Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase

Abstract

Mycobacterium tuberculosis adenosine kinase (MtbAdoK) is an essential enzyme of Mtb and forms part of the purine salvage pathway within mycobacteria. Evidence suggests that the purine salvage pathway might play a crucial role in Mtb survival and persistence during its latent phase of infection. In these studies, we adopted a structural approach to the discovery, structure-guided design, and synthesis of a series of adenosine analogues that displayed inhibition constants ranging from 5 to 120 nM against the enzyme. Two of these compounds exhibited low micromolar activity against Mtb with half maximal effective inhibitory concentrations of 1.7 and 4.0 μM. Our selectivity and preliminary pharmacokinetic studies showed that the compounds possess a higher degree of specificity against MtbAdoK when compared with the human counterpart and are well tolerated in rodents, respectively. Finally, crystallographic studies showed the molecular basis of inhibition, potency, and selectivity and revealed the presence of a potentially therapeutically relevant cavity unique to the MtbAdoK homodimer.

An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis

“…Recently, Crespo et al disclosed very potent and safe AdoK inhibitors by means of a structure-based drug design (SBDD) approach [ 29 ]. Several 6-substituted adenosine analogues complexed with AdoK, displaying high anti- Mtb activity in a whole-cell assay, were crystallized and solved revealing key insights into the region surrounding the active site.…”

“…Improved derivatives were prepared by Crespo et al based on the structural data, which suggested the presence of a size threshold conferring specificity to the active site vs the ATP site. This observation could be useful for the future design of bisubstrate-like inhibitors characterized by small substituents at the N6-position and bulky groups at the 5′-position, which increase the number of favorable contacts with the enzyme and sterically prevent the full closure of the lid domain [ 29 ]. Figure 29 reports the crystal structure of a second-generation inhibitor ( 72 ), together with a summary of the SAR obtained for this set of compounds.…”

“…Scheme 11. Phosphorylation of adenosine to AMP, catalyzed by adenosine kinase (AdoK).High-resolution structures for AdoK (PDB: 2PKM, 2PKF, 2PKK, and 2PKN) demonstrated that the apo form of the enzyme has the active site in an open conformation; after adenosine binding, a lid domain undergoes a conformational change, which leads to the formation of interactions with the substrate and residues of the active site.The purine salvage pathway in Mtb still leaves unexplored possibilities for drug development; therefore, structural data of enzyme-inhibitor complexes may provide a broader knowledge to drive the future search for chemical agents with novel mechanisms of action and a more selective biological activity.Recently, Crespo et al disclosed very potent and safe AdoK inhibitors by means of a structure-based drug design (SBDD) approach[29]. Several 6-substituted adenosine analogues complexed with AdoK, displaying high anti-Mtb activity in a whole-cell assay, were crystallized and solved revealing key insights into the region surrounding the active site.…”

Biosynthesis of Galactan in Mycobacterium tuberculosis as a Viable TB Drug Target?

“…In this review, we present the available information on the galactan component of the mycobacterial cell wall in a historical context; its structural characterization, discovery of the metabolic pathway, and the key enzymes involved in galactan polymerization, as well as a summary of the efforts towards their inhibition. Our aim is to provide inspiration for state-of-the-art targetbased approaches [4], which were already successfully applied for the development of potent inhibitors against selected enzymes from M. tuberculosis [12,13].…”

A Novel Adenosine Kinase from Bombyx mori: Enzymatic Activity, Structure, and Biological Function

“…ADK was first isolated from yeast in 1951. In the past decades, ADK properties including substrate specificity [8], inhibitors [9], metal ions [10], ATP, and inorganic phosphate [11] have been extensively investigated.…”