Peptide Deformylase Inhibitors as Potent Antimycobacterial Agents

Peptide deformylase (PDF) catalyzes the hydrolytic removal of the N-terminal formyl group from nascent proteins. This is an essential step in bacterial protein synthesis, making PDF an attractive target for antibacterial drug development. Essentiality of the def gene, encoding PDF from Mycobacterium tuberculosis, was demonstrated through genetic knockout experiments with Mycobacterium bovis BCG. PDF from M. tuberculosis strain H37Rv was cloned, expressed, and purified as an N-terminal histidine-tagged recombinant protein in Escherichia coli. A novel class of PDF inhibitors (PDF-I), the N-alkyl urea hydroxamic acids, were synthesized and evaluated for their activities against the M. tuberculosis PDF enzyme as well as their antimycobacterial effects. Several compounds from the new class had 50% inhibitory concentration (IC(50)) values of <100 nM. Some of the PDF-I displayed antibacterial activity against M. tuberculosis, including MDR strains with MIC(90) values of <1 μM. Pharmacokinetic studies of potential leads showed that the compounds were orally bioavailable. Spontaneous resistance towards these inhibitors arose at a frequency of ≤5 × 10(−7) in M. bovis BCG. DNA sequence analysis of several spontaneous PDF-I-resistant mutants revealed that half of the mutants had acquired point mutations in their formyl methyltransferase gene (fmt), which formylated Met-tRNA. The results from this study validate M. tuberculosis PDF as a drug target and suggest that this class of compounds have the potential to be developed as novel antimycobacterial agents

Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results.

Bacterial peptide deformylase (PDF) belongs to a subfamily of metalloproteases catalyzing the removal of the N-terminal formyl group from newly synthesized proteins. We report the synthesis and biological activity of highly potent inhibitors of Mycobacterium tuberculosis (Mtb) PDF enzyme as well as the first X-ray crystal structure of Mtb PDF. Structure-activity relationship and crystallographic data clarified the structural requirements for high enzyme potency and cell based potency. Activities against single and multi-drug-resistant Mtb strains are also reported

Discovery of Tetrahydropyrazolopyrimidine Carboxamide De-rivatives as Potent and Orally Active Novel Anti-Tubercular Agents

ABSTRACT: Tetrahydropyrazolopyrimidine scaffold was identified as a hit series from a Mycobacterium tuberculosis (Mtb) whole cell high through-put screening (HTS) campaign. A series of derivatives of this class were synthesized to evaluate their structure-activity relationship (SAR) and structure-property relationship (SPR). Compound 9 showed potent bactericidal effect and activity against multi-drug resistant tuberculosis (MDR TB) strains. Furthermore compound 9 had a promising in vivo DMPK profile in mouse and exhibited potent in vivo activity in a mouse efficacy model, achieving a reduction of 3.5 log CFU of Mtb after oral administration to infected mice once a day at 100 mg/kg for 28 days. Thus the compound 9 is a potential candidate for inclusion in combination therapies for both drug-sensitive and drug-resistant TB

Indolcarboxamide, a promising pre-clinical candidate for the treatment of multi drug resistant tuberculosis

To combat the drug resistance in tuberculosis, new chemotherapeutics active against multi-drug resistant Mycobacterium tuberculosis are urgently needed. We have identified and characterized the indolcarboxamides as a new class of anti-tubercular bactericidal agents. Genetics and lipid profiling studies identified the molecular target of indolcarboxamides as mmpL3, a transporter of TMM, a promiscuous target essential for mycobacterial cell wall biosynthesis. Two lead candidates NITD-304 and NITD-349 showed a significantly potent anti-TB activity against both drug sensitive and multi-drug resistant clinical Mtb isolates. Both compounds displayed favorable pharmacokinetic properties after oral administration in pre-clinical species. NITD-304 and NITD-349 showed no apparent inhibition of major CYP enzymes and are highly efficacious in both acute and chronic TB mouse efficacy models. Furthermore, we have assessed in vitro and in vivo safety profile of both candidates including two weeks exploratory rat toxicology studies. NITD-304 and NITD-349 show the adequate therapeutic index to justify further development for inclusion in the combination therapies for drug sensitive as well as drug resistant TB

A High-Throughput Screen To Identify Inhibitors of ATP Homeostasis in Non-replicating <i>Mycobacterium tuberculosis</i>

Growing evidence suggests that the presence of a subpopulation of hypoxic non-replicating, phenotypically drug-tolerant mycobacteria is responsible for the prolonged duration of tuberculosis treatment. The discovery of new antitubercular agents active against this subpopulation may help in developing new strategies to shorten the time of tuberculosis therapy. Recently, the maintenance of a low level of bacterial respiration was shown to be a point of metabolic vulnerability in <i>Mycobacterium tuberculosis</i>. Here, we describe the development of a hypoxic model to identify compounds targeting mycobacterial respiratory functions and ATP homeostasis in whole mycobacteria. The model was adapted to 1,536-well plate format and successfully used to screen over 600,000 compounds. Approximately 800 compounds were confirmed to reduce intracellular ATP levels in a dose-dependent manner in <i>Mycobacterium bovis</i> BCG. One hundred and forty non-cytotoxic compounds with activity against hypoxic non-replicating <i>M. tuberculosis</i> were further validated. The resulting collection of compounds that disrupt ATP homeostasis in <i>M. tuberculosis</i> represents a valuable resource to decipher the biology of persistent mycobacteria

A High-Throughput Screen To Identify Inhibitors of ATP Homeostasis in Non-replicating <i>Mycobacterium tuberculosis</i>

Growing evidence suggests that the presence of a subpopulation of hypoxic non-replicating, phenotypically drug-tolerant mycobacteria is responsible for the prolonged duration of tuberculosis treatment. The discovery of new antitubercular agents active against this subpopulation may help in developing new strategies to shorten the time of tuberculosis therapy. Recently, the maintenance of a low level of bacterial respiration was shown to be a point of metabolic vulnerability in <i>Mycobacterium tuberculosis</i>. Here, we describe the development of a hypoxic model to identify compounds targeting mycobacterial respiratory functions and ATP homeostasis in whole mycobacteria. The model was adapted to 1,536-well plate format and successfully used to screen over 600,000 compounds. Approximately 800 compounds were confirmed to reduce intracellular ATP levels in a dose-dependent manner in <i>Mycobacterium bovis</i> BCG. One hundred and forty non-cytotoxic compounds with activity against hypoxic non-replicating <i>M. tuberculosis</i> were further validated. The resulting collection of compounds that disrupt ATP homeostasis in <i>M. tuberculosis</i> represents a valuable resource to decipher the biology of persistent mycobacteria

A High-Throughput Screen To Identify Inhibitors of ATP Homeostasis in Non-replicating <i>Mycobacterium tuberculosis</i>

Growing evidence suggests that the presence of a subpopulation of hypoxic non-replicating, phenotypically drug-tolerant mycobacteria is responsible for the prolonged duration of tuberculosis treatment. The discovery of new antitubercular agents active against this subpopulation may help in developing new strategies to shorten the time of tuberculosis therapy. Recently, the maintenance of a low level of bacterial respiration was shown to be a point of metabolic vulnerability in <i>Mycobacterium tuberculosis</i>. Here, we describe the development of a hypoxic model to identify compounds targeting mycobacterial respiratory functions and ATP homeostasis in whole mycobacteria. The model was adapted to 1,536-well plate format and successfully used to screen over 600,000 compounds. Approximately 800 compounds were confirmed to reduce intracellular ATP levels in a dose-dependent manner in <i>Mycobacterium bovis</i> BCG. One hundred and forty non-cytotoxic compounds with activity against hypoxic non-replicating <i>M. tuberculosis</i> were further validated. The resulting collection of compounds that disrupt ATP homeostasis in <i>M. tuberculosis</i> represents a valuable resource to decipher the biology of persistent mycobacteria

Discovery of Tetrahydropyrazolopyrimidine Carboxamide Derivatives As Potent and Orally Active Antitubercular Agents

Tetrahydropyrazolo­[1,5-<i>a</i>]­pyrimidine scaffold was identified as a hit series from a <i>Mycobacterium tuberculosis</i> (Mtb) whole cell high through-put screening (HTS) campaign. A series of derivatives of this class were synthesized to evaluate their structure–activity relationship (SAR) and structure–property relationship (SPR). Compound <b>9</b> had a promising in vivo DMPK profile in mouse and exhibited potent in vivo activity in a mouse efficacy model, achieving a reduction of 3.5 log CFU of Mtb after oral administration to infected mice once a day at 100 mg/kg for 28 days. Thus, compound <b>9</b> is a potential candidate for inclusion in combination therapies for both drug-sensitive and drug-resistant TB

A high-throughput screen to identify inhibitors of ATP homeostasis in non-replicating mycobacterium tuberculosis

10.1021/cb2004884ACS Chemical Biology771190-1197ACBC