Facile synthesis of SAM–peptide conjugates through alkyl linkers targeting protein N-terminal methyltransferase 1

Abstract

We report the first chemical synthesis of SAM–peptide conjugates through alkyl linkers to prepare bisubstrate analogs for protein methyltransferases. We demonstrate its application by developing a series of bisubstrate inhibitors for protein N-terminal methyltransferase 1 and the most potent one exhibits a K_i value of 310 ± 55 nM.

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Protein methylation has been recognized as an important post-translational modification because of its implications in a variety of disorders including cancer, cardiovascular diseases, inflammation, metabolic and neurodegenerative diseases.^1–5 Consequently, protein methyltransferases that are responsible for this modification have drawn a lot of attention as potential therapeutic targets. The protein methyltransferase family consists of nearly fifty predicted protein lysine methyltransferases (PKMTs), over forty predicted protein arginine methyltransferases (PRMTs), and two newly discovered protein N-terminal methyltransferases (NTMTs). They all have two binding pockets: one for a protein substrate and the other for a methyl donor S-adenosyl-L-methionine (SAM). PKMTs, PRMTs, and NTMTs all utilize SAM as a methyl donor to transfer a methyl group from SAM to the nitrogen atom of the epsilon amine of lysine, guanidino group of arginine, and N-terminal α-amine, respectively. The methyl-transfer reaction generally undergoes an S_N2-like mechanism and involves a ternary complex formation.^6–9

The number of reports concerning protein methylation has undergone exponential growth since 2000. However, the majority of protein methyltransferases involved in specific physiological reactions remains elusive. Hence, specific probes are important to decipher the biological functions and therapeutic potentials of methyltransferase targets.^10–16 A general approach for the development of specific inhibitors of individual methyltransferases would greatly advance the field.

Bisubstrate analogs that simultaneously occupy the binding sites for both substrates to mimic a transition state and have the potential to offer high selectivity for individual enzymes of large and homologous families such as acetyltransferases, kinases, glycosyltransferases and methyltransferases.^17–26 Bisubstrate inhibitors can also be used in cellular studies if linked to cell-penetrating peptides including polyarginine and Tat peptide (GRKKRRQRRRPPQ) to improve the cellular uptake.²³ The protein methyltransferases share a common SAM binding site, therefore it imposes a big challenge for small SAM analogs to discriminate specific target unless there is a unique structural feature like DOT1L.² Since 2010, many efforts have been made to develop bisubstrate analogs for PRMTs and PKMTs by covalently linking a SAM analog with a guanidine functionality through various alkylamino groups or an ethylene linker.^20–22 They exhibited high selectivity and validated the feasibility of using an alkyl group to tether both substrate portions to develop specific inhibitors for protein methyltransferases. However, these prototype bisubstrate inhibitors either did not contain a peptide substrate moiety, or were obtained in situ via nitrogen mustard which restricted an ethylene group as the only linker.^27,28 Hence, there is an urgent need to address the synthetic challenge to chemically tether a SAM analog with a specific peptide substrate through various alkyl groups with different length to probe optimal length to generate more potent and specific probe for individual protein methyltransferase (Fig. 1). To fulfil this need, we describe herein a new synthetic route to connect a SAM analog with different peptides via alkyl linkers.

Fig. 1 SAM–peptide conjugates designed to occupy both SAM and protein substrate binding sites.

NTMT1, a new addition to the family of protein methyltransferases, recognizes and methylates proteins that have a canonical X-Pro-Lys motif (X = Ala, Gly, Pro, and Ser) at the N-terminus.^29,30 So far, there is only one specific inhibitor available for this enzyme, which was synthesized through a click chemistry and reported by our laboratory.²⁴ To explore a new scaffold, we initiated our efforts to design a series of SAM–peptide conjugates by linking a SAM analog with peptides that start with either Ala or Gly through an alkyl group as our model system. Our crystal structure suggested that the distance between the sulfonium ion and the α-N-terminal nitrogen atom is 4.7 Å.³⁰ And for most protein methyltransferases, this distance varies from 2.2 Å to 4.7 Å.^29–33 Hence, we chose an ethylene or a propylene group as a linker and designed a series of compounds 1a–f targeting NTMT1 with substrate peptides that start with GPK/R.^34,35 We also designed compounds 1g–j by adding either an Ala or Gly to an ethylene group to extend the linker length for two peptide substrates PPKR and SPKR to probe an optimal linker. In addition, successful preparation of 1g–j will further support that our synthetic route may be applied as a general approach to link different peptides to construct bisubstrate analogs for other protein methyltransferases.

We have successfully synthesized these SAM–peptide conjugates (Scheme 1). Compound 4 was synthesized from commercially available adenosine after protection of 2′- and 3′-hydroxyl groups by the isopropylidene group,³⁶ conversion to an azide,³⁷ and followed by a hydrogenation reaction.³⁸ Then 4 reacted with Boc-protected aspartic aldehyde gave 5 by reductive amination.²⁰ Amines of the amino alcohols were protected with a Cbz group by treatment of benzyl chloroformate (CbzCl).³⁹ Subsequent oxidation with Dess–Martin periodinane yielded 6a–b,⁴⁰ which were subjected to a reductive amination in the presence of 5 and sodium triacetoxyborohydride to produce 7a–b in 78–80% yield. Removal of the Cbz group by hydrogenation reaction from 7a–b led to 3a–b. Compound 3a–b reacted with α-bromo peptide 2 on resin and was cleaved from the resin with a cleavage cocktail containing trifluoroacetic acid (TFA)/2,2′-(ethylenedioxy)-diethanethiol (DODT)/H₂O/triisopropylsilane (TIPS) (94 : 2.5 : 2.5 : 1, v/v), and purified by RP-HPLC to afford the target compounds 1a–j. The α-bromo peptides were prepared by using 2-bromo acetic acid or 2-bromo propionic acid at the N-terminal position following general solid-phase peptide synthesis.

Scheme 1 Synthesis of SAM–peptide conjugates.

We evaluated the inhibitory activities of all synthesized compounds at both K_m values of SAM (8 μM) and RCC1-10 (0.9 μM) in a fluorescence-based assay.⁹ Among them, compounds 1a–f exhibited an IC₅₀ value ranging from 780 nM to 113 μM (Table 1). In particular, compound 1c displayed an IC₅₀ value of 0.94 ± 0.16 μM and a K_i value of 310 ± 55 nM. Structure–activity relationships indicate that a propylene group is an optimal linker for NTMT1, since 1b–c are more potent than 1e–f, respectively. These results further validated our structural discovery of the unique distance of 4.7 Å for NTMT1. As the peptide length extends to six residues like 1b–c and 1e–f, the NTMT1 inhibition activity increases. These results confirmed that the first six amino acids are important for NTMT1 recognition.⁹ In addition, peptide sequence specificity contributes to the inhibitory activity. For NTMT1, the second and third positions of peptide substrates are critical for NTMT1 recognition. Normally, Pro is at the second position and Lys or Arg is at the third position, respectively. As shown in Table 1, 1g–j barely showed any inhibition even at 100 μM, which suggested that addition of Gly or Ala to the linker failed to orient PPKR and SPKR to the peptide binding pocket. The bisubstrate analogs (1c and 1f) with peptide sequence GPRRRS showed higher potency than related compounds (1b and 1e), which suggests that GPRRRS can be well recognized by NTMT1. This result correlates with previous study of centromere protein A which contains a GPRRRS peptide at its N-terminus and has been shown to be predominantly trimethylated in mitosis.³⁴

Table 1 Inhibition activities against NTMT1

Compd	n	Peptide	IC50 (μM)	Ki (μM)
1a	2	GPKR	10 ± 2	2.6 ± 0.7
1b	2	GPKRIA	4.2 ± 1.2	1.1 ± 0.3
1c	2	GPRRRS	0.94 ± 0.16	0.31 ± 0.06
1d	1	GP	77 ± 36	19 ± 9
1e	1	GPKRIA	10 ± 3	2.6 ± 0.8
1f	1	GPRRRS	4.6 ± 1.5	1.2 ± 0.4
1g	1	APPKR	>100	—
1h	1	ASPKR	>100	—
1i	1	GPPKR	>100	—
1j	1	GSPKR	>100	—

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In order to assess the selectivity of 1c to serve as a valuable inhibitor of NTMT1, we evaluated its selectivity versus two closely related protein methyltransferases, protein arginine methyltransferase 1 and lysine methyltransferase G9a. At 30 μM, it did not show any significant inhibition of either G9a or PRMT1. We also examined how compound 1c affects the progression of α-N-amine methylation at 5 μM by MALDI-MS.^9,24,41 Triplicate samples of RCC1-10 peptide (SPKRIAKRRS) along with compound 1c were subjected to NTMT1 methylation assays. Following these assays, samples were analyzed at 20 min to monitor the methylation progression. Dimethylation and trimethylation of RCC1-10 were completely abolished. Monomethylated RCC1-10 was substantially reduced to 19% in the presence of 1c (Fig. 2).

Fig. 2 Inhibition on methylation states of RCC1-10 with 5 μM of compound 1c.

To understand the interactions between compound 1c and NTMT1, we performed molecular docking of 1c into the SAM and peptide substrate binding sites of NTMT1 using Gold 5.2. The result suggested that compound 1c can occupy both SAM and peptide substrate binding sites simultaneously. The SAM part in 1c was superimposed well with SAH and retained similar interactions with NTMT1. The Ser6 of the peptide interacts with GLU213 and the guanidino groups on the three Arg residues interact with LEU31, GLY32 and LEU176 (Fig. 3).

Fig. 3 (A) Docking study of 1c with carbons in yellow to crystal structure of NTMT1 complexed with SAH (PDB: 2EX4). (B) Superimposed structure of 1c (carbons in yellow, nitrogens in blue and oxygens in red) with SAH (purple) in the complex. Only interacting residues were labeled. Hydrogen bonds are shown as yellow dotted lines.

In summary, we successfully synthesized a series of SAM–peptide conjugates among which compound 1c exhibited a K_i value of 310 ± 55 nM for NTMT1 and barely inhibited PRMT1 and G9a at 30 μM. The optimal linker is a propylene group for NTMT1 in this series. This route is the first chemical synthesis to link a SAM analog with peptide through alkyl linkers. It has the potential to be adapted to build bisubstrate analogs for other PMTs since alkyl linkers have been proven to be viable linkers for both PRMTs and PKMTs.

Acknowledgements

We thank Dr Raymond Trievel for the SAH Hydrolase plasmid, and Dr George Yujun Zheng for the PRMT1 plasmid. We appreciate Dr Darrel L. Peterson for purifying NTMT1 and G9a. The authors acknowledge financial support from the VCU Presidential Research Quest Fund (R. H.).

Notes and references

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Footnote

† Electronic supplementary information (ESI) available: Organic synthesis, characterization, fluorescence-based assay procedure, and docking study. See DOI: 10.1039/c5ra20625a

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