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Inhibition of Nuclear Receptor Binding SET Domain 2/Multiple Myeloma SET Domain by LEM-06 Implication for Epigenetic Cancer Therapies.

di Luccio E - J Cancer Prev (2015)

Bottom Line: Thus, effective therapeutic strategies are greatly needed.We used homology modeling, molecular modeling simulations, virtual ligand screening, computational chemistry software for structure-activity relationship and performed in vitro H3K36 histone lysine methylation inhibitory assay using recombinant human NSD2-SET and human H3.1 histone.LEM-06 derivatives may pave the way to specific NSD2 inhibitors suitable for therapeutic efforts against malignancies.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, Korea.

ABSTRACT

Background: Multiple myeloma SET domain (MMSET)/nuclear receptor binding SET domain 2 (NSD2) is a lysine histone methyltransferase (HMTase) and bona fide oncoprotein found aberrantly expressed in several cancers, suggesting potential role for novel therapeutic strategies. In particular, MMSET/NSD2 is emerging as a target for therapeutic interventions against multiple myeloma, especially t(4;14) myeloma that is associated with a significantly worse prognosis than other biological subgroups. Multiple myeloma is the second most common hematological malignancy in the United States, after non-Hodgkin lymphoma and remains an incurable malignancy. Thus, effective therapeutic strategies are greatly needed. HMTases inhibitors are scarce and no NSDs inhibitors have been isolated.

Methods: We used homology modeling, molecular modeling simulations, virtual ligand screening, computational chemistry software for structure-activity relationship and performed in vitro H3K36 histone lysine methylation inhibitory assay using recombinant human NSD2-SET and human H3.1 histone.

Results: Here, we report the discovery of LEM-06, a hit small molecule inhibitor of NSD2, with an IC50 of 0.8 mM against H3K36 methylation in vitro.

Conclusions: We propose LEM-06 as a hit inhibitor that is useful to further optimize for exploring the biology of NSD2. LEM-06 derivatives may pave the way to specific NSD2 inhibitors suitable for therapeutic efforts against malignancies.

No MeSH data available.


Related in: MedlinePlus

Architecture of nuclear receptor binding SET domain 2 (NSD2)/multiple myeloma SET domain (MMSET) and model of the opened SET domain with LEM-06. (A) Schematic of the primary structure of NSD2: PWWP domain; PHD zinc fingers domain; SET histone methyl transferase (HMTase) with the preSET and postSET domains. The regulatory loop closing onto the histone-binding site is indicated in red. (B) Commassie staining on sodium dodecylsulfate-polyacrylamide gel electrophoresis gel of the recombinant expressed NSD2-SET after purification. (C) Molecular surface of the model of the opened NSD2-SET bound with the computed most favourable conformation of LEM-06 during virtual ligand screening. Electrostatic surface is coloured as follow: blue: positive charges; red: negative charges with unit +5/−5 kb.T.ec−1.
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f1-jcp-20-113: Architecture of nuclear receptor binding SET domain 2 (NSD2)/multiple myeloma SET domain (MMSET) and model of the opened SET domain with LEM-06. (A) Schematic of the primary structure of NSD2: PWWP domain; PHD zinc fingers domain; SET histone methyl transferase (HMTase) with the preSET and postSET domains. The regulatory loop closing onto the histone-binding site is indicated in red. (B) Commassie staining on sodium dodecylsulfate-polyacrylamide gel electrophoresis gel of the recombinant expressed NSD2-SET after purification. (C) Molecular surface of the model of the opened NSD2-SET bound with the computed most favourable conformation of LEM-06 during virtual ligand screening. Electrostatic surface is coloured as follow: blue: positive charges; red: negative charges with unit +5/−5 kb.T.ec−1.

Mentions: The catalytic mechanism of lysine-HMTase has been established and it proceeds through a linear SN2 nucleophilic attack between the cofactor S-Adenosyl methionine (SAM) and the lysine-NH3 substrate.1 The SAM binds into a small cavity immediately adjacent to the histone-tail large binding groove where the lysine substrate extends deep inside a channel at the interface between both binding areas.15 Previously, we demonstrated that the SET domain of NSD1 accommodates a 7-amino acid peptide, similarly as it was further identified in SET8.26,35 In addition, we demonstrated the opening mechanism of the SET domain of NSD1 through rotation of a small loop at the interface between the SET and postSET subdomain.26 This regulatory-loop is likely to participate in both the substrate recognition and the catalytic mechanism by acting as a seat belt for the lysine-substrate. The regulatory-loop sits on top of the lysine-substrate strongly anchoring the histone-tail in the SET domain.35 The histone-tail binding area involves areas from both the SET and postSET subdomains (Fig. 1). The SET domain sequence is highly conserved across the NSDs, thus it is likely that NSD2 and NSD3 proceed through the same mechanism as described for NSD1 (Fig. 2). Noteworthy, the NSDs are phylogenically distinct from other known HMTases (Fig. 2).


Inhibition of Nuclear Receptor Binding SET Domain 2/Multiple Myeloma SET Domain by LEM-06 Implication for Epigenetic Cancer Therapies.

di Luccio E - J Cancer Prev (2015)

Architecture of nuclear receptor binding SET domain 2 (NSD2)/multiple myeloma SET domain (MMSET) and model of the opened SET domain with LEM-06. (A) Schematic of the primary structure of NSD2: PWWP domain; PHD zinc fingers domain; SET histone methyl transferase (HMTase) with the preSET and postSET domains. The regulatory loop closing onto the histone-binding site is indicated in red. (B) Commassie staining on sodium dodecylsulfate-polyacrylamide gel electrophoresis gel of the recombinant expressed NSD2-SET after purification. (C) Molecular surface of the model of the opened NSD2-SET bound with the computed most favourable conformation of LEM-06 during virtual ligand screening. Electrostatic surface is coloured as follow: blue: positive charges; red: negative charges with unit +5/−5 kb.T.ec−1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492355&req=5

f1-jcp-20-113: Architecture of nuclear receptor binding SET domain 2 (NSD2)/multiple myeloma SET domain (MMSET) and model of the opened SET domain with LEM-06. (A) Schematic of the primary structure of NSD2: PWWP domain; PHD zinc fingers domain; SET histone methyl transferase (HMTase) with the preSET and postSET domains. The regulatory loop closing onto the histone-binding site is indicated in red. (B) Commassie staining on sodium dodecylsulfate-polyacrylamide gel electrophoresis gel of the recombinant expressed NSD2-SET after purification. (C) Molecular surface of the model of the opened NSD2-SET bound with the computed most favourable conformation of LEM-06 during virtual ligand screening. Electrostatic surface is coloured as follow: blue: positive charges; red: negative charges with unit +5/−5 kb.T.ec−1.
Mentions: The catalytic mechanism of lysine-HMTase has been established and it proceeds through a linear SN2 nucleophilic attack between the cofactor S-Adenosyl methionine (SAM) and the lysine-NH3 substrate.1 The SAM binds into a small cavity immediately adjacent to the histone-tail large binding groove where the lysine substrate extends deep inside a channel at the interface between both binding areas.15 Previously, we demonstrated that the SET domain of NSD1 accommodates a 7-amino acid peptide, similarly as it was further identified in SET8.26,35 In addition, we demonstrated the opening mechanism of the SET domain of NSD1 through rotation of a small loop at the interface between the SET and postSET subdomain.26 This regulatory-loop is likely to participate in both the substrate recognition and the catalytic mechanism by acting as a seat belt for the lysine-substrate. The regulatory-loop sits on top of the lysine-substrate strongly anchoring the histone-tail in the SET domain.35 The histone-tail binding area involves areas from both the SET and postSET subdomains (Fig. 1). The SET domain sequence is highly conserved across the NSDs, thus it is likely that NSD2 and NSD3 proceed through the same mechanism as described for NSD1 (Fig. 2). Noteworthy, the NSDs are phylogenically distinct from other known HMTases (Fig. 2).

Bottom Line: Thus, effective therapeutic strategies are greatly needed.We used homology modeling, molecular modeling simulations, virtual ligand screening, computational chemistry software for structure-activity relationship and performed in vitro H3K36 histone lysine methylation inhibitory assay using recombinant human NSD2-SET and human H3.1 histone.LEM-06 derivatives may pave the way to specific NSD2 inhibitors suitable for therapeutic efforts against malignancies.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Biosciences, Kyungpook National University, Daegu, Korea.

ABSTRACT

Background: Multiple myeloma SET domain (MMSET)/nuclear receptor binding SET domain 2 (NSD2) is a lysine histone methyltransferase (HMTase) and bona fide oncoprotein found aberrantly expressed in several cancers, suggesting potential role for novel therapeutic strategies. In particular, MMSET/NSD2 is emerging as a target for therapeutic interventions against multiple myeloma, especially t(4;14) myeloma that is associated with a significantly worse prognosis than other biological subgroups. Multiple myeloma is the second most common hematological malignancy in the United States, after non-Hodgkin lymphoma and remains an incurable malignancy. Thus, effective therapeutic strategies are greatly needed. HMTases inhibitors are scarce and no NSDs inhibitors have been isolated.

Methods: We used homology modeling, molecular modeling simulations, virtual ligand screening, computational chemistry software for structure-activity relationship and performed in vitro H3K36 histone lysine methylation inhibitory assay using recombinant human NSD2-SET and human H3.1 histone.

Results: Here, we report the discovery of LEM-06, a hit small molecule inhibitor of NSD2, with an IC50 of 0.8 mM against H3K36 methylation in vitro.

Conclusions: We propose LEM-06 as a hit inhibitor that is useful to further optimize for exploring the biology of NSD2. LEM-06 derivatives may pave the way to specific NSD2 inhibitors suitable for therapeutic efforts against malignancies.

No MeSH data available.


Related in: MedlinePlus