Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis

Abstract

The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analogue of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form π-stacking interactions with the catalytic Tyr24 have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19-24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.

The molecular biology of mycobacterial trehalose in the quest for advanced tuberculosis therapies

“…The enzymes for biosynthesis of SL-1 and PAT as well as those for LOS and the putative systems for their translocation to the outer layers of the cell envelope are also not conserved between M. tuberculosis and M. abscessus (Table 3). Investigation of their genuine functions in this organism in particular, and in NTM in general, will certainly advance our understanding about their metabolic abilities, their infection strategies and eventually the identification of novel drug targets, upon which we will need to intervene to fight these pathogens (Dias et al, 2011;Nessar et al, 2011). Application of the elegant trehalose-based imaging tools described above will be of paramount importance to assess the contribution of these apparent genomic 'incidents' to the M. abscessus successful lifestyle and pathogenesis.…”

“…For optimal progression towards new efficient TB chemotherapies, the genetic, functional and structural characterization of validated targets will accelerate drug discovery and unquestionably shorten the path from the laboratory bench to the patient (Dias et al, 2011;La Rosa et al, 2012). Interestingly, some antibiotics effective against M. smegmatis, namely cathomycin, circulin, diumycin and moenomycin, inhibited OtsA activity in vitro (Pan & Elbein, 1996).…”

“…Consequently, crystallization is a major bottleneck in structural mycobacteriology efforts and drug design (Dias et al, 2011;Tiago et al, 2012). The genome sequence of Mycobacterium hassiacum, the most thermophilic species of Mycobacterium known to date and presumably encoding intrinsically more stable proteins, may help overcome protein stability problems and facilitate structural studies and structure-guided drug design (Dias et al, 2011;Tiago et al, 2012).…”

Inhibition of Shikimate Kinase and Type II Dehydroquinase for Antibiotic Discovery: Structure-Based Design and Simulation Studies

“…Specifically, the 3-substituted cyclohexene derivatives 31-36, the tetrahydrobenzothiophene derivatives 37, the O-alkyl derivatives 38, and the 2,3-disubstituted compounds 39 were reported ( Fig. 9) [54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71]. A summary of the inhibition constants of these compounds against Mt-DHQ2 and Hp-DHQ2 are shown in Tables 1 and 2.…”

Structural Annotation of the Mycobacterium tuberculosis Proteome

“…The absence of the glyoxylate shunt pathway in mammals makes this an interesting target, and a number of interesting inhibitors-many of them mimics of metabolic intermediates in the pathway, such as succinate-have presented potential candidates showing inhibitory activity in the 0.10 μM range. Similarly, the structure of dehydroquinase from M. tuberculosis with bound ligand and inhibitors explained the molecular details of the reaction that could be used to design better inhibitors (93). Isoniazid, a frontline drug used in the treatment of TB, is known to be a prodrug, which is converted to the active species by catalase, which subsequently inhibits the function of InhA, a key enzyme in the mycolic acid biosynthetic pathway, by reacting nonenzymatically with NAD + and NADP + to form isonicotinoyl nucleotide adducts.…”