Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines

Hotra, Adam; Ragunathan, Priya; Ng, Pearly Shuyi; Seankongsuk, Pattarakiat; Harikishore, Amaravadhi; Sarathy, Jickky Palmae; Saw, Wuan‐Geok; Lakshmanan, Umayal; Sae‐Lao, Patcharaporn; Kalia, Nitin Pal; Shin, Joon; Kalyanasundaram, Revathy; Anbarasu, Sivaraj; Parthasarathy, Krupakar; Pradeep, Chaudhari Namrata; Makhija, Harshyaa; Dröge, Peter; Poulsen, Anders; Tan, Jocelyn Hui Ling; Pethe, Kévin; Dick, Thomas; Bates, Roderick W.; Grüber, Gerhard

doi:10.1002/anie.202002546

Cited by 29 publications

(35 citation statements)

References 42 publications

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“…Although BDQ has pharmacological and toxicological liabilities [ 4 , 5 ] and is shown to inhibit human mitochondrial F-ATP synthase [ 6 ], it demonstrated that the mycobacterial F-ATP synthase is a potent anti-TB drug target. This is also confirmed by recent discoveries of the novel mycobacterial F-ATP synthase inhibitors GaMF1, which is bactericidal and targets the mycobacterial extra loop of the rotary γ subunit [ 7 ] or EpNMF1/epigallocatechin gallate (EGCG), which inhibits the mycobacterial engine by binding to subunit ε and preventing coupling [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 75%

Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ

et al. 2021

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Mycobacteria regulate their energy (ATP) levels to sustain their survival even in stringent living conditions. Recent studies have shown that mycobacteria not only slow down their respiratory rate but also block ATP hydrolysis of the F-ATP synthase (α3:β3:γ:δ:ε:a:b:b’:c9) to maintain ATP homeostasis in situations not amenable for growth. The mycobacteria-specific α C-terminus (α533-545) has unraveled to be the major regulative of latent ATP hydrolysis. Its deletion stimulates ATPase activity while reducing ATP synthesis. In one of the six rotational states of F-ATP synthase, α533-545 has been visualized to dock deep into subunit γ, thereby blocking rotation of γ within the engine. The functional role(s) of this C-terminus in the other rotational states are not clarified yet and are being still pursued in structural studies. Based on the interaction pattern of the docked α533-545 region with subunit γ, we attempted to study the druggability of the α533-545 motif. In this direction, our computational work has led to the development of an eight-featured α533-545 peptide pharmacophore, followed by database screening, molecular docking, and pose selection, resulting in eleven hit molecules. ATP synthesis inhibition assays using recombinant ATP synthase as well as mycobacterial inverted membrane vesicles show that one of the hits, AlMF1, inhibited the mycobacterial F-ATP synthase in a micromolar range. The successful targeting of the α533-545-γ interaction motif demonstrates the potential to develop inhibitors targeting the α site to interrupt rotary coupling with ATP synthesis.

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Section: Introductionmentioning

confidence: 75%

Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ

et al. 2021

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“…[6a-c] These improved analogues include 5307, 5316, and 5377, [6c] which interact with the c-ring and subunit e of the mycobacterial F-ATP synthase [6d] (Figure 6C). Using am odified synthesis protocol (see the Supporting Information), racemates of 5307 [(AE)-5307],5 316 [(AE)-5316],a nd 5366 [(AE)-5366] were synthesized, [28] which inhibited M. smegmatis mc 2 155 growth with MIC 50 values of 1.6 nm,4 .4 nm and 1.0 nm, respectively ( Figure 6D). Thei mproved MIC 50 values of the racemates compared to BDQ were in line with improved IC 50 in ATPs ynthesis inhibition of M. smegmatis mc 2 155 IMVs, with values of 0.1 AE 0.01 nm,0 .2 AE 0.08 nm,a nd 0.6 AE 0.33 nm for the racemates of 5307, 5316, and 5366, respectively ( Figure 6E).…”

Section: Angewandte Chemiementioning

confidence: 99%

Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines

Hotra

Ragunathan

et al. 2020

Angewandte Chemie

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The F1FO‐ATP synthase is required for growth and viability of Mycobacterium tuberculosis and is a validated clinical target. A mycobacterium‐specific loop of the enzyme's rotary γ subunit plays a role in the coupling of ATP synthesis within the enzyme complex. We report the discovery of a novel antimycobacterial, termed GaMF1, that targets this γ subunit loop. Biochemical and NMR studies show that GaMF1 inhibits ATP synthase activity by binding to the loop. GaMF1 is bactericidal and is active against multidrug‐ as well as bedaquiline‐resistant strains. Chemistry efforts on the scaffold revealed a dynamic structure activity relationship and delivered analogues with nanomolar potencies. Combining GaMF1 with bedaquiline or novel diarylquinoline analogues showed potentiation without inducing genotoxicity or phenotypic changes in a human embryonic stem cell reporter assay. These results suggest that GaMF1 presents an attractive lead for the discovery of a novel class of anti‐tuberculosis F‐ATP synthase inhibitors.

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“…BDQ as a control revealed an IC 50 of 1.22 ± 0.06 nM, which is comparable to earlier published studies. 9,24 Likewise, DeMF1 also exhibited the ability to inhibit succinate-driven ATP synthesis with an IC 50 of 1.14 ± 0.07 μM. Because varying the electron donors that activate ATP synthesis via complexes I and -II has not abrogated the inhibitory effects, it can be inferred that both complexes were not involved in mediating the actions of DeMF1.…”

Section: ■ Results and Discussionmentioning

confidence: 98%

Mutational Analysis of Mycobacterial F-ATP Synthase Subunit δ Leads to a Potent δ Enzyme Inhibitor

et al. 2022

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While many bacteria are able to bypass the requirement for oxidative phosphorylation when grown on carbohydrates, Mycobacterium tuberculosis is unable to do so. Differences of amino acid composition and structural features of the mycobacterial F-ATP synthase (α 3 :β 3 :γ:δ:ε:a:b:b′:c 9 ) compared to its prokaryotic or human counterparts were recently elucidated and paved avenues for the discovery of molecules interfering with various regulative mechanisms of this essential energy converter. In this context, the mycobacterial peripheral stalk subunit δ came into focus, which displays a unique Nterminal 111-amino acid extension. Here, mutants of recombinant mycobacterial subunit δ were characterized, revealing significant reduction in ATP synthesis and demonstrating essentiality of this subunit for effective catalysis. These results provided the basis for the generation of a four-feature model forming a δ receptor-based pharmacophore and to identify a potent subunit δ inhibitor DeMF1 via in silico screening. The successful targeting of the δ subunit demonstrates the potential to advance δ's flexible coupling as a new area for the development of F-ATP synthase inhibitors.

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Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines

Cited by 29 publications

References 42 publications

Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ

Targeting Mycobacterial F-ATP Synthase C-Terminal α Subunit Interaction Motif on Rotary Subunit γ

Discovery of a Novel Mycobacterial F‐ATP Synthase Inhibitor and its Potency in Combination with Diarylquinolines

Mutational Analysis of Mycobacterial F-ATP Synthase Subunit δ Leads to a Potent δ Enzyme Inhibitor

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