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Exploring host epigenetic enzymes as targeted therapies for visceral leishmaniasis: in silico design and in vitro efficacy of KDM6B and ASH1L inhibitors

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Abstract

In order to combat various infectious diseases, the utilization of host-directed therapies as an alternative to chemotherapy has gained a lot of attention in the recent past, since it bypasses the existing limitations of conventional therapies. The use of host epigenetic enzymes like histone lysine methyltransferases and lysine demethylases as potential drug targets has successfully been employed for controlling various inflammatory diseases like rheumatoid arthritis and acute leukemia. In our earlier study, we have already shown that the functional knockdown of KDM6B and ASH1L in the experimental model of visceral leishmaniasis has resulted in a significant reduction of organ parasite burden. Herein, we performed a high throughput virtual screening against KDM6B and ASH1L using > 53,000 compounds that were obtained from the Maybridge library and PubChem Database, followed by molecular docking to evaluate their docking score/Glide Gscore. Based on their docking scores, the selected inhibitors were later assessed for their in vitro anti-leishmanial efficacy. Out of all inhibitors designed against KDM6B and ASH1L, HTS09796, GSK-J4 and AS-99 particularly showed promising in vitro activity with IC50 < 5 µM against both extracellular promastigote and intracellular amastigote forms of L. donovani. In vitro drug interaction studies of these inhibitors further demonstrated their synergistic interaction with amphotericin-B and miltefosine. However, GSK-J4 makes an exception by displaying an in different mode of interaction with miltefosine. Collectively, our in silico and in vitro studies acted as a platform to identify the applicability of these inhibitors targeted against KDM6B and ASH1L for anti-leishmanial therapy.

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Data availability

No datasets were generated or analysed during the current study.

Abbreviations

ASH1L:

Histone lysine N-methyltransferase

BLAST:

Basic local alignment search tool

CC50 :

50% Cytotoxicity concentration

CRK12:

Cell division cycle-2-related kinase 12

DNMT:

DNA methyltransferases

FDA:

Food and drug administration

GUI:

Graphical user interface

HDAC:

Histone deacetylases

IC50 :

Half-maximal inhibitory concentration

KMTs:

Histone lysine methyltransferases

KDMs:

Histone lysine demethylases

KDM6B:

Histone lysine demethylase 6B

MTT:

3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide

OPLS:

Optimized potentials for liquid simulations

PDB:

Protein data bank

QSAR:

Quantitative structure- activity relationship

RMSD:

Root mean square deviation

RLU:

Relative luminescence unit

VL:

Visceral leishmaniasis

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Acknowledgements

The authors would like to thank Dr. Neena Goyal, Division of Biochemistry and Structural Biology, CSIR-CDRI, Lucknow, India, for providing us with transgenic L. donovani promastigotes. The authors extend their gratitude to Dr. Sanjay Batra, Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, India, for providing the Maybridge library compounds (sourced from the chemical repository of CSIR-CDRI, Lucknow) for the in vitro assessment conducted in this study.

Funding

The study was funded by the Department of Biotechnology (BT/PR32490/MED/29/1457/2019) & Department of Science & Technology (DST, CRG/2020/002932), New Delhi, India and CSIR-CDRI in-house project. The author M.D. & U.K. is thankful to CSIR & UGC, New Delhi respectively for providing financial assistance in the form of fellowship. T.Q. acknowledges the Department of Science & Technology (DST, CRG/2020/002932), New Delhi, for the project fellowship.

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Author notes

  1. Tooba Qamar

    Present address: Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, 226014, India

  2. Mukul Dutta and Tooba Qamar have contributed equally to this work.

Authors and Affiliations

  1. Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India

    Mukul Dutta & Susanta Kar

  2. Molecular Microbiology & Immunology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India

    Mukul Dutta, Tooba Qamar & Susanta Kar

  3. Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India

    Unnati Kushavah & Mohammad Imran Siddiqi

  4. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India

    Mukul Dutta, Unnati Kushavah, Mohammad Imran Siddiqi & Susanta Kar

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Contributions

MD, TQ and SK conceived and designed the study. MD and TQ performed and analyzed the results of biological experiments. TQ, UK and MIS performed and analyzed the results of computational studies. MD and TQ prepared the figures and wrote the original manuscript. Overall supervision, conceptualization, acquisition of funding & manuscript editing was done by SK. All authors reviewed the manuscript.

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Correspondence to Susanta Kar.

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Dutta, M., Qamar, T., Kushavah, U. et al. Exploring host epigenetic enzymes as targeted therapies for visceral leishmaniasis: in silico design and in vitro efficacy of KDM6B and ASH1L inhibitors. Mol Divers (2024). https://doi.org/10.1007/s11030-024-10824-w

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