Evaluating the Impact of the Tyr158 pKa on the Mechanism and Inhibition of InhA, the Enoyl-ACP Reductase from Mycobacterium tuberculosis

Is Mycobacterial InhA a Suitable Target for Rational Drug Design?

InhA, an NAD-dependent enoyl-acyl carrier protein reductase, is involved in the biosynthesis of mycolic acids, specific lipids to mycobacteria. InhA is the target of isoniazid, a first-line antituberculosis drug used since the 1950s. Isoniazid is a prodrug that needs to be activated by the catalase-peroxidase KatG. Due to resistance problems, a substantial amount of work has been carried out to identify or design direct inhibitors of InhA, demonstrating that this enzyme is still considered a relevant target for the discovery of new antituberculosis drugs. Much of this work included the resolution of crystallographic structures. Indeed, over a hundred structures have been deposited in the Protein Data Bank for different forms of the enzyme (apo, holo, and complexes), demonstrating a real crystalline polymorphism. Taken together, these structures constitute a valuable dataset. However, the complete decoding of the enzyme's properties and its inhibition literally comes up against its molecular plasticity at the level of a motif essential to the definition of the active site: the substrate-binding loop. In this article, a detailed analysis of this structural dataset is proposed, describing in particular the different families of inhibitors and attempting to establish structural links of causality.

Mechanism of a novel metal-free carbonic anhydrase

The recently discovered metal-free carbonic anhydrase (CA) enzyme may significantly impact the global carbon dioxide (CO2) cycle, as it can irreversibly perform the CO2 hydration reaction. In this study, we investigated several key aspects of metal-free CA, including the identification of the catalytic site, the determination of the CO2 binding site, and the mechanism of catalysis. This is achieved through classical molecular dynamics (MD) simulations, quantum chemical density functional theory (DFT), and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our study indicates that the experimental structure based on X-ray crystallography, which shows the 'bicarbonate (HCO3-) product' trapped in the hydrophilic region of metal-free CA, might not accurately depict the actual enzyme-substrate interaction. Instead, the simulation reveals that CO2 prefers the hydrophobic zone, which serves as the primary catalytic site. It also highlights the strategic role of a gatekeeper residue (Phe504), which assists in regulating the transportation of CO2 by tilting its aromatic plane. Additionally, the hybrid QM/MM calculations establish that CO2 hydration is catalyzed within the hydrophobic zone by a deprotonated tyrosine with the help of an organized water chain.

Origin of the multi-phasic quenching dynamics in the BLUF domains across the species

Blue light using flavin (BLUF) photoreceptors respond to light via one of nature's smallest photo-switching domains. Upon photo-activation, the flavin cofactor in the BLUF domain exhibits multi-phasic dynamics, quenched by a proton-coupled electron transfer reaction involving the conserved Tyr and Gln. The dynamic behavior varies drastically across different species, the origin of which remains controversial. Here, we incorporate site-specific fluorinated Trp into three BLUF proteins, i.e., AppA, OaPAC and SyPixD, and characterize the percentages for the Wout, WinNHin and WinNHout conformations using 19F nuclear magnetic resonance spectroscopy. Using femtosecond spectroscopy, we identify that one key WinNHin conformation can introduce a branching one-step proton transfer in AppA and a two-step proton transfer in OaPAC and SyPixD. Correlating the flavin quenching dynamics with the active-site structural heterogeneity, we conclude that the quenching rate is determined by the percentage of WinNHin, which encodes a Tyr-Gln configuration that is not conducive to proton transfer.

Activity of Bacteriophage D29 Loaded on Nanoliposomes against Macrophages Infected with Mycobacterium tuberculosis

The search for new antimicrobial agents is a continuous struggle, mainly because more and more cases of resistant strains are being reported. Mycobacterium tuberculosis (MTB) is the main microorganism responsible for millions of deaths worldwide. The development of new antimicrobial agents is generally aimed at finding strong interactions with one or more bacterial receptors. It has been proven that bacteriophages have the ability to adhere to specific and selective regions. However, their transport and administration must be carefully evaluated as an excess could prevent a positive response and the bacteriophages may be eliminated during their journey. With this in mind, the mycobacteriophage D29 was encapsulated in nanoliposomes, which made it possible to determine its antimicrobial activity during transport and its stability in the treatment of active and latent Mycobacterium tuberculosis. The antimicrobial activity, the cytotoxicity in macrophages and fibroblasts, as well as their infection and time-kill were evaluated. Phage nanoencapsulation showed efficient cell internalization to induce MTB clearance with values greater than 90%. Therefore, it was shown that nanotechnology is capable of assisting in the activity of degradation-sensitive compounds to achieve better therapy and evade the immune response against phages during treatment.