Mycobacterium tuberculosis KasA as a drug target: Structure-based inhibitor design

Abstract

Recent studies have reported the β-ketoacyl-acyl carrier protein KasA as a druggable target for Mycobacterium tuberculosis. This review summarizes the current status of major classes of KasA inhibitors with an emphasis on significant contributions from structure-based design methods leveraging X-ray crystal structures of KasA alone and in complex with inhibitors. The issues addressed within each inhibitor class are discussed while detailing the characterized interactions with KasA and structure-activity relationships. A critical analysis of these findings should lay the foundation for new KasA inhibitors to study the basic biology of M. tuberculosis and to form the basis of new antitubercular molecules of clinical significance with activity against drug-sensitive and drug-resistant infections.

Keywords: KasA; medicinal chemistry; mycobacterium tuberculosis; structure-based drug discovery; β-ketoacyl synthase.

Figure 1

Depiction of mycolic acid biosynthesis through the FAS-I and FAS-II pathways. AcpM: mycobacterial acyl carrier protein. By each protein name, the number of corresponding X-ray crystal structures deposited in the Protein Data Bank is annotated.

Figure 2

General catalytic mechanism of the KasA and KasB enzymes.

Figure 3

Crystal structure of the KasA dimer  with inhibitors bound (GSK3011724A/DG167, JSF-3285, TLM) at different binding sites. The monomer on the left is represented as a ribbon tracing the alpha carbons and the monomer on the right is depicted as a surface. The dark blue surface indicates the cap region of KasA excluding the acyl channel whereas the light blue surface indicates the core domain; Light green surface, acyl binding site; pink surface, malonyl binding site; yellow sticks; phospholipid bound to KasA (PDB ID 4C6W); green sticks; DG167 (PDB ID 5W2P); brown sticks; JSF-3285 (PDB ID 6P9L); orange sticks; TLM (PDB ID 4C6U); pink sticks, Cys171; red sticks, Phe404; cyan sticks, His 311 and His 345. For clarity, only the KasA dimer from PDB ID 6P9L is shown.

Figure 4

Mechanism of KasA catalysis with emphasis on the catalytic triad. In the KasA resting state, Cys171 and His311 are proposed to be deprotonated and protonated, respectively. Acylation of KasA occurs by nucleophilic attack of Cys171 on the acyl-AcpM. Several theories have been offered to explain the decarboxylation step, and it is unclear as to the protonation state of His311. The ensuing condensation of this enolate with the Cys171 bound acyl moiety occurs to elongate the acyl chain length by two carbons and then release the product.

Figure 5

Thiolactomycin and its analogs. Noted are efforts, referenced within, regarding analogs at the specific positions of the thiophen-2(5H)-one ring system which are numbered.

Figure 6

Interaction profiles for TLM bound to (A) wild type KasA (PDB ID 2WGE) and (B) KasA-C171Q (PDB ID 2WGG). Hydrogen bonds are shown as green dashed lines and distances are measured in Angstroms.

Figure 7

Interaction profiles for KasA C171Q bound to the following TLM analogs: (A) 3-ethyl (PDB ID 4C6Z), (B) 3-n-propyl (PDB ID 4C70), (C) 4-azido-n-butyl (PDB ID 4C71), (D) 3-acetyl (PDB ID 4C72), and (E) 3-trifluoroacetyl (PDB ID 4C73). Hydrogen bonds are shown as green dashed lines and distances are measured in Angstroms.

Figure 8

DG167 and its analogs. The derivatives, as referenced herein, are noted with regard to alterations in the heterocyclic core and sulfonamide moiety.

Figure 9

Interaction profiles for wild type KasA bound to the following sulfonamides: (A) GSK3011724A (PDB ID 5LD8), (B) DG167 (PDB ID 5W2P), (C) JSF-3217 (PDB ID 5W2S), (D) JSF-3285 (PDB ID 6P9L), (E) JSF-3005 (PDB ID 6P9K), (F) JSF-3341 (PDB ID 6P9M), and (G) GSK Cmpd 80 (PDB ID 6Y2J). Hydrogen bonds are shown as green dashed lines and distances are measured in Angstroms.