Ipglycermides

Ipglycermide Ce-2
Chemical and physical data
Formula	C82H102N16O26S2
Molar mass	1791.92 g·mol−1
3D model (JSmol)	Interactive image;
	SMILES O=C(NC(CC1=CC=C(O)C=C1)C(NC(CC(C)C)C(NC(CC2=CC=C(O)C=C2)C(NCC(NC(C(O)C)C(NC(CS)C(NCC(N)=O)=O)=O)=O)=O)=O)=O)[C@@H]3CSCC(N[C@H](CC4=CC=C(O)C=C4)C(NC(CC(O)=O)C(N[C@H](CC5=CC=C(O)C=C5)C(N6C(CCC6)C(NCC(N[C@@H](CC(O)=O)C(N[C@@H](CC7=CC=C(O)C=C7)C(N3)=O)=O)=O)=O)=O)=O)=O)=O;

Ipglycermide Sa-D3
Chemical and physical data
Formula	C87H111N19O23S
Molar mass	1823.02 g·mol−1
3D model (JSmol)	Interactive image;
	SMILES OC(CC[C@H](NC([C@H](CC1=CNC2=C1C=CC=C2)NC([C@@H]3CCCN3C([C@H](CO)N(C)C([C@@H](NC([C@H](CC4=CNC5=C4C=CC=C5)NC([C@H](CC6=CNC7=C6C=CC=C7)NC([C@H](C(C)C)NC([C@]([H])([C@@H](C)O)NC([C@H](C(C)C)NC([C@H](CCC(N)=O)NC([C@@H](CC8=CC=C(O)C=C8)NC9=O)=O)=O)=O)=O)=O)=O)=O)C)=O)=O)=O)=O)C(N[C@@H](CC(O)=O)C(N[C@@H](CSC9)C(N)=O)=O)=O)=O;

Ipglycermide Ce-2 Y7F
Chemical and physical data
Formula	C82H102N16O25S2
Molar mass	1775.93 g·mol−1
3D model (JSmol)	Interactive image;
	SMILES O=C(NC(CC1=CC=C(O)C=C1)C(NC(CC(C)C)C(NC(CC2=CC=C(O)C=C2)C(NCC(NC(C(O)C)C(NC(CS)C(NCC(N)=O)=O)=O)=O)=O)=O)=O)[C@@H]3CSCC(N[C@H](CC4=CC=C(O)C=C4)C(NC(CC(O)=O)C(N[C@H](CC5=CC=C(O)C=C5)C(N6C(CCC6)C(NCC(N[C@@H](CC(O)=O)C(N[C@@H](CC7=CC=CC=C7)C(N3)=O)=O)=O)=O)=O)=O)=O)=O;

Ipglycermide Ce-2d
Chemical and physical data

Formula	C₇₁H₈₄N₁₂O₂₁S
Molar mass	1473.58 g·mol⁻¹
3D model (JSmol)	Interactive image
SMILES O=C(NC(CC1=CC=C(O)C=C1)C(NC(CC(C)C)C(NC(CC2=CC=C(O)C=C2)C(N)=O)=O)=O)[C@@H]3CSCC(N[C@H](CC4=CC=C(O)C=C4)C(NC(CC(O)=O)C(N[C@H](CC5=CC=C(O)C=C5)C(N6C(CCC6)C(NCC(N[C@@H](CC(O)=O)C(N[C@@H](CC7=CC=C(O)C=C7)C(N3)=O)=O)=O)=O)=O)=O)=O)=O

Ipglycermide Ce-1 NHOH
Chemical and physical data

Formula	C₇₄H₉₂N₁₆O₂₄S
Molar mass	1621.70 g·mol⁻¹
3D model (JSmol)	Interactive image
SMILES O=C(NC(CC1=CC=C(O)C=C1)C(NC(CC(C)C)C(NC(CC2=CC=C(O)C=C2)C(NCC(NC(C(O)C)C(NO)=O)=O)=O)=O)=O)[C@@H]3CSCC(N[C@H](CC4=CC=C(O)C=C4)C(NC(CC(O)=O)C(N[C@H](CC5=CC=C(O)C=C5)C(N6C(CCC6)C(NCC(N[C@@H](CC(O)=O)C(N[C@@H](CC7=CNC=N7)C(N3)=O)=O)=O)=O)=O)=O)=O)=O

Ipglycermide Sa-D2
Chemical and physical data

Formula	C₈₈H₁₁₉N₁₉O₂₃S₂
Molar mass	1875.15 g·mol⁻¹
3D model (JSmol)	Interactive image
SMILES O=C(NC(CC1=CC=C(O)C=C1)C(NC(CC(C)C)C(NC(CC2=CC=C(O)C=C2)C(N)=O)=O)=O)[C@@H]3CSCC(N[C@H](CC4=CC=C(O)C=C4)C(NC(CC(O)=O)C(N[C@H](CC5=CC=C(O)C=C5)C(N6C(CCC6)C(NCC(N[C@@H](CC(O)=O)C(N[C@@H](CC7=CC=C(O)C=C7)C(N3)=O)=O)=O)=O)=O)=O)=O)=O

Ipglycermides are non-natural macrocyclic peptide (MCP) inhibitors of cofactor independent phosphoglycerate mutases (iPGM) discovered by the research laboratories of Dr. James Inglese of the National Institutes of Health and Prof. Hiroaki Suga of the University of Tokyo. It is part of a class of drugs or potential drugs composed of a loop of amino acids with a molecular weight of 700 to 2000 daltons. Thus, compared to most small-molecule drugs, there are more interactions with the drug target that allow them to work at significantly lower concentrations.

Over eons Nature has evolved numerous cyclic peptides for signaling and host defense.^[1] This class of molecule has found therapeutic use as antibiotics (e.g., vancomycin, bacitracin), immunosuppressants (e.g., ciclosporin), and chemotherapeutics (e.g., romidepsin). The restricted conformations associated with cyclic peptides vs their linear counterparts bestow advantages in potency and stability. With advances in the generation of very large synthetic cyclic peptide libraries and in vitro affinity-based selection methods,^[2] scientists have begun to harness the potential of this molecular modality as a template for novel ligands in drug development and other applications. However, while approaches in de novo discovery of synthetic high affinity and selective cyclic peptides progressed significantly, properties including cell permeability and metabolic stability remain challenging to incorporate and represents an active area of study in the field ^[3]

Discovery

These high-affinity molecules were discovered using affinity selection from an RNA-encoded MCP library having a theoretical size of trillions of members, though in practice the numbers are several orders of magnitude lower. However, this is still significantly larger than anything possible with standard small molecule chemical libraries typically applied in high throughput screening (HTS). The initially RaPID-selected ipglycermides using C. elegans iPGM as the selection target were Ce-1 and Ce-2, 14 amino acid cyclic lariat peptides containing an 8-member peptide ring and a six amino acid linear sequence terminating in Cy14. Ce-1 and Ce-2 differed by a single amino acid at position 7, histidine vs. tyrosine, respectively.^[4] Subsequent sequence activity relationship studies demonstrated that additional amino acid sequence variation was possible ^[5] suggesting that the initially identified Ce-1 and Ce-2 reflected a fraction of the potential library size and diversity. The limited number of ipglycermides initially identified may reflect the restricted library size, selection efficiency, or a combination of both.

Ipglycermides bind at the interface of the iPGM phosphotransferase and phosphatase domains as revealed in several co-crystal structures obtained with C. elegans (5KGN, 7KNF, 7KNG, 7TL7) and Staphylococcus aureus (7TL8) iPGMs and a variety of ipglycermides. Lariate ipglycermides containing either a terminal cysteine or hydroxamic acid have sub-nanomolar affinity for C. elegans iPGM, while truncated analogs, such as ipglycermide Ce-2d bind potently in the low nanomolar range.

Identifiers

SMILES

SMILES is a chemical notation system that is used to describe the structure of a chemical or molecule.

To view the structures of these ipglycermides, copy the SMILES from the drug boxes to the right and use this online tool to generate the structure https://www.antvaset.com/smiles-to-structure

Co-crystal structures

iPGM apo structures (2) and five ipglycermide co-crystal structures have been determined by the Protein Structure and X-ray Crystallography Laboratory (PSXL) of Dr. Scott Lovell at the University of Kansas (PDB IDs) 5KGL (https://www.rcsb.org/structure/5KGL) -- 2.45A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (orthorhombic form) 5KGM (https://www.rcsb.org/structure/5KGM) -- 2.95A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (monoclinic form) 5KGN (https://www.rcsb.org/structure/5KGN) -- 1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2d) 7KNF (https://www.rcsb.org/structure/7KNF) -- 1.80A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-1 NHOH) 7KNG (https://www.rcsb.org/structure/7KNG) -- 2.10A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-2 Y7F) 7TL7 (https://www.rcsb.org/structure/7TL7) -- 1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Sa-D2) 7TL8 (https://www.rcsb.org/structure/7TL8) -- 1.95A resolution structure of independent phosphoglycerate mutase from Staphylococcus aureus in complex with a macrocyclic peptide inhibitor (Sa-D3)

Mechanism of Action

Ipglycermides bind at the interface of the iPGM phosphotransferase and phosphatase domains as revealed in several co-crystal structures obtained with C. elegans (5KGN, 7KNF, 7KNG, 7TL7) and Staphylococcus aureus (7TL8) ^[6] iPGMs and a variety of ipglycermides. Lariate ipglycermides containing either a terminal cysteine or hydroxamic acid have sub-nanomolar affinity for C. elegans iPGM, while truncated analogs, such as ipglycermide Ce-2d bind potently in the low nanomolar range.

Chemical synthesis

Ipglycermides are readily synthesized using automated solid phase peptide synthesis and incorporate the thioether macrocycle linkage via cyclization achieved between a free cysteine thiol and N-chloroacetyl containing tyrosine.

References

^ Abdalla, M.A.; McGaw, L.J. (2018). "Natural Cyclic Peptides as an Attractive Modality for Therapeutics: A Mini Review". Molecules. 23 (8): 2080. doi:10.3390/molecules23082080. PMC 6222632. PMID 30127265.
^ Schlippe, Y.V.G.; Hartman, M.C.T.; Josephson, K.; Szostak, J.W. (2012). "in Vitro Selection of Highly Modified Cyclic Peptides That Act as Tight Binding Inhibitors". Journal of the American Chemical Society. 134 (25): 10469–10477. Bibcode:2012JAChS.13410469G. doi:10.1021/ja301017y. PMC 3384292. PMID 22428867.
^ Faris, J.H.; Adaligil, E.; Popovych, N.; Ono, S.; Takahashi, M.; Nguyen, H.; Plise, E.; Taechalertpaisarn, J.; Lee, H.W.; Koehler, M.F.T.; Cunningham, C.N.; Lokey, R.S. (2024). "Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation". J Am Chem Soc. 146 (7): 4582–91. Bibcode:2024JAChS.146.4582F. doi:10.1021/jacs.3c10949. PMC 10885153. PMID 38330910.
^ Yu, H.; Dranchak, P.; MacArthur, R.; Munson, M.S.; Mehzabeen, N.; Baird, N.J.; Battaile, K.P.; Ross, D.; Lovell, S.; Carlow, C.K.S.; Suga, H.; Inglese, J. (2017). "Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases". Nat. Commun. 8: 14932. Bibcode:2017NatCo...814932Y. doi:10.1038/ncomms14932. PMC 5382265. PMID 28368002.
^ Weidmann, M.; Dranchak, P.K.; Aitha, M.; Lamy, L.; Collmus, C.D.; Queme, B.; Kanter, L.; Battaile, K.P.; Rai, G.; Lovell, S.; Suga, H.; Inglese, J. (2021). "Structure–activity relationship of ipglycermide binding to phosphoglycerate mutases". J. Biol. Chem. 296: 100628. doi:10.1016/j.jbc.2021.100628. PMC 8113725. PMID 33812994.
^ van Neer, R.H.P.; Dranchak, P.K.; Liu, L.; Aitha, M.; Queme, B.; Kimura, H.; Katoh, T.; Battaile, K.P.; Lovell, S.; Inglese, J.; Suga, H. (2022). "Serum-stable and selective backbone-N-methylated cyclic peptides that inhibit prokaryotic glycolytic mutases". ACS Chemical Biology. 17 (8): 2284–95. doi:10.1021/acschembio.2c00403. PMC 9900472. PMID 35904259.

[1] Abdalla, M.A.; McGaw, L.J. (2018). "Natural Cyclic Peptides as an Attractive Modality for Therapeutics: A Mini Review". Molecules. 23 (8): 2080. doi:10.3390/molecules23082080. PMC 6222632. PMID 30127265.

[2] Schlippe, Y.V.G.; Hartman, M.C.T.; Josephson, K.; Szostak, J.W. (2012). "in Vitro Selection of Highly Modified Cyclic Peptides That Act as Tight Binding Inhibitors". Journal of the American Chemical Society. 134 (25): 10469–10477. Bibcode:2012JAChS.13410469G. doi:10.1021/ja301017y. PMC 3384292. PMID 22428867.

[3] Faris, J.H.; Adaligil, E.; Popovych, N.; Ono, S.; Takahashi, M.; Nguyen, H.; Plise, E.; Taechalertpaisarn, J.; Lee, H.W.; Koehler, M.F.T.; Cunningham, C.N.; Lokey, R.S. (2024). "Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation". J Am Chem Soc. 146 (7): 4582–91. Bibcode:2024JAChS.146.4582F. doi:10.1021/jacs.3c10949. PMC 10885153. PMID 38330910.

[4] Yu, H.; Dranchak, P.; MacArthur, R.; Munson, M.S.; Mehzabeen, N.; Baird, N.J.; Battaile, K.P.; Ross, D.; Lovell, S.; Carlow, C.K.S.; Suga, H.; Inglese, J. (2017). "Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases". Nat. Commun. 8: 14932. Bibcode:2017NatCo...814932Y. doi:10.1038/ncomms14932. PMC 5382265. PMID 28368002.

[5] Weidmann, M.; Dranchak, P.K.; Aitha, M.; Lamy, L.; Collmus, C.D.; Queme, B.; Kanter, L.; Battaile, K.P.; Rai, G.; Lovell, S.; Suga, H.; Inglese, J. (2021). "Structure–activity relationship of ipglycermide binding to phosphoglycerate mutases". J. Biol. Chem. 296: 100628. doi:10.1016/j.jbc.2021.100628. PMC 8113725. PMID 33812994.

[6] van Neer, R.H.P.; Dranchak, P.K.; Liu, L.; Aitha, M.; Queme, B.; Kimura, H.; Katoh, T.; Battaile, K.P.; Lovell, S.; Inglese, J.; Suga, H. (2022). "Serum-stable and selective backbone-N-methylated cyclic peptides that inhibit prokaryotic glycolytic mutases". ACS Chemical Biology. 17 (8): 2284–95. doi:10.1021/acschembio.2c00403. PMC 9900472. PMID 35904259.

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