Catalytic properties of the metal ion variants of mandelate racemase reveal alterations in the apparent electrophilicity of the metal cofactor

Drug targeting of aminopeptidases: importance of deploying a right metal cofactor

Aminopeptidases are metal co-factor-dependent hydrolases releasing N-terminal amino acid residues from peptides. Many of these enzymes, particularly the M24 methionine aminopeptidases (MetAPs), are considered valid drug targets in the fight against many parasitic and non-parasitic diseases. Targeting MetAPs has shown promising results against the malarial parasite, Plasmodium, which is regarded as potential anti-cancer targets. While targeting these essential enzymes represents a potentially promising approach, many challenges are often ignored by scientists when designing drugs or inhibitory scaffolds against the MetAPs. One such aspect is the metal co-factor, with inadequate attention paid to its role in catalysis, folding and remodeling of the catalytic site, and its role in inhibitor binding or potency. Knowing that a metal co-factor is essential for aminopeptidase enzyme activity and active site remodeling, it is intriguing that most computational biologists often ignore the metal ion while screening millions of potential inhibitors to find hits. Ironically, a similar trend is followed by biologists who avoid metal promiscuity of these enzymes while screening inhibitor libraries in vitro which may lead to false positives. This review highlights the importance of considering a physiologically relevant metal co-factor during the drug discovery processes targeting metal-dependent aminopeptidases.

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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.

Bacterial mandelic acid degradation pathway and its application in biotechnology

Mandelic acid and its derivatives are an important class of chemical synthetic blocks, which is widely used in drug synthesis and stereochemistry research. In nature, mandelic acid degradation pathway has been widely identified and analyzed as a representative pathway of aromatic compounds degradation. The most studied mandelic acid degradation pathway from Pseudomonas putida consists of mandelate racemase, S-mandelate dehydrogenase, benzoylformate decarboxylase, benzaldehyde dehydrogenase and downstream benzoic acid degradation pathways. Because of the ability to catalyze various reactions of aromatic substrates, pathway enzymes have been widely used in biocatalysis, kinetic resolution, chiral compounds synthesis or construction of new metabolic pathways. In this paper, the physiological significance and the existing range of the mandelic acid degradation pathway were introduced first. Then each of the enzymes in the pathway is reviewed one by one, including the researches on enzymatic properties and the applications in biotechnology as well as efforts that have been made to modify the substrate specificity or improving catalytic activity by enzyme engineering to adapt different applications. The composition of the important metabolic pathway of bacterial mandelic acid degradation pathway as well as the researches and applications of pathway enzymes is summarized in this review for the first time.

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.

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.

Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition

Racemases and epimerases catalyse changes in the stereochemical configurations of chiral centres and are of interest as model enzymes and as biotechnological tools. They also occupy pivotal positions within metabolic pathways and, hence, many of them are important drug targets. This review summarises the catalytic mechanisms of PLP-dependent, enolase family and cofactor-independent racemases and epimerases operating by a deprotonation/reprotonation (1,1-proton transfer) mechanism and methods for measuring their catalytic activity. Strategies for inhibiting these enzymes are reviewed, as are specific examples of inhibitors. Rational design of inhibitors based on substrates has been extensively explored but there is considerable scope for development of transition-state mimics and covalent inhibitors and for the identification of inhibitors by high-throughput, fragment and virtual screening approaches. The increasing availability of enzyme structures obtained using X-ray crystallography will facilitate development of inhibitors by rational design and fragment screening, whilst protein models will facilitate development of transition-state mimics.