Avoiding Antibiotic Inactivation in Mycobacterium tuberculosis by Rv3406 through Strategic Nucleoside Modification

Abstract

5'-[ N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine (Bio-AMS, 1) possesses selective activity against Mycobacterium tuberculosis ( Mtb) and arrests fatty acid and lipid biosynthesis through inhibition of the Mycobacterium tuberculosis biotin protein ligase ( MtBPL). Mtb develops spontaneous resistance to 1 with a frequency of at least 1 × 10 by overexpression of Rv3406, a type II sulfatase that enzymatically inactivates 1. In an effort to circumvent this resistance mechanism, we describe herein strategic modification of the nucleoside at the 5'-position to prevent enzymatic inactivation. The new analogues retained subnanomolar potency to MtBPL ( K = 0.66-0.97 nM), and 5' R- C-methyl derivative 6 exhibited identical antimycobacterial activity toward: Mtb H37Rv, MtBPL overexpression, and an isogenic Rv3406 overexpression strain (minimum inhibitory concentration, MIC = 1.56 μM). Moreover, 6 was not metabolized by recombinant Rv3406 and resistant mutants to 6 could not be isolated (frequency of resistance <1.4 × 10) demonstrating it successfully overcame Rv3406-mediated resistance.

Advanced Resistance Studies Identify Two Discrete Mechanisms in Staphylococcus aureus to Overcome Antibacterial Compounds that Target Biotin Protein Ligase

“…The incidence rate for the generation of spontaneous resistance was low, with no resistant colonies growing after 24 hours, resulting in a resistance rate of less than 1 × 10 −9 . Similar low spontaneous resistance rates have been reported for another anti-BPL compound active against M. tuberculosis (less than 1.4 × 10 −10 ) [33]. This highlights BPL as an important antibacterial target with low potential for resistance to develop.…”

“…Several groups have reported on the development of anti-BPL compounds with antibacterial activity [15][16][17][18][19][30][31][32][33][34]. Bisubstrate analogs that occupy both the biotin and ATP-binding pockets and mimic the mode of binding adopted by biotinyl-5 -AMP have been particularly promising.…”

Acylated sulfonamide adenosines as potent inhibitors of the adenylate-forming enzyme superfamily

“…In general, mimicking the acyl-AMP intermediates by hydrolytically stable competitive inhibitors has proven a potent way of targeting the adenylate-forming enzymes from the different structural classes [12][13][14]. Focusing on aaRSs, enzymes which catalyse the activation and esterification of amino acids to their cognate tRNA, there have been many successful approaches to enhance the stability of the aminoacyl-adenylate intermediate by substitution of the mixed phosphoanhydride linker with a sulfur based isoster [15][16][17][18].…”

“…Alternative stabilization strategies have been applied to sulfamate based acyl-AMP bioisosteres targeting other adenylate-forming enzymes. In an attempt to limit disproportionation of biotinoyl-sulfamoyladenosine, a potent inhibitor of the Class II member biotin ligase, modifications of the adenine base [12] or addition of a methyl group to the C5′-position of the ribose [13] resulted in stabilization of the compounds. This was rationalized as likely the result of steric hindrance, preventing the syn-conformation required for the adenine N3 attack on the C5′ atom.…”

“…Substitution with an amine, yielding biotinoyl-AMS resulted in a more stable compound that is a potent and selective antitubercular [12]. Although chemically more difficult, replacement of the same atom with a methylene group also resulted in a potent inhibitor that was resistant to chemical and biochemical induced degradation [12,13].…”