques are the only hope to speed up the inhibitor design. In this study, we applied different ligand-based modeling techniques on a diverse set of HDAC10 inhibitors (n = 484). Machine learning (ML) models were developed that could be used to screen unknown compounds as HDAC10 inhibitors from a large chemical database. Moreover, Bayesian classification and Recursive partitioning models were used to identify the structural fingerprints regulating the HDAC10 inhibitory activity. Additionally, a molecular docking study was performed to understand the binding pattern of the identified structural fingerprints towards the active site of HDAC10. Overall, the modeling insight might offer helpful information for medicinal chemists to design and develop efficient HDAC10 inhibitors.
    MeSH term(s) Humans ; Molecular Docking Simulation ; Ligands ; Bayes Theorem ; Histone Deacetylases/chemistry ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylase Inhibitors/chemistry ; Machine Learning
    Chemical Substances Ligands ; Histone Deacetylases (EC 3.5.1.98) ; Histone Deacetylase Inhibitors ; HDAC10 protein, human (EC 3.5.1.98)
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1396450-1
    ISSN 1873-4243 ; 1093-3263
    ISSN (online) 1873-4243
    ISSN 1093-3263
    DOI 10.1016/j.jmgm.2023.108510
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    Zs.A 3491: Show issues Location:
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  8. Article ; Online: A critical analysis of urea transporter B inhibitors: molecular fingerprints, pharmacophore features for the development of next-generation diuretics.

    Amin, Sk Abdul / Nandi, Sudipta / Kashaw, Sushil Kumar / Jha, Tarun / Gayen, Shovanlal

    Molecular diversity

    2022  Volume 26, Issue 5, Page(s) 2549–2559

    Abstract: Urea transporter is a membrane transport protein. It is involved in the transferring of urea across the cell membrane in humans. Along with urea transporter A, urea transporter B (UT-B) is also responsible for the management of urea concentration and ... ...

    Abstract Urea transporter is a membrane transport protein. It is involved in the transferring of urea across the cell membrane in humans. Along with urea transporter A, urea transporter B (UT-B) is also responsible for the management of urea concentration and blood pressure of human. The inhibitors of urea transporters have already generated a huge attention to be developed as alternate safe class of diuretic. Unlike conventional diuretics, these inhibitors are suitable for long-term therapy without hampering the precious electrolyte imbalance in the human body. In this study, UT-B inhibitors were analysed by using multi-chemometric modelling approaches. The possible pharmacophore features along with favourable and unfavourable sub-structural fingerprints for UT-B inhibition are extracted. This information will guide the medicinal chemist to design potent UT-B inhibitors in future.
    MeSH term(s) Diuretics/chemistry ; Diuretics/pharmacology ; Electrolytes/metabolism ; Humans ; Membrane Transport Proteins ; Urea/pharmacology ; Urea Transporters
    Chemical Substances Diuretics ; Electrolytes ; Membrane Transport Proteins ; Urea (8W8T17847W)
    Language English
    Publishing date 2022-01-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-021-10353-w
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  9. Article ; Online: Updated chemical scaffolds of ABCG2 inhibitors and their structure-inhibition relationships for future development.

    Moinul, Md / Amin, Sk Abdul / Jha, Tarun / Gayen, Shovanlal

    European journal of medicinal chemistry

    2022  Volume 241, Page(s) 114628

    Abstract: ATP-binding cassette (ABC) transporters are pivotal for cell detoxification and survival. Overexpression of ABC transporter in tumor cells lead to chemoresistance through the efflux of chemotherapeutic agents. P-glycoprotein (Pgp/ABCB1), multidrug ... ...

    Abstract ATP-binding cassette (ABC) transporters are pivotal for cell detoxification and survival. Overexpression of ABC transporter in tumor cells lead to chemoresistance through the efflux of chemotherapeutic agents. P-glycoprotein (Pgp/ABCB1), multidrug resistance protein 1 (MRP1/ABCC1) and breast cancer resistance protein (BCRP/ABCG2) are the major ABC transporters involved in multidrug resistance (MDR) of cancer cells against anticancer drugs. ABCG2 is one of the major transporters involved in the efflux of different cytotoxic agents. Hence, inhibition of ABCG2-mediated transport is considered a prime target to resist MDR of cancer cells. Here, brief structural biology and functions of ABCG2 were discussed with the aim to identify key pharmacophoric elements to design potent and selective as well as non-toxic ABCG2 inhibitors. Structure-inhibition relationships (SIRs) of the earlier reported compounds were also explored. Taken together, this study offers insight for further development of ABCG2 inhibitors.
    MeSH term(s) ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism ; ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism ; ATP-Binding Cassette Transporters/metabolism ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Drug Resistance, Multiple ; Drug Resistance, Neoplasm ; Neoplasm Proteins/metabolism
    Chemical Substances ATP Binding Cassette Transporter, Subfamily B, Member 1 ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; ATP-Binding Cassette Transporters ; Antineoplastic Agents ; Neoplasm Proteins
    Language English
    Publishing date 2022-07-31
    Publishing country France
    Document type Journal Article ; Review
    ZDB-ID 188597-2
    ISSN 1768-3254 ; 0009-4374 ; 0223-5234
    ISSN (online) 1768-3254
    ISSN 0009-4374 ; 0223-5234
    DOI 10.1016/j.ejmech.2022.114628
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  10. Article ; Online: Host P2X

    Mukherjee, Niladri / Banerjee, Saswati / Amin, Sk Abdul / Jha, Tarun / Datta, Sriparna / Das Saha, Krishna

    Experimental parasitology

    2022  Volume 241, Page(s) 108365

    Abstract: Current drugs are inefficient for the treatment of visceral leishmaniasis an immunosuppressive ailment caused by Leishmania donovani. Regrettably, there is no plant-origin antileishmanial drug present. ... ...

    Abstract Current drugs are inefficient for the treatment of visceral leishmaniasis an immunosuppressive ailment caused by Leishmania donovani. Regrettably, there is no plant-origin antileishmanial drug present. P2X
    MeSH term(s) Animals ; Carrier Proteins/metabolism ; Leishmania donovani/metabolism ; Leishmaniasis, Visceral/drug therapy ; Macrophages/metabolism ; Mice ; Mice, Inbred BALB C ; Receptors, Purinergic P2X7/metabolism ; Signal Transduction ; Spleen/metabolism ; p38 Mitogen-Activated Protein Kinases/metabolism
    Chemical Substances Carrier Proteins ; Receptors, Purinergic P2X7 ; p38 Mitogen-Activated Protein Kinases (EC 2.7.11.24)
    Language English
    Publishing date 2022-08-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 391089-1
    ISSN 1090-2449 ; 0014-4894
    ISSN (online) 1090-2449
    ISSN 0014-4894
    DOI 10.1016/j.exppara.2022.108365
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