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. 2021 Dec 8;14(12):1282.
doi: 10.3390/ph14121282.

Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis: A Crystallographic and Molecular Modelling Study

Romain Galy  1 , Stéphanie Ballereau  2 , Yves Génisson  2 , Lionel Mourey  1 , Jean-Christophe Plaquevent  2 , Laurent Maveyraud  1
Affiliations

Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis: A Crystallographic and Molecular Modelling Study

Romain Galy et al. Pharmaceuticals (Basel). .

Abstract

The mycolic acid biosynthetic pathway represents a promising source of pharmacological targets in the fight against tuberculosis. In Mycobacterium tuberculosis, mycolic acids are subject to specific chemical modifications introduced by a set of eight S-adenosylmethionine dependent methyltransferases. Among these, Hma (MmaA4) is responsible for the introduction of oxygenated modifications. Crystallographic screening of a library of fragments allowed the identification of seven ligands of Hma. Two mutually exclusive binding modes were identified, depending on the conformation of residues 147-154. These residues are disordered in apo-Hma but fold upon binding of the S-adenosylmethionine (SAM) cofactor as well as of analogues, resulting in the formation of the short η1-helix. One of the observed conformations would be incompatible with the presence of the cofactor, suggesting that allosteric inhibitors could be designed against Hma. Chimeric compounds were designed by fusing some of the bound fragments, and the relative binding affinities of initial fragments and evolved compounds were investigated using molecular dynamics simulation and generalised Born and Poisson-Boltzmann calculations coupled to the surface area continuum solvation method. Molecular dynamics simulations were also performed on apo-Hma to assess the structural plasticity of the unliganded protein. Our results indicate a significant improvement in the binding properties of the designed compounds, suggesting that they could be further optimised to inhibit Hma activity.

Keywords: Mycobacterium tuberculosis; binding energies; fragment-based ligand discovery; molecular modelling; mycolic acid methyltransferases.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Structures of the fragments bound to Hma.
Figure 2
Figure 2
Ribbon representation of the Hma protein (PDB ID 2FK8) in the presence of the S-adenosylmethionine cofactor, represented as sticks with black carbon atoms, with all observed bound fragments represented as sticks with coloured carbon atoms. The protein is represented as a ribbon coloured from blue at the N-terminus to red at the C-terminus and secondary structure elements are labelled according to [30].
Figure 3
Figure 3
Detailed representation of binding of ZT218 (A, pink), ZT260 (B, beige), and ZT585 (C, yellow) at the substrate binding site. The protein backbone is represented as a tube, the side chains of residues involved in ligand binding are shown as sticks and labelled, water molecules as red spheres, and hydrogen bonds as blue dotted lines. Residues 148–151 forming helix η1 are coloured orange.
Figure 4
Figure 4
2D interaction maps of fragments ZT218 (A), ZT260 (B), ZT585 (C), ZT275 (D), ZT320 (E), and ZT424 (F) bound to the Hma protein. Hydrogen bonds are represented with dashed black lines and their lengths are indicated. Residues/atoms involved in van der Waals contacts are represented by notched semicircles (figure adapted from LigPlot+ [34]).
Figure 5
Figure 5
Detailed representation of binding of ZT275 ((A), pale green) and ZT320 ((B), turquoise) at the substrate binding site. The protein is represented as a ribbon, the side chains of residues involved in ligand biding are shown as sticks and labelled, water molecules as red spheres, and hydrogen bonds as blue dotted lines. Residues 148–151 forming helix η1 are coloured orange.
Figure 6
Figure 6
Detailed representation of binding of ZT424 (light pink) at the cofactor binding site. The protein is represented as a ribbon, the side chains of residues involved in ligand biding are shown as sticks and labelled, water molecules as red spheres, and hydrogen and halogen bonds as blue and green dotted lines, respectively. Residues 148–151 forming helix η1 are coloured orange. The position of ZT260, coloured beige, in the substrate binding site is also indicated for easier comparison with Figure 4 and Figure 5.
Figure 7
Figure 7
Detailed representation of binding of ZT260 (A), ZT320 (B), ZT726 (C), and ZT585 (D) at the protein surface. The protein is represented as a ribbon, the side chains of residues involved in ligand biding are shown as sticks and labelled, water molecules as red spheres, and hydrogen bonds as blue dotted lines. Residues 148–151 forming helix η1 are coloured orange. In D, the symmetry-related molecule is represented in beige and labelled in italics.
Figure 8
Figure 8
Chimeric compounds derived from merged fragments.
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