Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 13 de 13
Filter
Add more filters










Publication year range
1.
Proc Natl Acad Sci U S A ; 117(29): 16782-16789, 2020 07 21.
Article in English | MEDLINE | ID: mdl-32641511

ABSTRACT

DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).


Subject(s)
DNA/chemistry , DNA/metabolism , Drug Discovery , Gene Library , Protease Inhibitors/pharmacology , Small Molecule Libraries/pharmacology , Thrombin/antagonists & inhibitors , Combinatorial Chemistry Techniques , Humans , Protease Inhibitors/chemistry , Small Molecule Libraries/chemistry
2.
ACS Infect Dis ; 4(7): 1102-1113, 2018 07 13.
Article in English | MEDLINE | ID: mdl-29663798

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 × 10-7 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 ( KD = 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 × 10-10) demonstrating it successfully overcame Rv3406-mediated resistance.


Subject(s)
Antitubercular Agents/pharmacology , Carbon-Nitrogen Ligases/metabolism , Drug Resistance, Bacterial , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Nucleosides/metabolism , Antitubercular Agents/chemistry , Microbial Sensitivity Tests , Molecular Structure , Nucleosides/chemistry , Structure-Activity Relationship , Substrate Specificity
3.
ACS Med Chem Lett ; 9(4): 386-391, 2018 Apr 12.
Article in English | MEDLINE | ID: mdl-29670706

ABSTRACT

5'-O-[N-(Salicyl)sulfamoyl]adenosine (Sal-AMS, 1) is a nucleoside antibiotic that inhibits incorporation of salicylate into siderophores required for bacterial iron acquisition and has potent activity against Mycobacterium tuberculosis (Mtb). Cinnolone analogues exemplified by 5 were designed to replace the acidic acyl-sulfamate functional group of 1 (pKa = 3) by a more stable sulfonamide linkage (pKa = 6.0) in an attempt to address potential metabolic liabilities and improve membrane permeability. We showed 5 potently inhibited the mycobacterial salicylate ligase MbtA (apparent Ki = 12 nM), blocked production of the salicylate-capped siderophores in whole-cell Mtb, and exhibited excellent antimycobacterial activity under iron-deficient conditions (minimum inhibitor concentration, MIC = 2.3 µM). To provide additional confirmation of the mechanism of action, we demonstrated the whole-cell activity of 5 could be fully antagonized by the addition of exogenous salicylate to the growth medium. Although the total polar surface area (tPSA) of 5 still exceeds the nominal threshold value (140 Å) typically required for oral bioavailability, we were pleasantly surprised to observe introduction of the less acidic and conformationally constrained cinnolone moiety conferred improved drug disposition properties as evidenced by the 7-fold increase in volume of distribution in Sprague-Dawley rats.

4.
Sci Transl Med ; 10(438)2018 04 25.
Article in English | MEDLINE | ID: mdl-29695454

ABSTRACT

Successful drug treatment for tuberculosis (TB) depends on the unique contributions of its component drugs. Drug resistance poses a threat to the efficacy of individual drugs and the regimens to which they contribute. Biologically and chemically validated targets capable of replacing individual components of current TB chemotherapy are a major unmet need in TB drug development. We demonstrate that chemical inhibition of the bacterial biotin protein ligase (BPL) with the inhibitor Bio-AMS (5'-[N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine) killed Mycobacterium tuberculosis (Mtb), the bacterial pathogen causing TB. We also show that genetic silencing of BPL eliminated the pathogen efficiently from mice during acute and chronic infection with Mtb Partial chemical inactivation of BPL increased the potency of two first-line drugs, rifampicin and ethambutol, and genetic interference with protein biotinylation accelerated clearance of Mtb from mouse lungs and spleens by rifampicin. These studies validate BPL as a potential drug target that could serve as an alternate frontline target in the development of new drugs against Mtb.


Subject(s)
Antitubercular Agents/pharmacology , Bacterial Proteins/metabolism , Tuberculosis/metabolism , Animals , Biotinylation/drug effects , Female , Mice , Mice, Inbred C57BL , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , Sulfurtransferases/metabolism , Tuberculosis/drug therapy
5.
Nat Commun ; 9(1): 1003, 2018 03 08.
Article in English | MEDLINE | ID: mdl-29520101

ABSTRACT

Trimethoprim (TMP)-sulfamethoxazole (SMX) is a widely used synergistic antimicrobial combination to treat a variety of bacterial and certain fungal infections. These drugs act by targeting sequential steps in the biosynthetic pathway for tetrahydrofolate (THF), where SMX inhibits production of the THF precursor dihydropteroate, and TMP inhibits conversion of dihydrofolate (DHF) to THF. Consequently, SMX potentiates TMP by limiting de novo DHF production and this mono-potentiation mechanism is the current explanation for their synergistic action. Here, we demonstrate that this model is insufficient to explain the potent synergy of TMP-SMX. Using genetic and biochemical approaches, we characterize a metabolic feedback loop in which THF is critical for production of the folate precursor dihydropterin pyrophosphate (DHPPP). We reveal that TMP potentiates SMX activity through inhibition of DHPPP synthesis. Our study demonstrates that the TMP-SMX synergy is driven by mutual potentiation of the action of each drug on the other.


Subject(s)
Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology , Drug Synergism , Escherichia coli , Feedback, Physiological , Microbial Sensitivity Tests , Pterins/metabolism , Tetrahydrofolates/biosynthesis
6.
Org Lett ; 19(19): 5220-5223, 2017 10 06.
Article in English | MEDLINE | ID: mdl-28926267

ABSTRACT

The mechanism of action of para-aminosalicylic acid (PAS), a drug used to treat drug-resistant tuberculosis (TB), has been confirmed through the first synthesis and biochemical characterization of its active metabolite 7. The synthesis features the coupling of N2-acetyl-6-formylpterin obtained from the degradation of folic acid and appropriately functionalized arylamines to form Schiff bases. The sequential chemoselective reduction of the imine and pterin ring led to the formation of dihydrofolate analogue 7 and two other dihydropteroate species.


Subject(s)
Folic Acid/chemistry , Aminosalicylic Acid , Antitubercular Agents , Drug Resistance, Bacterial , Folic Acid Antagonists , Kinetics , Molecular Structure , Mutation , Mycobacterium tuberculosis
7.
J Med Chem ; 60(19): 8131-8144, 2017 10 12.
Article in English | MEDLINE | ID: mdl-28858511

ABSTRACT

The cellular delivery of nucleotides through various pronucleotide strategies has expanded the utility of nucleosides as a therapeutic class. Although highly successful, the highly popular ProTide system relies on a four-step enzymatic and chemical process to liberate the corresponding monophosphate. To broaden the scope and reduce the number of steps required for monophosphate release, we have developed a strategy that depends on initial chemical activation by a sulfur atom of a methylthioalkyl protecting group, followed by enzymatic hydrolysis of the resulting phosphoramidate monoester. We have employed this ProTide strategy for intracellular delivery of a nucleotide antagonist of eIF4E in mantle cell lymphoma (MCL) cells. Furthermore, we demonstrated that chemical inhibition of cap-dependent translation results in suppression of c-Myc expression, increased p27 expression, and enhanced chemosensitization to doxorubicin, dexamethasone, and ibrutinib. In addition, the new ProTide strategy was shown to enhance oral bioavailability of the corresponding monoester phosphoramidate.


Subject(s)
Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Lymphoma, Mantle-Cell/drug therapy , Nuclear Cap-Binding Protein Complex/drug effects , Peptides/chemical synthesis , Peptides/pharmacology , Animals , Antineoplastic Agents/pharmacokinetics , Cell Line, Tumor , Cell Survival/drug effects , Cyclin-Dependent Kinase Inhibitor p27/antagonists & inhibitors , Cyclin-Dependent Kinase Inhibitor p27/biosynthesis , Drug Design , Eukaryotic Initiation Factor-4E/antagonists & inhibitors , Female , Humans , Lymphoma, Mantle-Cell/pathology , Proto-Oncogene Proteins c-myc/antagonists & inhibitors , Rats , Rats, Sprague-Dawley
8.
J Med Chem ; 60(13): 5507-5520, 2017 07 13.
Article in English | MEDLINE | ID: mdl-28594172

ABSTRACT

The pyridoxal 5'-phosphate (PLP)-dependent transaminase BioA catalyzes the second step in the biosynthesis of biotin in Mycobacterium tuberculosis (Mtb) and is an essential enzyme for bacterial survival and persistence in vivo. A promising BioA inhibitor 6 containing an N-aryl, N'-benzoylpiperazine scaffold was previously identified by target-based whole-cell screening. Here, we explore the structure-activity relationships (SAR) through the design, synthesis, and biological evaluation of a systematic series of analogues of the original hit using a structure-based drug design strategy, which was enabled by cocrystallization of several analogues with BioA. To confirm target engagement and discern analogues with off-target activity, each compound was evaluated against wild-type (WT) Mtb in biotin-free and -containing medium as well as BioA under- and overexpressing Mtb strains. Conformationally constrained derivative 36 emerged as the most potent analogue with a KD of 76 nM against BioA and a minimum inhibitory concentration of 1.7 µM (0.6 µg/mL) against Mtb in biotin-free medium.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacterial Proteins/antagonists & inhibitors , Biotin/biosynthesis , Mycobacterium tuberculosis/drug effects , Piperazines/pharmacology , Pyridoxal Phosphate/metabolism , Transaminases/antagonists & inhibitors , Anti-Bacterial Agents/chemical synthesis , Anti-Bacterial Agents/chemistry , Bacterial Proteins/metabolism , Biocatalysis , Dose-Response Relationship, Drug , Microbial Sensitivity Tests , Molecular Structure , Mycobacterium tuberculosis/metabolism , Piperazines/chemical synthesis , Piperazines/chemistry , Structure-Activity Relationship , Transaminases/metabolism
9.
Bioorg Med Chem ; 24(14): 3133-43, 2016 07 15.
Article in English | MEDLINE | ID: mdl-27265685

ABSTRACT

A series of 5'-O-[N-(salicyl)sulfamoyl]-2-aryl-8-aza-3-deazaadenosines were designed to block mycobactin biosynthesis in Mycobacterium tuberculosis (Mtb) through inhibition of the essential adenylating enzyme MbtA. The synthesis of the 2-aryl-8-aza-3-deazaadenosine nucleosides featured sequential copper-free palladium-catalyzed Sonogashira coupling of a precursor 4-cyano-5-iodo-1,2,3-triazolonucleoside with terminal alkynes and a Minakawa-Matsuda annulation reaction. These modified nucleosides were shown to inhibit MbtA with apparent Ki values ranging from 6.1 to 25nM and to inhibit Mtb growth under iron-deficient conditions with minimum inhibitory concentrations ranging from 12.5 to >50µM.


Subject(s)
Antitubercular Agents/chemistry , Antitubercular Agents/pharmacology , Mycobacterium tuberculosis/drug effects , Siderophores/biosynthesis , Tubercidin/chemistry , Mycobacterium tuberculosis/metabolism , Spectrum Analysis/methods , Structure-Activity Relationship
10.
Bioorg Med Chem ; 24(6): 1314-21, 2016 Mar 15.
Article in English | MEDLINE | ID: mdl-26875934

ABSTRACT

The nucleoside antibiotic, 5'-O-[N-(salicyl)sulfamoyl]adenosine (1), possesses potent whole-cell activity against Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB). This compound is also active in vivo, but suffers from poor drug disposition properties that result in poor bioavailability and rapid clearance. The synthesis and evaluation of a systematic series of lipophilic ester prodrugs containing linear and α-branched alkanoyl groups from two to twelve carbons at the 3'-position of a 2'-fluorinated analog of 1 is reported with the goal to improve oral bioavailability. The prodrugs were stable in simulated gastric fluid (pH 1.2) and under physiological conditions (pH 7.4). The prodrugs were also remarkably stable in mouse, rat, and human serum (relative serum stability: human∼rat≫mouse) displaying a parabolic trend in the SAR with hydrolysis rates increasing with chain length up to eight carbons (t1/2=1.6 h for octanoyl prodrug 7 in mouse serum) and then decreasing again with higher chain lengths. The permeability of the prodrugs was also assessed in a Caco-2 cell transwell model. All of the prodrugs were found to have reduced permeation in the apical-to-basolateral direction and enhanced permeation in the basolateral-to-apical direction relative to the parent compound 2, resulting in efflux ratios 5-28 times greater than 2. Additionally, Caco-2 cells were found to hydrolyze the prodrugs with SAR mirroring the serum stability results and a preference for hydrolysis on the apical side. Taken together, these results suggest that the described prodrug strategy will lead to lower than expected oral bioavailability of 2 and highlight the contribution of intestinal esterases for prodrug hydrolysis.


Subject(s)
Drug Design , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , Nucleosides/pharmacology , Prodrugs/chemical synthesis , Prodrugs/pharmacology , Siderophores/biosynthesis , Animals , Caco-2 Cells , Dose-Response Relationship, Drug , Humans , Mice , Molecular Structure , Nucleosides/blood , Nucleosides/chemical synthesis , Nucleosides/chemistry , Prodrugs/chemistry , Rats , Structure-Activity Relationship
11.
Tetrahedron Lett ; 56(23): 3534-3537, 2015 Jun 03.
Article in English | MEDLINE | ID: mdl-26236053

ABSTRACT

Oxidation of hydroxy substituted phosphono allylic carbonates gave the aldehyde substituted phosphonates in good yield. Stereospecific palladium (0)-catalyzed cyclization in the presence of methanol or water gave acetal tetrahydrofuran and tetrahydropyran vinyl phosphonate products derived from hemiacetal trapping. The tetrahydrofuran acetals undergo Lewis acid catalyzed addition of nucleophiles to give diastereoisomeric mixtures of substituted tetrahydrofurans.

12.
J Med Chem ; 58(14): 5459-75, 2015 Jul 23.
Article in English | MEDLINE | ID: mdl-26110337

ABSTRACT

MbtA catalyzes the first committed biosynthetic step of the mycobactins, which are important virulence factors associated with iron acquisition in Mycobacterium tuberculosis. MbtA is a validated therapeutic target for antitubercular drug development. 5'-O-[N-(Salicyl)sulfamoyl]adenosine (1) is a bisubstrate inhibitor of MbtA and exhibits exceptionally potent biochemical and antitubercular activity. However, 1 suffers from suboptimal drug disposition properties resulting in a short half-life (t(1/2)), low exposure (AUC), and low bioavailability (F). Four strategies were pursued to address these liabilities including the synthesis of prodrugs, increasing the pK(a) of the acyl-sulfonyl moiety, modulation of the lipophilicity, and strategic introduction of fluorine into 1. Complete pharmacokinetic (PK) analysis of all compounds was performed. The most successful modifications involved fluorination of the nucleoside that provided substantial improvements in t(1/2) and AUC. Increasing the pK(a) of the acyl-sulfonyl linker yielded incremental enhancements, while modulation of the lipophilicity and prodrug approaches led to substantially poorer PK parameters.


Subject(s)
Antitubercular Agents/chemical synthesis , Antitubercular Agents/pharmacology , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , Siderophores/biosynthesis , Animals , Antitubercular Agents/metabolism , Antitubercular Agents/pharmacokinetics , Caco-2 Cells , Chemistry Techniques, Synthetic , Drug Stability , Humans , Hydrophobic and Hydrophilic Interactions , Ligases/antagonists & inhibitors , Mice , Microbial Sensitivity Tests , Prodrugs/metabolism , Prodrugs/pharmacokinetics , Rats , Structure-Activity Relationship , Tissue Distribution
13.
J Org Chem ; 80(10): 4835-50, 2015 May 15.
Article in English | MEDLINE | ID: mdl-25916415

ABSTRACT

Antibiotic resistance represents one of the greatest threats to public health. The adenylation inhibitor 5'-O-[N-(salicyl)sulfamoyl]adenosine (SAL-AMS) is the archetype for a new class of nucleoside antibiotics that target iron acquisition in pathogenic microorganisms and is especially effective against Mycobacterium tuberculosis, the causative agent of tuberculosis. Strategic incorporation of fluorine at the 2' and 3' positions of the nucleoside was performed by direct fluorination to enhance activity and improve drug disposition properties. The resulting SAL-AMS analogues were comprehensively assessed for biochemical potency, whole-cell antitubercular activity, and in vivo pharmacokinetic parameters. Conformational analysis suggested a strong preference of fluorinated sugar rings for either a 2'-endo, 3'-exo (South), or a 3'-endo,2'-exo (North) conformation. The structure-activity relationships revealed a strong conformational bias for the C3'-endo conformation to maintain potent biochemical and whole-cell activity, whereas improved pharmacokinetic properties were associated with the C2'-endo conformation.


Subject(s)
Adenosine/analogs & derivatives , Anti-Bacterial Agents/chemistry , Antitubercular Agents/chemistry , Mycobacterium tuberculosis/chemistry , Nucleosides/chemistry , Nucleosides/chemical synthesis , Siderophores/biosynthesis , Adenosine/chemistry , Adenosine/pharmacology , Anti-Bacterial Agents/pharmacology , Antitubercular Agents/pharmacology , Halogenation , Humans , Models, Molecular , Molecular Conformation , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/metabolism , Nucleic Acid Conformation , Siderophores/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL
...