Discovery and Characterization of Potent Dual P-Glycoprotein and CYP3A4 Inhibitors: Design, Synthesis, Cryo-EM Analysis, and Biological Evaluations.

Targeted concurrent inhibition of intestinal drug efflux transporter P-glycoprotein (P-gp) and drug metabolizing enzyme cytochrome P450 3A4 (CYP3A4) is a promising approach to improve oral bioavailability of their common substrates such as docetaxel, while avoiding side effects arising from their pan inhibitions. Herein, we report the discovery and characterization of potent small molecule inhibitors of P-gp and CYP3A4 with encequidar (minimally absorbed P-gp inhibitor) as a starting point for optimization. To aid in the design of these dual inhibitors, we solved the high-resolution cryo-EM structure of encequidar bound to human P-gp. The structure guided us to prudently decorate the encequidar scaffold with CYP3A4 pharmacophores, leading to the identification of several analogues with dual potency against P-gp and CYP3A4. In vivo, dual P-gp and CYP3A4 inhibitor 3a improved the oral absorption of docetaxel by 3-fold as compared to vehicle, while 3a itself remained poorly absorbed.

Discovery of Encequidar, First-in-Class Intestine Specific P-glycoprotein Inhibitor.

Many chemotherapeutics, such as paclitaxel, are administered intravenously as they suffer from poor oral bioavailability, partly because of efflux mechanism of P-glycoprotein in the intestinal epithelium. To date, no drug has been approved by the U.S. Food and Drug Administration (FDA) that selectively blocks this efflux pump. We sought to identify a compound that selectively inhibits P-glycoprotein in the gastrointestinal mucosa with poor oral bioavailability, thus eliminating the issues such as bone marrow toxicity associated with systemic inhibition of P-glycoprotein. Here, we describe the discovery of highly potent, selective, and poorly orally bioavailable P-glycoprotein inhibitor 14 (encequidar). Clinically, encequidar was found to be well tolerated and minimally absorbed; and importantly, it enabled the oral delivery of paclitaxel.

Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors.

Here we report the discovery of tetracyclic benzothiazepines (BTZs) as highly potent and selective antimalarials along with the identification of the Plasmodium falciparum cytochrome bc(1) complex as the primary functional target of this novel compound class. Investigation of the structure activity relationship within this previously unexplored chemical scaffold has yielded inhibitors with low nanomolar activity. A combined approach employing genetically modified parasites, biochemical profiling, and resistance selection validated inhibition of cytochrome bc(1) activity, an essential component of the parasite respiratory chain and target of the widely used antimalarial drug atovaquone, as the mode of action of this novel compound class. Resistance to atovaquone is eroding the efficacy of this widely used antimalarial drug. Intriguingly, BTZ-based inhibitors retain activity against atovaquone resistant parasites, suggesting this chemical class may provide an alternative to atovaquone in combination therapy.

Aminoindoles, a novel scaffold with potent activity against Plasmodium falciparum.

This study characterizes aminoindole molecules that are analogs of Genz-644442. Genz-644442 was identified as a hit in a screen of ~70,000 compounds in the Broad Institute's small-molecule library and the ICCB-L compound collection at Harvard Medical School. Genz-644442 is a potent inhibitor of Plasmodium falciparum in vitro (50% inhibitory concentrations [IC50s], 200 to 285 nM) and inhibits P. berghei in vivo with an efficacy of > 99% in an adapted version of Peters' 4-day suppressive test (W. Peters, Ann. Trop. Med. Parasitol. 69:155-171, 1975). Genz-644442 became the focus of medicinal chemistry optimization; 321 analogs were synthesized and were tested for in vitro potency against P. falciparum and for in vitro absorption, distribution, metabolism, and excretion (ADME) properties. This yielded compounds with IC50s of approximately 30 nM. The lead compound, Genz-668764, has been characterized in more detail. It is a single enantiomer with IC50s of 28 to 65 nM against P. falciparum in vitro. In the 4-day P. berghei model, when it was dosed at 100 mg/kg of body weight/day, no parasites were detected on day 4 postinfection. However, parasites recrudesced by day 9. Dosing at 200 mg/kg/day twice a day resulted in cures of 3/5 animals. The compound had comparable activity against P. falciparum blood stages in a human-engrafted NOD-scid mouse model. Genz-668764 had a terminal half-life of 2.8 h and plasma trough levels of 41 ng/ml when it was dosed twice a day orally at 55 mg/kg/day. Seven-day rat safety studies showed a no-observable-adverse-effect level (NOAEL) at 200 mg/kg/day; the compound was not mutagenic in Ames tests, did not inhibit the hERG channel, and did not have potent activity against a broad panel of receptors and enzymes. Employing allometric scaling and using in vitro ADME data, the predicted human minimum efficacious dose of Genz-668764 in a 3-day once-daily dosing regimen was 421 mg/day/70 kg, which would maintain plasma trough levels above the IC90 against P. falciparum for at least 96 h after the last dose. The predicted human therapeutic index was approximately 3, on the basis of the exposure in rats at the NOAEL. We were unable to select for parasites with >2-fold decreased sensitivity to the parent compound, Genz-644442, over 270 days of in vitro culture under drug pressure. These characteristics make Genz-668764 a good candidate for preclinical development.

A concise silylamine approach to 2-amino-3-hydroxy-indoles with potent in vivo antimalaria activity.

The development of a concise strategy to access 2-amino-3-hydroxy-indoles, which are disclosed as novel antimalarials with potent in vivo activity, is reported. Starting from isatins the target compounds are synthesized in 2 steps and in good yields via oxoindole intermediates by employing tert-butyldimethylsilyl amine (TBDMSNH(2)) as previously unexplored ammonia equivalent.

Identification and characterization of small molecule inhibitors of a class I histone deacetylase from Plasmodium falciparum.

A library of approximately 2000 small molecules biased toward inhibition of histone deacetylases was assayed for antimalarial activity in a high-throughput P. falciparum viability assay. Active compounds were cross-analyzed for induction of histone hyperacetylation in a human myeloma cell line to identify HDAC inhibitors with selectivity for P. falciparum over the human host. To verify on-target selectivity, pfHDAC-1 was expressed and purified and a biochemical assay for pfHDAC-1 activity was established.

Water solubilization of DDGS via derivatization with phosphite esters.

Ethanol production from corn starch in the corn dry milling process leaves Distillers' Dry Grains and Solubles (DDGS) as a major by-product from which additional ethanol may be economically obtained from its glucan content. A challenge in processing the cellulose content of this material lies in its extensive inter-cellulose chain hydrogen bonding, which inhibits access of enzymes capable of cleaving glycosidic bonds, a transformation required for providing fermentable sugars. The phosphitylation of cellulosic OH groups using a reactive bicyclic phosphite ester is utilized to disrupt cellulosic hydrogen bonds, thus providing access to cellulose chains for further processing. We describe a method of pretreating DDGS with commercially available trimethylolpropane phosphite [P(OCH2)3CEt] in the presence of a slight molar excess of water to afford greater than 90% DDGS solubility in the reaction mixture in methanol and in water. Preliminary results using a model compound [D-(+)-permethylated cellobiose] indicate that glycosidic bonds are cleaved as a consequence of this pretreatment.

N-Benzyl-3-sulfonamidopyrrolidines as novel inhibitors of cell division in E. coli.

A new small molecule inhibitor of bacterial cell division has been discovered using a high-throughput screen in Escherichia coli. Although the lead screening hit (534F6) exhibited modest inhibition of the GTPase activity of FtsZ (20+/-5% at 100microM of compound), a primary target for bacterial cell division inhibitors, several analogs caused potent bacterial growth inhibition with negligible antagonism of FtsZ GTPase activity. A library of analogs has been prepared and several alkyne-tagged photoaffinity probes have been synthesized for use in experiments to elucidate the primary target of this compound.

Synthesis of kaempferitrin.

A short synthesis of Kaempferitrin (1), a 3,7-diglycosylflavone, is reported. Key features include the synthesis of a protected form of kaempferol in which all four hydroxy groups are differentiated and the first bis-glycosylation of a dihydroxyflavone. This synthesis will allow the preparation of derivatives for further explorations into the origins of this compound's biological activity.

Synthesis of antimicrobial natural products targeting FtsZ: (+/-)-dichamanetin and (+/-)-2' ''-hydroxy-5' '-benzylisouvarinol-B.

[chemical structure: see text]. Two natural products have been synthesized using a ZnCl2-mediated benzylic coupling reaction. Both are potent inhibitors of the GTPase activity of FtsZ, a highly conserved protein that is essential for bacterial cytokinesis.

A highly effective catalyst system for the Pd-catalyzed amination of vinyl bromides and chlorides.

[reaction: see text] A highly efficient synthesis of enamines and imines by Pd-catalyzed amination of vinyl bromides or chlorides with amines is described using the Pd2(dba)3/P(i-BuNCH2CH2)3N catalyst system.

Separation and characterization of underivatized oligosaccharides using liquid chromatography and liquid chromatography-electrospray ionization mass spectrometry.

Native cyclodextrin-based columns are particularly useful for the analysis of oligosaccharides because the retention of these carbohydrates is based mainly on the hydrogen bonding interactions of oligosaccharide hydroxyl groups with the stationary phase. Thus, the retention time predictably increases with the number of analyte hydroxyl groups, which corresponds to the elongation of the oligosaccharide chain. High-performance liquid chromatography (HPLC) coupled to electrospray ionization (ESI) mass spectrometry (MS) was used for the separation and characterization of underivatized oligosaccharide mixtures. With the limits of detection as low as 50 pg, all individual components of oligosaccharide mixtures (up to 11 glucose units long) were baseline resolved on a Cyclobond I 2000 column and detected using ESI-MS. Low flow rates and narrow I.D. columns increase the ESI-MS sensitivity significantly. The method showed potential usefulness for the sensitive and quick analysis of hydrolysis products of polysaccharides, and for trace levels of individual oligosaccharide or oligosaccharide isomers from biological systems.

P(i-BuNCH2CH2)3N: an efficient promoter for the nucleophilic aromatic substitution reaction of aryl fluorides with aryl TBDMS (or TMS) ethers.

[reaction: see text]. The nucleophilic aromatic substitution reaction between electron-deficient aryl fluorides and aryl TBDMS (or TMS) ethers has been shown to be efficiently promoted by proazaphosphatranes such as P(i-BuNCH(2)CH(2))(3)N (3). Excellent yields of diaryl ether products were obtained under unusually mild conditions.

Highly active palladium catalysts supported by bulky proazaphosphatrane ligands for Stille cross-coupling: coupling of aryl and vinyl chlorides, room temperature coupling of aryl bromides, coupling of aryl triflates, and synthesis of sterically hindered biaryls.

A family of proazaphosphatrane ligands [P(RNCH2CH2)2N(R'NCH2CH2): R = R' = i-Bu, 1; R = Bz, R' = i-Bu, 3; R = R' = Bz, 4] for palladium-catalyzed Stille reactions of aryl chlorides is described. Catalysts derived from ligands 1 and 4 efficiently catalyze the coupling of electronically diverse aryl chlorides with an array of organotin reagents. The catalyst system based on the ligand 3 is active for the synthesis of sterically hindered biaryls (di-, tri-, and tetra-ortho substituted). The use of ligand 4 allows room-temperature coupling of aryl bromides and it also permits aryl triflates and vinyl chlorides to participate in Stille coupling.

Scope and limitations of Pd2(dba)3/P(i-BuNCH2CH2)3N-catalyzed Buchwald-Hartwig amination reactions of aryl chlorides.

Proazaphosphatrane ligands in combination with Pd(2)(dba)(3) generate highly active catalysts for Buchwald-Hartwig amination of aryl chlorides. In particular, commercially available P(i-BuNCH(2)CH(2))(3)N is a highly general and efficient ligand, allowing the coupling of an electronically diverse set of aryl chlorides, including chloropyridines, with a wide variety of amines using 1 mol % of Pd at 100 degrees C. Either a 1:1 or 2:1 ratio of ligand to Pd was found to be effective. This catalyst system performs exceptionally well for sterically hindered substrates, even with only 0.25 mol % of Pd. It is shown that NaOH can also be used as the base (instead of NaO-t-Bu) allowing functionalized substrates to participate in these reactions.

Ligand-, copper-, and amine-free sonogashira reaction of aryl iodides and bromides with terminal alkynes.

Conditions for an efficient ligand-, copper-, and amine-free palladium-catalyzed Sonogashira reaction of aryl iodides and bromides with terminal alkynes have been developed. Critical to the success of this new protocol is the use of tetrabutylammonium acetate as the base. Noteworthy features of this method are room-temperature conditions and the tolerance of a broad range of functional groups in both reaction partners.

Pd2(dba)3/P(i-BuNCH2CH2)3N-catalyzed Stille cross-coupling of aryl chlorides.

[reaction: see text] The Pd(2)(dba)(3)/P(i-BuNCH(2)CH(2))(3)N (1d) catalyst system is highly effective for the Stille cross-coupling of aryl chlorides with organotin compounds. This method represents only the second general method for the coupling of aryl chlorides. Other proazaphosphatranes possessing benzyl substituents also generate very active catalysts for Stille reactions. Noteworthy features of the method are: (a) commercial availability of ligand 1d, (b) the wide array of aryl chlorides that can be coupled, and (c) applicability to aryl, vinyl, and allyl tin reagents.

Application of a new bicyclic triaminophosphine ligand in Pd-catalyzed Buchwald-Hartwig amination reactions of aryl chlorides, bromides, and iodides.

The new bicyclic triaminophosphine ligand P(i-BuNCH2)3CMe (3) has been synthesized in three steps from commercially available materials and its efficacy in palladium-catalyzed reactions of aryl halides with an array of amines has been demonstrated. Electron-poor, electron-neutral, and electron-rich aryl bromides, chlorides, and iodides participated in the process. The reactions encompassed aromatic amines (primary or secondary) and secondary amines (cyclic or acyclic). It has also been shown that the weak base Cs2CO3 can be employed with ligand 3, allowing a variety of functionalized substrates (e.g., those containing esters and nitro groups) to be utilized in our amination protocols. This ligand provides a remarkably general, efficient, and mild palladium catalyst for aryl iodide amination. Although 3 is slightly air and moisture sensitive, easy procedures can be adopted that avoid the need of a glovebox. Comparisons of the efficacy of 3 in these reactions with that of the proazaphosphatrane P(i-BuNCH2CH2)3N (2) reveal that in addition to the opportunity for transannulation in 2 (but not in 3), other significant stereoelectronic contrasts exist between these two ligands which help account for differences in the activities of the Pd/2 and Pd/3 catalytic systems.

P[N(i-Bu)CH2CH2]3N: a versatile ligand for the Pd-catalyzed amination of aryl chlorides.

[reaction: see text] Palladium-catalyzed amination reactions of aryl chlorides with amines proceeded in the presence of the bicyclic triaminophosphine P[N(i-Bu)CH(2)CH(2)](3)N to afford the corresponding arylamines in good to excellent yields. Electron-poor, electron-neutral, and electron-rich aryl chlorides all participated with equal ease.