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Flavaglines such as silvestrol (1) and rocaglamide (2) constitute an interesting class of natural products with promising anticancer activities. Their mode of action is based on inhibition of eukaryotic initiation factor 4A (eIF4A) dependent translation through formation of a stable ternary complex with eIF4A and mRNA, thus blocking ribosome scanning. Herein we describe initial SAR studies in a novel series of 1-aminomethyl substituted flavagline-inspired eIF4A inhibitors. We discovered that a variety of N-substitutions at the 1-aminomethyl group are tolerated, making this position pertinent for property and ADME profile tuning. The findings presented herein are relevant to future drug design efforts towards novel eIF4A inhibitors with drug-like properties.

As a continuation of our efforts to discover novel apoptosis inducers as anticancer agents using a cell-based caspase HTS assay, 2-phenyl-oxazole-4-carboxamide derivatives were identified. The structure–activity relationships of this class of molecules were explored. Compound 1k , with EC 50 of 270 nM and GI 50 of 229 nM in human colorectal DLD-1 cells, was selected and demonstrated the ability to cleave PARP and displayed DNA laddering, the hallmarks of apoptosis. Compound 1k showed 63% tumor growth inhibition in human colorectal DLD-1 xenograft mouse model at 50 mpk, bid.

The synthesis of novel [1,2,4]oxadiazoles and their structure-activity relationship (SAR) for the inhibition of tryptase and related serine proteases is presented. Elaboration of the P'-side afforded potent, selective, and orally bioavailable tryptase inhibitors.

A series of novel α-keto-[1,2,4]-oxadiazoles has been synthesized as human tryptase inhibitors for evaluation as a new class of anti-asthmatic agent. The inhibitor design is focused on using a prime-side hydrophobic pocket and the S2 pocket of β-tryptase to achieve inhibition potency and selectivity over other serine proteases.

The discovery and development of 5-azaindole factor VIIa inhibitors will be described.

Structure-activity relationships and binding mode of novel heterocyclic factor VIIa inhibitors will be described. In these inhibitors, a highly basic 5-amidinoindole moiety has been successfully replaced with a less basic 5-aminopyrrolo[3,2-b]pyridine scaffold.

Inhibition of coagulation proteases such as thrombin, fXa, and fVIIa has been a focus of ongoing research to produce safe and effective antithrombotic agents. Herein, we describe a unique zinc-mediated chelation strategy to streamline the discovery of potent inhibitors of fIIa, fXa, and fVIIa. SAR studies that led to the development of selective inhibitors of fXa will also be detailed.

Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.

In the current studies, we used the single-crystal X-ray analysis and Kakisawa–Kashman modification of the Mosher NMR method to determine the complete relative and absolute stereochemistries of the (+)-macrosphelides A (+)-1 and B (+)-2 . The stereostructure of (+)-2 was determined by chemical comparison with artificial (+)-2 from (+)-1 . We also report the convergent total synthesis of (+)-1 and (+)-3 , as well as their antipodes, utilizing an asymmetric dihydroxylation for introduction of chirality and Yamaguchi macrocyclization to form the 16-membered trilactone macrolides.

A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences present in comparisons of natural proteases. Crystallography and enzymology involving WT and Ala190 uPA were used to calculate free energy binding contributions of hydrogen bonds involving the Ser190 hydroxyl group (O(gamma)(Ser190)) responsible for the remarkable selectivity of 6-halo-5-amidinoindole and 6-halo-5-amidinobenzimidazole inhibitors toward uPA and against natural Ala190 protease anti-targets. Crystal structures of uPA complexes of novel, active site-directed arylguanidine and 2-aminobenzimidazole inhibitors of WT uPA, together with associated K(i) values for WT and Ala190 uPA, also indicate a significant role of Ser190 in the binding of these classes of uPA inhibitors. Structures and associated K(i) values for a lead inhibitor (CA-11) bound to uPA and to five other proteases, as well as for other leads bound to multiple proteases, help reveal the features responsible for the potency (K(i)=11nM) and selectivity of the remarkably small inhibitor, CA-11. The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets.

An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog. Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.

The development of potent and selective urokinase-type plasminogen activator (uPA) inhibitors based on the lead molecule 2-(2-hydroxy-3-ethoxyphenyl)-1H-benzimidazole-5-carboxamidine (3a) is described.

The structure-based design and progression of a screening lead to a 3 nM factor VIIa/TF inhibitor with improved selectivity versus related enzymes is described.

The development of potent and selective small molecule inhibitors of factor Xa is described.

We describe a new serine protease inhibition motif in which binding is mediated by a cluster of very short hydrogen bonds (

The discovery of somatostatin antagonists at one or more receptor subtypes remains an important goal. We therefore undertook the synthesis of the homodetic tricyclic peptide ( 1 ) hoping to cause conformational distortion and thereby achieve this biological goal. The synthetic strategy called for five dimensional orthogonal amino protection. The carboxyl and amino protecting groups were selected to assure the desired selective ring closures. The amino protecting groups were also chosen to permit differentiation between the two lysine e-amino groups. An improved general cyclization procedure was achieved, which provided the complex c -octapeptide 13 in 93% yield. Biological assay results for 1 are also presented.

Plasma kallikrein is a serine protease that is involved in pathways of inflammation, complement fixation, coagulation, and fibrinolysis. Herein, we describe the SAR and structural binding modes of a series of inhibitors of plasma kallikrein as well as the pharmacokinetics of a lead analog 11 in rat.

To access mimics of peptidal β-strands ( 1 ), scalemic 3,5,5-trisubstituted pyrrolin-4-ones bearing the tyrosine, serine, and lysine side-chains have been generated via cyclization of metalated imino esters and deprotection. The functionalized imino esters were prepared by asymmetric alkylation of a common oxazolidinone precursor ( 2 ) derived from L-prenylglycine.

In an effort to cause significant conformational distortion and thereby possibly generate a pure SRIF antagonist, we undertook the synthesis of 2 , the first homodetic tricyclic peptide. This required five dimensional orthogonal amino protection and three carboxyl protecting groups to allow the selective closure of the three rings and to differentiate the e-amino groups of the two lysines. We also exploited acid catalyzed removal from the resin to achieve selective deprotection of a side chain carboxyl moiety simultaneously with its partner amino group for subsequent cyclization.

The design and synthesis of peptidomimetic 1 employing the novel cyclopentanoperhydrophenanthrene skeleton is described. The large body of steroid literature allows for the introduction of diverse peptidal side chains with precise regio- and stereoselective control. Compound 1 binds to the fibrinogen receptor on blood platelets (GP IIb/IIIa), for which it was designed, with an IC50 of ca. 100 μM.

A new two-step method employs the intramolecular cyclization of metalated imino esters for the construction of scalemic 3,5,5-trisubstituted pyrrolin-4-ones (4). The imino esters in turn derive from α-disubstituted amino acids, the latter readily available via a new protocol exploiting the enantioretentive alkylation of oxazolidinones.

Iodine monobromide (IBr) induces efficient electrophilic cyclizations of homoallylic t-butyl carbonates in toluene or methylene chloride at low temperature, affording significantly better diastereoselectivity than iodine (I2) in acetonitrile.

The four stereoisomers of 3-hydroxyleucine have been prepared in high overall yield and enantiomeric purity. Key steps include Sharpless asymmetric epoxidation, benzyl isocyanate-induced epoxide opening, and epimerization of an intermediate oxazolidinone ester.

Organodilithium reagents derived from 2-alkyl-N-trimethylsilyl anilines undergo condensation with esters of carboxylic acids to afford substituted indoles. A total of 16 examples are reported; yields in general were good. In conjunction with this program, a convenient, large-scale procedure for preparation of monosilylated anilines was also developed. To demonstrate the utility of the new indole protocol in natural products synthesis, efficient syntheses of ( + )-cinchonamine and ( + )-epi-cinchonamine as well as a tetracyclic model system for the architecturally complex penitrem mycotoxins were completed in regio- and stereoselective fashion.