Slow-Binding Inhibition of Mycobacterium tuberculosis Shikimate Kinase by Manzamine Alkaloids

Abstract

Tuberculosis represents a significant public health crisis. There is an urgent need for novel molecular scaffolds against this pathogen. We screened a small library of marine-derived compounds against shikimate kinase from Mycobacterium tuberculosis ( MtSK), a promising target for antitubercular drug development. Six manzamines previously shown to be active against M. tuberculosis were characterized as MtSK inhibitors: manzamine A (1), 8-hydroxymanzamine A (2), manzamine E (3), manzamine F (4), 6-deoxymanzamine X (5), and 6-cyclohexamidomanzamine A (6). All six showed mixed noncompetitive inhibition of MtSK. The lowest K values were obtained for 6 across all MtSK-substrate complexes. Time-dependent analyses revealed two-step, slow-binding inhibition. The behavior of 1 was typical; initial formation of an enzyme-inhibitor complex (EI) obeyed an apparent K of ∼30 μM with forward ( k) and reverse ( k) rate constants for isomerization to an EI* complex of 0.18 and 0.08 min, respectively. In contrast, 6 showed a lower K for the initial encounter complex (∼1.5 μM), substantially faster isomerization to EI* ( k = 0.91 min), and slower back conversion of EI* to EI ( k = 0.04 min). Thus, the overall inhibition constants, K*, for 1 and 6 were 10 and 0.06 μM, respectively. These findings were consistent with docking predictions of a favorable binding mode and a second, less tightly bound pose for 6 at MtSK. Our results suggest that manzamines, in particular 6, constitute a new scaffold from which drug candidates with novel mechanisms of action could be designed for the treatment of tuberculosis by targeting MtSK.

A Systematic Review of Recently Reported Marine Derived Natural Product Kinase Inhibitors

“…In 2018, the manzamine alkaloids were isolated from Indo-Pacific marine sponges Acanthostrongylophora sp., including manzamine A ( 98 ), 8-hydroxymanzamine A ( 99 ), manzamine E ( 100 ), manzamine F ( 101 ), 6-deoxymanzamine X ( 102 ), and the synthetic analogue 6-cyclohexamidomanzamine A ( 103 ) was also generated [115,116]. These compounds (Figure 25) showed mixed noncompetitive inhibition of MtSK, and the synthetic compound 103 takes advantage of the structural features to pursue applications of anti-inflammatory, antiparasitic, insecticidal, and antibacterial activities with potential for development against malaria and tuberculosis [115,116]. In 2014, Nag S. Kumar et al reported the discovery of a series of bis-indole alkaloids based on the structure of a marine alkaloid isolated from the marine sponge Topsentia pachastrelloides , of which compound 104 (Figure 26) is a promising PK inhibitor [117].…”

Anti‐Tubercular Insights of Carbolines – A Decade Critique

“…Kinetic profiling has shown that multiple manzamines (1–6) represented in table 6 inhibit MtSK. 6‐cyclohexamido derivative of manzamine A was found to be the most superior inhibitor of MtSK [19] …”

“…Consequently, these compounds are promising candidates for further studies leading to the development of new drug candidates specific to the M. tuberculosis pathogen. A compound 6‐cycloheximide derivative, compound ( 49 ), is the most prominent derivative because of its inhibition profile, in vitro anti‐bacterial activity, and lack of cytotoxicity [19] …”

“…[18] Carbolines being an important N-heterocycle class, has been classified as α, β, γ, and δ carboline, according to the ABC skeleton system (Figure 2), which are present in many naturally occurring and pharmaceutically active compounds. These are ubiquitous structural motifs having essential and wide-ranging biological activities such as anti-tubercular, [19] anti-viral, [20] anti-tumor, [21] anti-inflammatory, [22] and central nervous system stimulating activities (Figure 3). [20]…”

Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs

“…Different researches have been making efforts to find a potent molecule against this enzyme, which could help in the treatment of TB. Recently, six new compounds were characterized as MtSK inhibitors-manzamine A, 8-hydroxymanzamine A, manzamine E, manzamine F, 6-deoxymanzamine X and 6-cyclohexamidomanzamine A. Inhibition studies demonstrated that these molecules show a mixed noncompetitive type of inhibition [127]. Another study showed a collection of 14 hits (out of 404 compounds) containing oxadiazole-amide and aminobenzothiazole scaffolds, which displayed >90% inhibition at concentrations below 50 μM against MtSK [123,128] Experimental and computational studies have shown that catalysis may occur under specific conditions.…”