Innovations in Antifungal Drug Discovery among Cell Envelope Synthesis Enzymes through Structural Insights

Abstract

Life-threatening systemic fungal infections occur in immunocompromised patients at an alarming rate. Current antifungal therapies face challenges like drug resistance and patient toxicity, emphasizing the need for new treatments. Membrane-bound enzymes account for a large proportion of current and potential antifungal targets, especially ones that contribute to cell wall and cell membrane biosynthesis. Moreover, structural biology has led to a better understanding of the mechanisms by which these enzymes synthesize their products, as well as the mechanism of action for some antifungals. This review summarizes the structures of several current and potential membrane-bound antifungal targets involved in cell wall and cell membrane biosynthesis and their interactions with known inhibitors or drugs. The proposed mechanisms of action for some molecules, gleaned from detailed inhibitor-protein studeis, are also described, which aids in further rational drug design. Furthermore, some potential membrane-bound antifungal targets with known inhibitors that lack solved structures are discussed, as these might be good enzymes for future structure interrogation.

Keywords: antifungal development; cryo-EM; drug resistance; membrane-bound enzymes; rational drug design; structure biology.

Figure 1

The interaction between nikkomycin Z and Phytophthora sojae Chs1. (A) Chemical and 3D structure of nikkomycin Z (NikZ). (B) The left is a sliced-surface view of the NikZ-binding site of PsChs and the right is detailed interactions between NikZ and PsChs1. The reaction chamber and translocating channel are pointed out by the arrow. Hydrogen bonds are labeled as black dashed lines. Figures originally generated in [42] (under Creative Commons CC BY license) and adapted for this review.

Figure 2

Binding models of UDP-GlcNAc, nikkomycin Z, and polyoxin D to C. albicans Chs2. (A) Overlay of substrate binding sites: one with UDP-GlcNAc (in brown) and the other with nikkomycin Z-bound (in green) in CaChs2. The aminohexuronic acid moiety is noted by a red arrow. (B) Overlay of the substrate binding sites of CaChs2: one bound with nikkomycin Z (in green) and the other with polyoxin D (in magenta). Hydrogen bonds and π-π stacking interactions between the substrate or ligand and CaChs2 are marked with dashed lines in their respective colors. Figures originally generated in [39] and adapted for this review with permission (License Number: 5697420844040).

Figure 3

Chemical structures of the three FDA-approved echinocandins.

Figure 4

Structural interpretation of echinocandin-resistant mutations in ScFKS1 structure. (A) The ScFKS1 structure with three distinct hotspot regions (colored in red) labeled as HS1–3. These regions are associated with mutations that confer resistance to echinocandins. (B) A detailed view of echinocandin-resistant mutations is provided, as referenced in (A). The mutations’ alpha carbon (Cα) atoms are illustrated as red spheres. (C) Conformational changes and lipid re-arrangements, marked by red arrows, in wildtype ScFKS1 (grey) and drug-resistant mutation S643P ScFKS1 (blue). Potential polar interaction is indicated by the black dashed line. Figures were originally generated in [48], and are reused in this review with permission (License Number: 5697430533684).

Figure 5

Binding of itraconazole to S. cerevisiae Erg11. (A) Structure of itraconazole. (B) S. cerevisiae Erg11 structure originally printed in [97] and reused in this review with permission (License Number: 5697681298825). The left-hand image shows a cartoon representation of the overall fold of S. cerevisiae Erg11 and its predicted position in the lipid membrane(PDBID:5EQB). The right-hand image shows the binding of itraconazole within the S. cerevisiae Erg11. Itraconazole is shown in purple and heme moiety is shown in pink. (ITC: itraconazole; FSL: fungus-specific loop; SEC: substrate entry channel; PPEC: putative product exit channel; LBP: ligand-binding pocket; MH1: amphipathic helix; TMH1: transmembrane helix).

Figure 6

Binding model of terbinafine to squalene epoxidase. (A) Structure of terbinafine. (B) The upper panel shows a superposition of terbinafine (orange) with NB-598 (cyan) in human squalene epoxidase (PDBID:6C6P). The lower panel shows the positions of the known terbinafine-resistant mutations (pink) with respect to terbinafine (orange) in human squalene epoxidase with a superposed terbinafine model. (C) Superposition of human squalene epoxidase structure (blue) and S. cerevisiae squalene epoxidase homology model (yellow). The extended loop on S. cerevisiae Erg1 is pointed to by an arrow. Figure (B) was originally generated in [101] (under Creative Commons CC BY license), and Figure (C) was originally generated in [129] (under Creative Commons CC BY license).

Figure 7

De novo synthesis of sphingolipids in S. cerevisiae and known inhibitors targeting each enzyme. This figure is adapted and modified from [91] (under Creative Commons CC BY license). IPC: Inositolphosphoryl-ceramide; MIPC: mannose inositol-P-ceramide; M(IP)₂C: mannose-(inositol-P)₂-ceramide.

Figure 8

Phospholipid biosynthesis pathways for C. albicans (A) and mammals/parasites (B). Known inhibitors to certain targets are also shown. Both the de novo pathway and Kennedy pathway exist in each scenario. This figure is adapted and modified from [193] (under Creative Commons CC BY license). PA: phosphatidic acid; CDP-DAG: cytidine diphosphate diacylglycerol; Ser: serine; Cho1/PSS1/PSS2: PS synthase; PI: phosphatidylinositol; PS: phosphatidylserine; PE: phosphatidylethanolamine; PC: phosphatidylcholine; Etn: ethanolamine; Cho: choline; Etn-P: phosphoethanolamine; Cho-P: phosphocholine; CDP-Etn: cytidyldiphosphate-ethanolamine; CDP-Cho: cytidyldiphosphatecholine; PSD: PS decarboxylase; Eki1: ethanolamine kinase; Ect1: ethanolamine-phosphate cytidylyltransferase; Ept1: ethanolamine phosphotransferase; Cki1: choline kinase; Pct1: choline-phosphate cytidylyltransferase; SDC: serine decarboxylase; Cpt1: choline phosphotransferase.