Loss of Catalytic Activity in the E134D, H67A, and H349A Mutants of DapE: Mechanistic Analysis with QM/MM Investigation

The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets

BACKGROUND

Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings.

SCOPE OF REVIEW

The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species.

MAJOR CONCLUSIONS

LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success.

GENERAL SIGNIFICANCE

This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.

Deciphering the role of the two metal-binding sites of DapE enzyme via metal substitution

DapE is a microbial metalloenzyme that hosts two Zn ions in its active site, although it shows catalytic activity with varying efficiency when the Zn ions in one or both of its metal-binding sites (MBS) are replaced by other transition-metal ions. The metal-ion promiscuity of DapE is believed to be a microbial strategy to overcome the homeostatic regulation of Zn ions by the mammalian host. Here, a hybrid QM/MM study is performed on a series of mixed-metal DapEs, where the Zn ion in the first MBS (MBS-1) is substituted by Mn, Co, Ni, and Cu ions, while the MBS-2 is occupied by Zn(II). The substrate binding affinity and the mechanism of catalytic action are estimated by optimizing the intermediates and the transition states with hybrid QM/MM method. Comparison of the binding affinity of the MBS-1 and MBS-2 substituted DapEs reveals that the MBS-1 substitution does not affect the substrate binding affinity in the mixed-metal DapEs, while a strong metal specificity was observed in MBS-2 substituted DapEs. On the contrary, the activation energy barriers show a high metal specificity at MBS-1 compared to MBS-2. Taken together, the QM/MM studies indicate that MBS-2 leads the substrate binding process, while MBS-1 steers the catalytic activity of the DapE enzyme.

Metal-ion promiscuity of microbial enzyme DapE at its second metal-binding site

Metalloenzymes are ubiquitous in nature catalyzing a number of crucial biochemical processes in animal and plant kingdoms. For better adaptation to the relative abundance of different metal ions in different cellular fluids, many of these enzymes exhibit metal promiscuity. The microbial enzyme DapE, an essential enzyme for bacterial growth and survival and a potentially safe target for antibiotics, continues to show enzyme activity when the two zinc ions in its active site are replaced by other transition metal ions. The effect of metal-ion substitution at the second metal-binding site of DapE on its substrate affinity and catalytic efficiency is investigated by QM/MM treatment of the enzyme-substrate complex, by modelling the enzyme with Mn(II), Co(II), Ni(II), or Cu(II) ion in place of Zn(II) at its second metal-binding site, while retaining Zn(II) ion at the first metal-binding site. On the basis of substrate binding energy and activation energy barrier for the chemical catalysis, it is found that Zn-Mn DapE shows poor binding affinity as well as inefficient chemical catalysis. Although Zn-Cu and Zn-Ni DapEs show activation energy barriers comparable to that of wild-type Zn-Zn DapE, their weaker substrate affinity renders these mixed-metal enzymes less efficient. On the other hand, Zn-Co DapE is found to outperform the naturally occurring Zn-Zn DapE, both in terms of substrate affinity and chemical catalysis. The observed metal promiscuity may have played an important role in the survival of bacteria even in those cellular media where Zn ions are in limited supply. Metal nonspecificity in the catalysis of DapE enzyme allows bacteria to thrive in different cellular media.

L-Captopril and its derivatives as potential inhibitors of microbial enzyme DapE: A combined approach of drug repurposing and similarity screening

The perils of antimicrobial drug resistance can be overcome by finding novel antibiotic targets and corresponding small molecule inhibitors. Microbial enzyme DapE is a promising antibiotic target due to its importance to the bacterial survival. The potency of L-Captopril, a well known angiotensin-converting enzyme inhibitor, as an inhibitor of DapE enzyme has been evaluated by analyzing its binding modes and binding affinity towards DapE enzyme. L-Captopril is found to bind the metal centers of DapE enzyme either via its thiolate group or through its carboxylate group. While the latter binding mode is found to be thermodynamically favorable, the former binding mode, also seen in the crystal structure, is kinetically favored. To optimize the binding affinity of the inhibitor towards DapE enzyme, a series of L-Captopril-based inhibitors have been modelled by changing the side groups of L-Captopril. The introduction of a bipolar functional group at the C4 position of the pyrrolidine ring of L-Captopril and the substitution of the thiol group with a carboxylate group, have been shown to provide excellent enzyme affinity that supersedes the binding affinity of DapE enzyme towards its natural substrate, thus making this molecule a potential inhibitor with great promise.