Three-dimensional QSAR analysis and design of new 1,2,4-oxadiazole antibacterials.

The oxadiazole antibacterials, a class of newly discovered compounds that are active against Gram-positive bacteria, target bacterial cell-wall biosynthesis by inhibition of a family of essential enzymes, the penicillin-binding proteins. Ligand-based 3D-QSAR analyses by comparative molecular field analysis (CoMFA), comparative molecular shape indices analysis (CoMSIA) and Field-Based 3D-QSAR evaluated a series of 102 members of this class. This series included inactive compounds as well as compounds that were moderately to strongly antibacterial against Staphylococcus aureus. Multiple models were constructed using different types of energy minimization and charge calculations. CoMFA derived contour maps successfully defined favored and disfavored regions of the molecules in terms of steric and electrostatic properties for substitution.

Exploration of the structure-activity relationship of 1,2,4-oxadiazole antibiotics.

We have recently disclosed the discovery of the class of 1,2,4-oxadiazole antibiotics, which emerged from in silico docking and scoring efforts. This class of antibacterials exhibits Gram-positive activity, particularly against Staphylococcus aureus. We define the structure-activity relationship (SAR) of this class of antibiotics with the synthesis and evaluation of a series of 59 derivatives with variations in the C ring or C and D rings. A total of 17 compounds showed activity against S. aureus. Four derivatives were evaluated against a panel of 16 Gram-positive strains, inclusive of several methicillin-resistant S. aureus strains. These compounds are broadly active against Gram-positive bacteria.

Discovery of a new class of non-ß-lactam inhibitors of penicillin-binding proteins with Gram-positive antibacterial activity.

Infections caused by hard-to-treat methicillin-resistant Staphylococcus aureus (MRSA) are a serious global public-health concern, as MRSA has become broadly resistant to many classes of antibiotics. We disclose herein the discovery of a new class of non-ß-lactam antibiotics, the oxadiazoles, which inhibit penicillin-binding protein 2a (PBP2a) of MRSA. The oxadiazoles show bactericidal activity against vancomycin- and linezolid-resistant MRSA and other Gram-positive bacterial strains, in vivo efficacy in a mouse model of infection, and have 100% oral bioavailability.

Unlocking the potential of water-soluble gold(i)-NHC complexes: unveiling the role of carboxylic acid in cycloisomerization of alkynyl amino acid derivatives.

Hydrocarboxylation of alkyne-containing amino acid derivatives using water-soluble gold(i)-NHC complexes in an aqueous biphasic system at room temperature is described. Addition of silver salts is not required as the carboxylic acid group of the substrate is responsible for the activation of the gold catalyst at room temperature. Our results confirm that the steric bulk of the N-heterocyclic carbene ligands is an important factor in both the stability and the catalytic activity of gold(i) complexes in aqueous medium, and consequently in the recycling (at least 15 times without any loss of activity). The catalytic activity of our most active water-soluble gold(i)-NHC complex has been demonstrated in the cycloisomerization of amino acids derivatives with terminal and internal alkynes in aqueous media at room temperature.

Step-Economic Total Synthesis of Melosatin A from Eugenol.

An efficient and straightforward route toward the isatin-type natural product melosatin A is reported, employing a trisubstituted aniline as a key intermediate. The latter was synthesized in 4 steps and 60% overall yield from eugenol, through its regioselective nitration, sequentially followed by a Williamson methylation, an olefin cross-metathesis with 4-phenyl-1-butene and the simultaneous reduction of olefin and nitro groups. The final step, a Martinet cyclocondensation of the key aniline with diethyl 2-ketomalonate, provided the natural product with 68% yield.

Hydrolytic mechanism of OXA-58 enzyme, a carbapenem-hydrolyzing class D ß-lactamase from Acinetobacter baumannii.

Carbapenem-hydrolyzing class D ß-lactamases (CHDLs) represent an emerging antibiotic resistance mechanism encountered among the most opportunistic Gram-negative bacterial pathogens. We report here the substrate kinetics and mechanistic characterization of a prominent CHDL, the OXA-58 enzyme, from Acinetobacter baumannii. OXA-58 uses a carbamylated lysine to activate the nucleophilic serine used for ß-lactam hydrolysis. The deacylating water molecule approaches the acyl-enzyme species, anchored at this serine (Ser-83), from the α-face. Our data show that OXA-58 retains the catalytic machinery found in class D ß-lactamases, of which OXA-10 is representative. Comparison of the homology model of OXA-58 and the recently solved crystal structures of OXA-24 and OXA-48 with the OXA-10 crystal structure suggests that these CHDLs have evolved the ability to hydrolyze imipenem, an important carbapenem in clinical use, by subtle structural changes in the active site. These changes may contribute to tighter binding of imipenem to the active site and removal of steric hindrances from the path of the deacylating water molecule.

Gold catalysis on immobilized substrates: a heteroannulation approach to the solid-supported synthesis of indoles.

A gold-catalyzed cyclization of immobilized 2-alkynylanilines was developed as the key step in the synthetic sequence for the preparation of 2-substituted indoles. These results demonstrate the potential of the unexplored combination of gold catalysis and solid-phase organic synthesis.

Exploration of mild copper-mediated coupling of organotrifluoroborates in the synthesis of thiirane-based inhibitors of matrix metalloproteinases.

The copper-mediated and non-basic oxidative cross-coupling of organotrifluoroborates with phenols was applied to elaboration of the structures of thiirane-based inhibitors of matrix metalloproteinases. By revision of the synthetic sequence to allow this cross-coupling as the final step, and taking advantage of the neutral nature of organotrifluoroborate cross-coupling, a focussed series of inhibitors showing aryloxy and alkenyloxy replacement of the phenoxy substituent was prepared. This reaction shows exceptional promise as an alternative to the classic copper-mediated but strongly basic Ullmann reaction, for the diversification of ether segments within base-labile lead structures.

Mechanistic basis for the emergence of catalytic competence against carbapenem antibiotics by the GES family of beta-lactamases.

A major mechanism of bacterial resistance to beta-lactam antibiotics (penicillins, cephalosporins, carbapenems, etc.) is the production of beta-lactamases. A handful of class A beta-lactamases have been discovered that have acquired the ability to turn over carbapenem antibiotics. This is a disconcerting development, as carbapenems are often considered last resort antibiotics in the treatment of difficult infections. The GES family of beta-lactamases constitutes a group of extended spectrum resistance enzymes that hydrolyze penicillins and cephalosporins avidly. A single amino acid substitution at position 170 has expanded the breadth of activity to include carbapenems. The basis for this expansion of activity is investigated in this first report of detailed steady-state and pre-steady-state kinetics of carbapenem hydrolysis, performed with a class A carbapenemase. Monitoring the turnover of imipenem (a carbapenem) by GES-1 (Gly-170) revealed the acylation step as rate-limiting. GES-2 (Asn-170) has an enhanced rate of acylation, compared with GES-1, and no longer has a single rate-determining step. Both the acylation and deacylation steps are of equal magnitude. GES-5 (Ser-170) exhibits an enhancement of the rate constant for acylation by a remarkable 5000-fold, whereby the enzyme acylation event is no longer rate-limiting. This carbapenemase exhibits k(cat)/K(m) of 3 x 10(5) m(-1)s(-1), which is sufficient for manifestation of resistance against imipenem.

Structure-Activity Relationship for the Oxadiazole Class of Antibacterials.

A structure-activity relationship (SAR) for the oxadiazole class of antibacterials was evaluated by syntheses of 72 analogs and determination of the minimal-inhibitory concentrations (MICs) against the ESKAPE panel of bacteria. Selected compounds were further evaluated for in vitro toxicity, plasma protein binding, pharmacokinetics (PK), and a mouse model of methicillin-resistant Staphylococcus aureus (MRSA) infection. Oxadiazole 72c shows potent in vitro antibacterial activity, exhibits low clearance, a high volume of distribution, and 41% oral bioavailability, and shows efficacy in mouse models of MRSA infection.

Metal-mediated synthesis of pyrrolines.

The five-membered, nitrogen-containing pyrroline ring is a privileged structure. This ring is present in many bioactive compounds from natural sources. Pyrrolines-the dihydro derivatives of pyrroles-have three structural isomer classes, depending on the location of the double bond: 1-pyrrolines (3,4-dihydro-2H-pyrroles), 2-pyrrolines (2,3-dihydro-1H-pyrroles) and 3-pyrrolines (2,5-dihydro-1H-pyrroles). This review aims to describe the latest advances for the synthesis of pyrrolines by transition metal-catalyzed cyclizations. Only reactions in which the pyrroline ring is formed by metal promotion are described. Transformations of the pyrroline ring in other heterocycles, and the structural manipulations of the pyrroline itself are not discussed. The review is organized into three parts, each covering the metal-mediated synthesis of the three pyrroline isomers. Each part is subdivided according to the metal involved, and concludes with a brief description of notable biological activities within the class.

Discovery of Mechanism-Based Inactivators for Human Pancreatic Carboxypeptidase A from a Focused Synthetic Library.

Metallocarboxypeptidases (MCPs) are involved in many biological processes such as fibrinolysis or inflammation, development, Alzheimer's disease, and various types of cancer. We describe the synthesis and kinetic characterization of a focused library of 22 thiirane- and oxirane-based potential mechanism-based inhibitors, which led to discovery of an inhibitor for the human pro-carboxypeptidase A1. Our structural analyses show that the thiirane-based small-molecule inhibitor penetrates the barrier of the pro-domain to bind within the active site. This binding leads to a chemical reaction that covalently modifies the catalytic Glu270. These results highlight the importance of combined structural, biophysical, and biochemical evaluation of inhibitors in design strategies for the development of spectroscopically nonsilent probes as effective beacons for in vitro, in cellulo, and/or in vivo localization in clinical and industrial applications.

Enantiospecific approach toward pentalenolactone.

[reaction: see text] The enantiospecific assembly of the pentalenolactones' carbon skeleton was achieved in 17 steps and 16% overall yield from methyl alpha-D-glucopyranoside. The synthetic strategy relies on two highly efficient key steps: an exo-diastereoselective Diels-Alder reaction and a nonsymmetric ozonolysis.

Synthesis of 3-(aryl)alkenyl-beta-lactams by an efficient application of olefin cross-metathesis on solid support.

[reaction: see text] An efficient cross-metathesis on solid support for the synthesis of beta-lactam analogues of cholesterol absorption inhibitors is described. The applied strategy allows the introduction of diversity in positions 3 and 4 of the beta-lactam ring with excellent 3,4-trans selectivity and complete E selectivity at the C-3 side chain.

A simple and mild synthesis of a 4,5-cyclopropanated carbohydrate.

The synthesis of a 4,5-cyclopropanated carbohydrate was achieved in five steps from methyl alpha-D-mannopyranoside under mild conditions that avoid the use of carbene chemistry.

Synthesis of a Small Library of Imidazolidin-2-ones using Gold Catalysis on Solid Phase.

An efficient and high-yielding solid phase synthesis of a small library of imidazolidin-2-ones and imidazol-2-ones was carried out employing a high chemo- and regioselective gold-catalyzed cycloisomerization as a key step. Polymer-supported amino acids derivatized with several alkyne functionalities combined with tosyl- and phenylureas have been subjected to gold-catalysis exhibiting exclusively C-N bond formation. The present work proves the potential of solid phase synthesis and homogeneous gold catalysis as an efficient and powerful synthetic tool for the generation of drug-like heterocycles.

Structure-activity relationship for the oxadiazole class of antibiotics.

The structure-activity relationship (SAR) for the newly discovered oxadiazole class of antibiotics is described with evaluation of 120 derivatives of the lead structure. This class of antibiotics was discovered by in silico docking and scoring against the crystal structure of a penicillin-binding protein. They impair cell-wall biosynthesis and exhibit activities against the Gram-positive bacterium Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA) and vancomycin-resistant and linezolid-resistant S. aureus. 5-(1H-Indol-5-yl)-3-(4-(4-(trifluoromethyl)phenoxy)phenyl)-1,2,4-oxadiazole (antibiotic 75b) was efficacious in a mouse model of MRSA infection, exhibiting a long half-life, a high volume of distribution, and low clearance. This antibiotic is bactericidal and is orally bioavailable in mice. This class of antibiotics holds great promise in recourse against infections by MRSA.

The non-metathetic role of Grubbs' carbene complexes: from hydrogen-free reduction of α,ß-unsaturated alkenes to solid-supported sequential cross-metathesis/reduction.

An efficient and high-yielding "hydrogen-free" reduction of α,ß-unsaturated alkenes was carried out employing Grubbs' catalyst in a non-metathetic role and Et(3)SiH. Conditions were optimized under microwave irradiation. Application to the solid-phase organic synthesis allows a facile construction of sp(3)-sp(3) carbon bonds through a sequential cross metathesis/olefin reduction.

Exploring the functional space of thiiranes as gelatinase inhibitors using click chemistry.

A series of 4-[(triazolyl)methoxy]phenyl analogs of the phenoxyphenyl-substituted thiirane SB-3CT 1 was evaluated for its ability to inhibit gelatinases, members of the matrix metalloproteinase family of enzymes. The triazole segment of these inhibitors was assembled using the Meldal-Sharpless copper-catalyzed Huisgen dipolar cycloaddition of an azide and a terminal alkyne. While these triazole derivatives possessed fair activity as gelatinase inhibitors, an intermediate used in the dipolar cycloaddition, 4-(propargyloxy)phenyl derivative 2, showed very good activity (>50% inhibitory activity following a 3 h pre-incubation of 2 at a concentration of 3 µM) as an inhibitor of human matrix metalloproteinase-2.