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Identification of potential natural compound inhibitors and drug like molecules against human METTL3 by docking and molecular dynamics simulation

Shibambika Manna, Pragati Samal, Rohini Basak, Anushka Mitra, Arijit Kumar Roy, Raima Kundu, Amrita Ahir, View ORCID ProfileAmlan Roychowdhury, View ORCID ProfileDitipriya Hazra
doi: https://doi.org/10.1101/2022.06.19.496750
Shibambika Manna
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Pragati Samal
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Rohini Basak
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Anushka Mitra
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Arijit Kumar Roy
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Raima Kundu
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Amrita Ahir
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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Amlan Roychowdhury
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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  • ORCID record for Amlan Roychowdhury
  • For correspondence: ditipriya.hazra@jisuniversity.ac.in amlan.roychowdhury@jisuniversity.ac.in
Ditipriya Hazra
Department of Bioscience, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
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  • ORCID record for Ditipriya Hazra
  • For correspondence: ditipriya.hazra@jisuniversity.ac.in amlan.roychowdhury@jisuniversity.ac.in
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Abstract

Nucleotide level chemical modification in transcriptome is critical in regulating different cellular processes, including cancer. The most investigated epitranscriptomic modification is methylation at the N6- position of adenosine (m6A). This dynamic modification process is carried out by: writer, reader and eraser proteins. Writers are methyltransferases, METTL3 is the major writer that works in association with METTL14, an accessory protein. Extensive study revealed that cancer progression for acute myeloid leukaemia, gastric cancer, colorectal cancer, hepatocellular carcinoma, and lung cancer is directly contributed by irregular expression of METTL3. Targeting METTL3, has opened a new window in the development of new inhibitors/drugs. In this study, 80 commercially available compounds were found from an unbiased screening by molecular docking, showing better score when compared with the existing substrate/substrate-analogue and the inhibitor bound crystal structures in terms of docking score and binding energy calculation. Among this pool of compounds, the best seven small molecules, AMF, RAD, JNJ, MEH, ECP, MHN, SGI, have been selected and further validated by different computational tools like binding energy calculation, molecular dynamics simulation etc. The novel hits found in this study can function as lead compounds which can be developed into inhibitors as well as drugs, specific against METTL3.

Competing Interest Statement

The authors have declared no competing interest.

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Posted June 20, 2022.
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Identification of potential natural compound inhibitors and drug like molecules against human METTL3 by docking and molecular dynamics simulation
Shibambika Manna, Pragati Samal, Rohini Basak, Anushka Mitra, Arijit Kumar Roy, Raima Kundu, Amrita Ahir, Amlan Roychowdhury, Ditipriya Hazra
bioRxiv 2022.06.19.496750; doi: https://doi.org/10.1101/2022.06.19.496750
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Identification of potential natural compound inhibitors and drug like molecules against human METTL3 by docking and molecular dynamics simulation
Shibambika Manna, Pragati Samal, Rohini Basak, Anushka Mitra, Arijit Kumar Roy, Raima Kundu, Amrita Ahir, Amlan Roychowdhury, Ditipriya Hazra
bioRxiv 2022.06.19.496750; doi: https://doi.org/10.1101/2022.06.19.496750

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