A stereoselective synthesis of trans-1,2,3,6-tetrahydropyridines 8 is described. This synthesis proceeds via intramolecular Mistunobu reactions of 1,5-syn-(Z)-amino alcohols 7, which were prepared by a highly diastereo- and enantioselective double-allylboration reaction of aldehyde 5 and silylimine 6. The chiral bifunctional γ-borylallylborane 9E was generated in situ by hydroboration of allene 3 with (diisopinocampheyl)borane 4. This strategy was applied to the total synthesis of andrachcine 1, thus establishing with certainty the absolute and relative configuration of the natural product.

We describe the use of comparative structural analysis and structure-guided molecular design to develop potent and selective inhibitors (10d and (S)-17b) of matrix metalloproteinase 13 (MMP-13). We applied a three-step process, starting with a comparative analysis of the X-ray crystallographic structure of compound 5 in complex with MMP-13 with published structures of known MMP-13·inhibitor complexes followed by molecular design and synthesis of potent but nonselective zinc-chelating MMP inhibitors (e.g., 10a and 10b). After demonstrating that the pharmacophores of the chelating inhibitors (S)-10a, (R)-10a, and 10b were binding within the MMP-13 active site, the Zn2+ chelating unit was replaced with nonchelating polar residues that bridged over the Zn2+ binding site and reached into a solvent accessible area. After two rounds of structural optimization, these design approaches led to small molecule MMP-13 inhibitors 10d and (S)-17b, which bind within the substrate-binding site of MMP-13 and surround the catalytically active Zn2+ ion without chelating to the metal. These compounds exhibit at least 500-fold selectivity versus other MMPs.

Stolonidiol, a marine natural product, has been reported to potentiate the activity of choline acetyltransferase (ChAT), the enzyme that produces the neurotransmitter acetylcholine. Here we report the total synthesis of stolonidiol starting from (R)-(+)-limonene. To identify the mechanism by which ChAT activity is increased, we sought to identify the biological target of stolonidiol. We show that stolonidiol binds to the phorbol ester binding site of protein kinase C (PKC), induces translocation of PKC to the cell membrane, and activates kinase activity. Furthermore, we confirmed the increase in ChAT activity observed upon treatment of cells with stolonidiol and show that this effect is mediated by PKC. Collectively, our data strongly suggest that PKC activation by stolonidiol is responsible for the resulting potentiation of ChAT activity.

Conventional antibody–drug conjugates (ADCs) are heterogeneous mixtures that have poor pharmacokinetic properties and decreased efficacy relative to homogenous ADCs. Furthermore, ADCs that are maleimide-based often have inadequate circulatory stability, which can result in premature drug release with consequent off-target toxicities. Selenocysteine-modified antibodies have been developed that allow site-specific antibody conjugation, yielding homogeneous ADCs. Herein, we survey several electrophilic functional groups that react with selenocystine with high efficiency. Several of these result in conjugates with stabilities that are superior to maleimide conjugates. Among these, the allenamide functional group reacts with notably high efficiency, leads to conjugates with remarkable stability, and shows exquisite selectivity for selenocysteine conjugation.

A series of oxyguanidine analogues of the cysteine protease inhibitor WRR-483 were synthesized and evaluated against cruzain, the major cysteine protease of the protozoan parasite Trypanosoma cruzi. Kinetic analyses of these analogues indicated that they have comparable potency to previously prepared vinyl sulfone cruzain inhibitors. Co-crystal structures of the oxyguanidine analogues WRR-666 (4) and WRR-669 (7) bound to cruzain demonstrated different binding interactions with the cysteine protease, depending on the aryl moiety of the P1′ inhibitor subunit. Specifically, these data demonstrate that WRR-669 is bound noncovalently in the crystal structure. This represents a rare example of noncovalent inhibition of a cysteine protease by a vinyl sulfone inhibitor.Keywords: Chagas’ disease; cysteine protease inhibitor; kinetics; noncovalent inhibitor; vinyl sulfone; X-ray crystallography

A highly enantio- and diastereoselective synthesis of morpholine syn-β-hydroxy-α-alkenyl carboxamides 11 via the reductive aldol reaction of allenyl carboxamide 8 with diisopinocampheylborane is described.

CYP51 is a P450 enzyme involved in the biosynthesis of the sterol components of eukaryotic cell membranes. CYP51 inhibitors have been developed to treat infections caused by fungi, and more recently the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease. To specifically optimize drug candidates for T. cruzi CYP51 (TcCYP51), we explored the structure–activity relationship (SAR) of a N-indolyl-oxopyridinyl-4-aminopropanyl-based scaffold originally identified in a target-based screen. This scaffold evolved via medicinal chemistry to yield orally bioavailable leads with potent anti-T. cruzi activity in vivo. Using an animal model of infection with a transgenic T. cruzi Y luc strain expressing firefly luciferase, we prioritized the biaryl and N-arylpiperazine analogues by oral bioavailability and potency. The drug–target complexes for both scaffold variants were characterized by X-ray structure analysis. Optimization of both binding mode and pharmacokinetic properties of these compounds led to potent inhibitors against experimental T. cruzi infection.

Chagas disease is a chronic infection in humans caused by Trypanosoma cruzi and manifested in progressive cardiomyopathy and/or gastrointestinal dysfunction. Limited therapeutic options to prevent and treat Chagas disease put 8 million people infected with T. cruzi worldwide at risk. CYP51, involved in the biosynthesis of the membrane sterol component in eukaryotes, is a promising drug target in T. cruzi. We report the structure–activity relationships (SAR) of an N-arylpiperazine series of N-indolyloxopyridinyl-4-aminopropanyl-based inhibitors designed to probe the impact of substituents in the terminal N-phenyl ring on binding mode, selectivity and potency. Depending on the substituents at C-4, two distinct ring binding modes, buried and solvent-exposed, have been observed by X-ray structure analysis (resolution of 1.95–2.48 Å). The 5-chloro-substituted analogs 9 and 10 with no substituent at C-4 demonstrated improved selectivity and potency, suppressing ≥99.8% parasitemia in mice when administered orally at 25 mg/kg, b.i.d., for 4 days.

Sterol 14α-demethylase (CYP51) is an important therapeutic target for fungal and parasitic infections due to its key role in the biosynthesis of ergosterol, an essential component of the cell membranes of these pathogenic organisms. We report the development of potent and selective d-tryptophan-derived inhibitors of T. cruzi CYP51. Structural information obtained from the cocrystal structure of CYP51 and (R)-2, which is >1000-fold more potent than its enantiomer (S)-1, was used to guide design of additional analogues. The in vitro efficacy data presented here for (R)-2–(R)-8, together with preliminary in vitro pharmacokinetic data suggest that this new CYP51 inhibitor scaffold series has potential to deliver drug candidates for treatment of T. cruzi infections.Keywords: CYP51; inhibitors; R-configuration; T. cruzi;

A highly diastereoselective synthesis of N-acetyl dihydrotetrafibricin methyl ester (34) is described. The synthesis features three enantioselective double allylboration reactions and an intramolecular hydrosilylation/Fleming–Tamao oxidation sequence to establish seven of the hydroxy-bearing stereocenters of 34. Especially noteworthy is the fragment-assembly double allyboration reaction of 2 and 7 using reagent 3, which provides the advanced intermediate 6 with >20:1 diastereoselectivity.

Kinetically controlled hydroboration of allenylboronate 5 followed by double allylboration with the resulting allylborane (Z)-7 gave (Z)-2-methyl-1,5-anti-pentenediols 6 in good yield and high enantioselectivity in the presence of 10% BF3·OEt2 as the catalyst in the second allylboration step. Under thermodynamically controlled isomerization conditions, (Z)-7 can readily isomerize to (E)-7. Double allylboration of representative aldehydes with allylborane (E)-7 gave (E)-2-methyl-1,5-anti-pentenediols 4 in good yield and high enantioselectivity without requiring use of the BF3·OEt2 catalyst. Thus, 2-methyl-1,5-anti-pentenediols with either olefin geometry can be synthesized from the same allenylboronate precursor 5. Furthermore, 1,5-pentenediols 4 and 6 can be easily converted to 1,3,5-triols with excellent diastereoselectivity in one step.

A chiral phosphoric acid catalyzed kinetic resolution/allenylboration of racemic allenylboronates with aldehydes is described. Allenylboration of aldehydes with 2.8 equiv of allenylboronate (±)-1 in the presence of 10 mol % of catalyst (R)-2 provided anti-homopropargyl alcohols 3 in 83–95% yield with 9:1 to 20:1 diastereoselectivity and 73–95% ee. The catalyst enables the kinetic resolution of the racemic allenylboronate (±)-1 to set the methyl stereocenter and biases the facial attack of the aldehyde to set the stereochemistry of the hydroxyl group in 3.

The (diisopinocampheyl)borane promoted reductive aldol reaction of acrylate esters 4 is described. Isomerization of the kinetically formed Z(O)-enolborinate 5Z to the thermodynamic E(O)-enolborinate 5E via 1,3-boratropic shifts, followed by treatment with representative achiral aldehydes, leads to anti-α-methyl-β-hydroxy esters 9 or 10 with excellent diastereo- (up to ≥20:1 dr) and enantioselectivity (up to 87% ee). The results of double asymmetric reactions of 5E with several chiral aldehydes are also presented.

A stereoselective synthesis of a fully protected version of the disaccharide unit (2) of incednine (1) is described. The synthesis of 2 proceeds in 4.7% overall yield from commercially available allyl α-d-galactopyranoside over the longest linear sequence.

A convergent synthesis of the protected C(1)–C(11) fragment 6 of the targeted enantiomer of tedanolide C is described. The key step of the synthesis is the Felkin–Ahn addition of vinyl iodide 7 to aldehyde 8 that proceeds in 80% yield with 4:1 diastereoselectivity.

The enantioselective hydroboration of racemic allenylsilane (±)-4 with (dIpc)2BH proceeds via enantiodivergent pathways to give vinylborane 11 and crotylborane intermediate (S)-E-5. Subsequent crotylboration of aldehyde substrates with (S)-E-5 at −78 °C provides (E)-δ-silyl-anti-homoallylic alcohols in 71–89% yield and with 93–96% ee.

An enantio- and diastereoselective synthesis of syn-β-hydroxy-α-vinyl carboxylate esters 3 via the reductive aldol reaction of ethyl allenecarboxylate (2) with 10-trimethylsilyl-9-borabicyclo[3.3.2]decane (1R) has been developed. Density functional theory calculations suggest that the allene hydroboration involves the 1,4-reduction of 2 with the 1R, leading directly to dienolborinate Z-(O)-8a.

A new series of 4-aminopyridyl-based lead inhibitors targeting Trypanosoma cruzi CYP51 (TcCYP51) has been developed using structure-based drug design as well as structure–property relationship (SPR) analyses. The screening hit starting point, LP10 (KD ≤ 42 nM; EC50 = 0.65 μM), has been optimized to give the potential leads 14t, 27i, 27q, 27r, and 27t, which have low-nanomolar binding affinity to TcCYP51 and significant activity against T. cruzi amastigotes cultured in human myoblasts (EC50 = 14–18 nM for 27i and 27r). Many of the optimized compounds have improved microsome stability, and most are selective against human CYPs 1A2, 2D6, and 3A4 (<50% inhibition at 1 μM). A rationale for the improvement in microsome stability and selectivity of inhibitors against human metabolic CYP enzymes is presented. In addition, the binding mode of 14t with the Trypanosoma brucei CYP51 (TbCYP51) orthologue has been characterized by X-ray structure analysis.

The development of a series of potent and highly selective casein kinase 1δ/ε (CK1δ/ε) inhibitors is described. Starting from a purine scaffold inhibitor (SR-653234) identified by high throughput screening, we developed a series of potent and highly kinase selective inhibitors, including SR-2890 and SR-3029, which have IC50 ⩽ 50 nM versus CK1δ. The two lead compounds have ⩽100 nM EC50 values in MTT assays against the human A375 melanoma cell line and have physical, in vitro and in vivo PK properties suitable for use in proof of principle animal xenograft studies against human cancer cell lines.

Syntheses of the C(15)-C(27) fragments of chaxamycins A/D, rifamycin S, and the C(12)-C(24) fragment of salinisporamycin have been accomplished in 10 steps from commercially available starting materials. Three crotylboron reagents were utilized to construct the seven contiguous stereocenters in these fragments with excellent stereoselectivity.

The stereocontrolled synthesis of the β-branched anti,anti-dipropionate stereotriad 4 via aldol or crotylmetal chemistry represents a historical challenge to the organic synthesis community. Here we describe a general solution to the long-standing problem associated with the synthesis of 4 by utilizing mismatched double asymmetric crotylboration reactions of enantioenriched α-methyl substituted aldehydes with the chiral, nonracemic crotylborane reagent (S)-(E)-22 (or its enantiomer). This method not only provides direct access to anti,anti-dipropionate stereotriads 24 [a synthetic equivalent of 4] with very good (5–8:1) if not excellent (≥15:1) diastereoselectivity from β-branched chiral aldehydes with ≤50:1 intrinsic diastereofacial selectivity preferences but also provides a vinylstannane unit in the products that is properly functionalized for use in subsequent C–C bond-forming events. We anticipate that this method will be widely applicable and will lead to substantial simplification of strategies for synthesis of polyketide natural products.

Chiral Brønsted acid catalyzed asymmetric allenylboration reactions are described. Under optimized conditions, anti-homopropargyl alcohols 2 are obtained in high yields with excellent diastereo- and enantioselectivities from stereochemically matched aldehyde allenylboration reactions with (M)-1 catalyzed by the chiral phosphoric acid (S)-4. The syn-isomers 3 can also be obtained in good diastereoselectivities and excellent enantioselectivities from the mismatched allenylboration reactions of aromatic aldehydes using (M)-1 in the presence of the enantiomeric phosphoric acid (R)-4. The stereochemistry of the methyl group introduced into 2 and 3 is controlled by the chirality of the allenylboronate (M)-1, whereas the configuration of the new hydroxyl stereocenter is controlled by the enantioselectivity of the chiral phosphoric acid catalyst used in these reactions. The synthetic utility of this methodology was further demonstrated in highly diastereoselective syntheses of a variety of anti, anti-stereotriads, the direct synthesis of which has constituted a significant challenge using previous generations of aldol and crotylmetal reagents.

Basiliskamide A is an antifungal polyketide natural product isolated by Andersen and co-workers from a Bacillus laterosporus isolate, PNG-276. A nine-step enantioselective synthesis of (−)-basiliskamide A is reported, starting from commercially available β-hydroxy ester 7. The synthesis features a highly diastereoselective mismatched double asymmetric δ-stannylallylboration reaction of aldehyde 5 with the bifunctional allylborane reagent 4.

A concise, enantioselective synthesis of (+)-crocacin C is described, featuring a highly diastereoselective mismatched double asymmetric δ-stannylcrotylboration of the stereochemically demanding chiral aldehyde 9 with the bifunctional crotylborane reagent (S)-E-10. The total synthesis of (+)-crocacin C was accomplished in seven steps (longest linear sequence) starting from commercially available precursors.

Enantioselective hydroboration of racemic allenylboronate (±)-1 with 0.48 equiv of (dIpc)2BH at −25 °C proceeds with efficient kinetic resolution and provides allylborane (R)-Z-4. When heated to 95 °C, allylborane (R)-Z-4 isomerizes to the thermodynamically more stable allylborane isomer (S)-E-7. Subsequent allylboration of aldehydes with (R)-Z-4 or (S)-E-7 at −78 °C followed by oxidative workup provides 1,2-syn- or 1,2-anti-diols, 2 or 3, respectively, in 87–94% ee.

Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogues, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC50 = 58 μM), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP5A in a PaTMK homology model. This hit (1) was cocrystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC50 = 100–200 nM) were synthesized using computer-aided design approaches including virtual synthesis/screening, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs but not with human TMK, which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray cocrystal structures, homology models, and structure–activity relationship results.

The enantioconvergent hydroboration of racemic allenylstannane (±)-1 with (dIpc)2BH converts both enantiomers of (±)-1 into the enantioenriched crotylborane (S)-E-3. Subsequent crotylboration of aldehydes with (S)-E-3 provides (E)-stannyl-homoallylic alcohols 5 in good yields and with excellent enantioselectivity.

The kinetic hydroboration of allenylsilane 5 with (dIpc)2BH at −40 °C provides allylborane 9Z with ≥12:1 selectivity. When the hydroboration is performed at temperatures above −40 °C, 9Z isomerizes to the thermodynamically more stable allylborane 9E with >20:1 selectivity. Subsequent treatment of 9Z or 9E with aldehydes at −78 °C provides syn- or anti-β-hydroxyallylsilanes, 7 or 8, respectively.

A stereoselective synthesis of the decahydrofluorene core of the hirsutellones was accomplished in eight steps and in 43% overall yield. The key step of the synthesis is the highly stereoselective intramolecular Diels–Alder cyclization of the siloxacyclopentene-constrained tetraene 1.

Matrix metalloproteinase-13 (MMP-13) has been implicated as the protease responsible for collagen degradation in cartilage during osteoarthritis (OA). Compounds that inhibit the metalloproteinase at the Zn binding site typically lack specificity among MMP family members. Analogs of the low-micromolar lead MMP-13 inhibitor 4, discovered through high-throughput screening, were synthesized to investigate structure–activity relationships in this inhibitor series. Systematic modifications of 4 led to the discovery of MMP-13 inhibitors 20 and 24 which are more selective than 4 against other MMPs. Compound 20 is also approximately fivefold more potent as an MMP-13 inhibitor than the original HTS-derived lead compound 4.

A highly enantioselective synthesis of (E)-δ-stannyl homoallylic alcohols 4 via aldehyde allylboration reactions of the double-chiral allylborane reagent 2a is reported. Allylborane 2a was generated from the hydroboration of commercially available allenylstannane 1 with (dIpc)2BH at −40 to −20 °C followed by a kinetically controlled and highly diastereoselective 1,3-boratropic shift in intermediate 3a.

An enantioselective synthesis of α-methylene-β-hydroxy carboxylic acid derivatives via a highly diastereoselective, one-pot syn-aldol and β-elimination sequence utilizing the chiral β-(phenylselenyl)propionyl imide 15 is described. This new method, which constitutes an alternative to the Baylis−Hillman reaction, has been applied to the synthesis of the C(15)−C(21) fragment of tedanolide C.

δ-Methyl-substituted homoallylic alcohols 2 were prepared in 71−88% yield, E:Z >30:1 and 93% to >95% ee via BF3·Et2O-promoted allylboration with α-Me-allylboronate 1. The origin of high (E)-selectivity is proposed.

The enantioselective synthesis of (Z)-1,2-anti-2,5-anti-triol monosilyl ethers via a two-step sequence involving olefin cross-metathesis of β-alkoxyallylboronate 4 and subsequent allylboration of the derived bisboryl intermediate 6 provides triol monoethers 7 with good to excellent diastereoselectivity.

Kinetically controlled hydroboration of allenes 8 and 14a−d with the readily accessible Soderquist borane 7, which is generated in situ from borohydride 6, constitutes a convenient and preparatively useful method for synthesis of (Z)-γ-(substituted)allylboranes 9 and 15a−d. These allylboranes undergo highly diastereo- (≥90: 10) and enantioselective (typically 89−96% e.e.) allylboration reactions with representative aldehydes to give syn-β-functionalized homoallylic alcohols.

The hydroboration of allene 7 with (dIpc)2BH at 0 °C provides the kinetic allylborane 12Z with >20:1 selectivity. However, when the hydroboration is performed at 85 °C, the kinetically formed allylborane isomerizes to give the thermodynamic allylborane 12E with ≥12:1 selectivity. Subsequent treatment of 12Z or 12E with aldehydes at −78 °C, followed by oxidative workup, provides the 2-methyl-1,2-diols 8 and 9 in good yield and with 80−92% e.e.

A stereoselective method for synthesis of syn,syn- and syn,anti-1,3,5-triols based on a double allylboration−intramolecular hydrosilylation sequence has been developed. The 1,3-syn stereocontrol is achieved in the intramolecular hydrosilylation of monoprotected (Z)-1,5-syn-diols and (E)-1,5-anti-diols with 87:13 to 95:5 and 86:14 to 88:12 diastereomeric ratios, respectively, by using 0.5 mol % of Karstedt’s catalyst in toluene.

Density functional theory was used to locate transition states for hydroboration reactions of allenes with 9-borabicyclo[3.3.1]nonane and 10-R-9-borabicyclo[3.3.2]decane, as well as transition states for [1,3]-boratropic shift and aldehyde addition reactions of the derived allylboranes. The origin of kinetic versus thermodynamic control in the allene hydroboration step is described.

Three synthetic routes were developed for structure–activity relationship (SAR) studies of HTS-derived isoquinolinone inhibitor probes for the orphan nuclear receptor steroidogenic factor-1 (NR5A1). Among the new analogs reported herein, 31 and 32 have improved potency, lower cellular toxicity, and improved selectivity compared to the initial HTS-derived leads 1 and 2.

The importance of cysteine proteases in parasites, compounded with the lack of redundancy compared to their mammalian hosts makes proteases attractive targets for the development of new therapeutic agents. The binding mode of K11002 to cruzain, the major cysteine protease of Trypanosoma cruzi was used in the design of conformationally constrained inhibitors. Vinyl sulfone-containing macrocycles were synthesized via olefin ring-closing metathesis and evaluated against cruzain and the closely related cysteine protease, rhodesain.

Conventional antibody–drug conjugates (ADCs) are heterogeneous mixtures that have poor pharmacokinetic properties and decreased efficacy relative to homogenous ADCs. Furthermore, ADCs that are maleimide-based often have inadequate circulatory stability, which can result in premature drug release with consequent off-target toxicities. Selenocysteine-modified antibodies have been developed that allow site-specific antibody conjugation, yielding homogeneous ADCs. Herein, we survey several electrophilic functional groups that react with selenocystine with high efficiency. Several of these result in conjugates with stabilities that are superior to maleimide conjugates. Among these, the allenamide functional group reacts with notably high efficiency, leads to conjugates with remarkable stability, and shows exquisite selectivity for selenocysteine conjugation.