The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening.

Computationally screening chemical libraries to discover molecules with desired properties is a common technique used in early-stage drug discovery. Recent progress in the field now enables the efficient exploration of billions of molecules within days or hours, but this exploration remains confined within the boundaries of the accessible chemistry space. While the number of commercially available compounds grows rapidly, it remains a limited subset of all druglike small molecules that could be synthesized. Here, we present a workflow where chemical reactions typically developed in academia and unconventional in drug discovery are exploited to dramatically expand the chemistry space accessible to virtual screening. We use this process to generate a first version of the Pan-Canadian Chemical Library, a collection of nearly 150 billion diverse compounds that does not overlap with other ultra-large libraries such as Enamine REAL or SAVI and could be a resource of choice for protein targets where other libraries have failed to deliver bioactive molecules.

Synthesis of N-Hydroxysuccinimide Esters, N-Acylsaccharins, and Activated Esters from Carboxylic Acids Using I2/PPh3.

A method for the syntheses of isolable, active esters is described in which carboxylic acids are treated with triphenylphosphine, iodine, and triethylamine. Active esters accessible in this way include N-hydroxysuccinimide esters, N-hydroxyphthalimide esters (N-(acyloxy)phthalimides), N-acylsaccharins, pentafluorophenol esters, pentachlorophenol esters, N-hydroxybenzotriazole esters, and hexafluoro-2-propanol esters. The approach can be similarly applied toward the formation of N-acylsaccharins and N-acylimidazoles. The method is suitable for the formation of isolable active esters of aromatic and aliphatic activated acids as well as α-amino acid derivatives. These products are widely used reagents in organic synthesis, peptide synthesis, medicinal chemistry, and chemical biology (e.g., for bioconjugations). The method has broad substrate scope, uses simple and inexpensive reagents, avoids the use of carbodiimides or other coupling agents, and occurs at room temperature. Additionally, the diastereomers of compound Boc-Ala-NHCHPh are demonstrated to be distinguishable by 1H NMR (in DMSO-d6), allowing for a straightforward NMR method to establish the degree of racemization of activated esters of Boc-Ala or amide bond formations using Boc-Ala.

Total Synthesis of the 2,5-Disubstituted γ-Pyrone E1 UAE Inhibitor Himeic Acid A.

The first total synthesis of the E1 ubiquitin-activating enzyme inhibitor, himeic acid A, is reported. A McCombie reaction was used to form the core γ-pyrone via a 6π-electrocyclization. A dioxenone ring-opening/acyl ketene trapping reaction with a primary amide provided the unusual unsymmetrical imide functionality. Other key steps include the use of an Evans auxiliary alkylation (d.r. ≥ 95:5) to install the (S)-2-methyl succinic acid fragment and a cross-metathesis to install the unsaturated side-chain.

High Accuracy Prediction of PROTAC Complex Structures.

The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a method for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. The method is dependent on two computational innovations: adding a "silent" convolution term to an efficient protein-protein docking program to eliminate protein poses that do not have acceptable linker conformations and clustering models of multiple PROTACs that use the same E3 ligase and target the same protein. Results show that the largest consensus clusters always have high predictive accuracy and that the ensemble of models can be used to predict the dissociation rate and cooperativity of the ternary complex that relate to the degrading activity of the PROTAC. The method is demonstrated by applications to known PROTAC structures and a blind test involving PROTACs against BRAF mutant V600E. The results confirm that PROTACs function by stabilizing a favorable interaction between the E3 ligase and the target protein but do not necessarily exploit the most energetically favorable geometry for interaction between the proteins.

Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4.

Targeted protein degradation (TPD) strategies exploit bivalent small molecules to bridge substrate proteins to an E3 ubiquitin ligase to induce substrate degradation. Few E3s have been explored as degradation effectors due to a dearth of E3-binding small molecules. We show that genetically induced recruitment to the GID4 subunit of the CTLH E3 complex induces protein degradation. An NMR-based fragment screen followed by structure-guided analog elaboration identified two binders of GID4, 16 and 67, with Kd values of 110 and 17 µM in vitro. A parallel DNA-encoded library (DEL) screen identified five binders of GID4, the best of which, 88, had a Kd of 5.6 µM in vitro and an EC50 of 558 nM in cells with strong selectivity for GID4. X-ray co-structure determination revealed the basis for GID4-small molecule interactions. These results position GID4-CTLH as an E3 for TPD and provide candidate scaffolds for high-affinity moieties that bind GID4.

N-Alkyl Carbamoylimidazoles as Isocyanate Equivalents: Exploration of the Reaction Scope for the Synthesis of Ureas, Hydantoins, Carbamates, Thiocarbamates, and Oxazolidinones.

The reaction of the HCl or trifluoroacetic acid salts of primary amines with carbonyldiimidazole (CDI) is shown to be a preparatively useful method for forming monosubstituted carbamoylimidazoles (28 examples) without the formation of symmetrical urea side products. The utility of these air- and water-stable crystalline carbamoylimidazole reagents was demonstrated by their reactions as blocked or masked isocyanate equivalents. Reaction with various classes of nucleophiles provides access to useful functional groups including ureas, carbamates, thiocarbamates, hydantoins, and oxazolidinones. A parallel synthesis library of 30 ureas was generated by the reaction of 6× carbamoylimidazole intermediates with 5× amines and triethylamine. The unsymmetrical urea-containing natural products macaurea A and pygmaniline A were also prepared in good yields (95% over four steps and 79% over three steps, respectively) using this approach. The reaction of carbamoylimidazoles with amino acid methyl esters followed by microwave irradiation in aqueous media gives hydantoins in high yields, further demonstrating the ability of carbamoylimidazoles as isocyanate surrogates. Three hydantoin-containing natural products including macahydantoin D and meyeniihydantoin A were prepared in nearly quantitative yields from proline methyl ester and carbamoylimidazoles. The reaction of carbamoylimidazoles with alcohols and thiols under basic conditions affords carbamates and thiocarbamates, respectively, in good yields. Lastly, a method for the preparation of chiral oxazolidinone heterocycles from chiral epoxy alcohols is demonstrated using a double displacement approach. The reactions occur with high regio- and stereoselectivity (dr ≥ 15:1 by 1H NMR) via a domino attack of the corresponding alkoxides with carbamoylimidazoles followed by an intramolecular attack of the in situ generated urea anion at the proximal position of the epoxide group.

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.

One aspirational goal of computational chemistry is to predict potent and drug-like binders for any protein, such that only those that bind are synthesized. In this Roadmap, we describe the launch of Critical Assessment of Computational Hit-finding Experiments (CACHE), a public benchmarking project to compare and improve small molecule hit-finding algorithms through cycles of prediction and experimental testing. Participants will predict small molecule binders for new and biologically relevant protein targets representing different prediction scenarios. Predicted compounds will be tested rigorously in an experimental hub, and all predicted binders as well as all experimental screening data, including the chemical structures of experimentally tested compounds, will be made publicly available, and not subject to any intellectual property restrictions. The ability of a range of computational approaches to find novel binders will be evaluated, compared, and openly published. CACHE will launch 3 new benchmarking exercises every year. The outcomes will be better prediction methods, new small molecule binders for target proteins of importance for fundamental biology or drug discovery, and a major technological step towards achieving the goal of Target 2035, a global initiative to identify pharmacological probes for all human proteins.

Development of Antibiotics That Dysregulate the Neisserial ClpP Protease.

Evolving antimicrobial resistance has motivated the search for novel targets and alternative therapies. Caseinolytic protease (ClpP) has emerged as an enticing new target since its function is conserved and essential for bacterial fitness, and because its inhibition or dysregulation leads to bacterial cell death. ClpP protease function controls global protein homeostasis and is, therefore, crucial for the maintenance of the bacterial proteome during growth and infection. Previously, acyldepsipeptides (ADEPs) were discovered to dysregulate ClpP, leading to bactericidal activity against both actively growing and dormant Gram-positive pathogens. Unfortunately, these compounds had very low efficacy against Gram-negative bacteria. Hence, we sought to develop non-ADEP ClpP-targeting compounds with activity against Gram-negative species and called these activators of self-compartmentalizing proteases (ACPs). These ACPs bind and dysregulate ClpP in a manner similar to ADEPs, effectively digesting bacteria from the inside out. Here, we performed further ACP derivatization and testing to improve the efficacy and breadth of coverage of selected ACPs against Gram-negative bacteria. We observed that a diverse collection of Neisseria meningitidis and Neisseria gonorrhoeae clinical isolates were exquisitely sensitive to these ACP analogues. Furthermore, based on the ACP-ClpP cocrystal structure solved here, we demonstrate that ACPs could be designed to be species specific. This validates the feasibility of drug-based targeting of ClpP in Gram-negative bacteria.

Functional characterization of a PROTAC directed against BRAF mutant V600E.

The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.

Di-tert-butyl Ethynylimidodicarbonate as a General Synthon for the ß-Aminoethylation of Organic Electrophiles: Application to the Formal Synthesis of Pyrrolidinoindoline Alkaloids (±)-CPC-1 and (±)-Alline.

The reagent di-tert-butyl ethynylimidodicarbonate is demonstrated as a ß-aminoethyl anion synthetic equivalent. It can be used to install ethyleneamine groups by exploiting its terminal alkyne reactivity with common organic electrophiles. Reactions exemplified with this terminal ynimide reagent include additions to imines, aldehydes, ketones, pyridinium salts, Michael acceptors, epoxides, and Pd-catalyzed Sonogashira couplings. Subsequent regioselective [3 + 2] cycloadditions of the alkynyl-imides (ynimides) generate N,N-di-Boc imide-functionalized triazole and isoxazole heterocycles. Reduction of the ynimides with Pd-catalyzed hydrogenation generates ethyleneimides with easily removable N,N-di-Boc-carbamate protecting groups, allowing for a flexible ynimide-based approach to ethyleneamine installation. The utility of this two-step aminoethylation strategy was demonstrated in the short formal syntheses of pyrrolidinoindoline alkaloids (±)-CPC-1 and (±)-alline. Analogously, the reagent (N,N,N')-tri-Boc 2-ethynylhydrazine serves as a ß-hydrazinoethyl anion synthetic equivalent.

Stereocontrolled Microwave-Assisted Domino [3,3]-Sigmatropic Reactions: A Winstein-Overman Rearrangement for the Formation of Differentiated Contiguous C-N Bonds.

A domino [3,3]-sigmatropic rearrangement sequence employing a sequential reversible allylic azide rearrangement followed by an irreversible Overman reaction provides a new route to the formation of two contiguous C-N bonds. The reaction occurs in a stereocontrolled fashion in two steps from readily available alkenyl epoxides via initial azide anion ring opening of the epoxides.

ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores.

Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.

An Approach to the 9-Oxo-10-oxabicyclo[5.3.0]dec-2-ene Core of the Guaianolide and Pseudoguaianolide Sesquiterpenes via a Domino Electrocyclic Ring-Opening/Carboxylic Acid Trapping of a gem-Dibromocyclopropane.

A domino silver(I)-promoted electrocyclic 2π-disrotatory electrocyclic ring-opening/intramolecular nucleophilic trapping of [ n.1.0]-dibromocyclopropanes by tethered carboxylic acids results in cyclization to butyrolactones fused to six- and seven-membered carbocycles. In the case of bicyclic [4.3.0] lactones the cis-fused stereoisomer was formed, whereas for the bicyclic [5.3.0] lactones the trans-fused stereoisomer was formed. Optimal conditions for the reaction used silver(I) trifluoroacetate (2.0 equiv) in trifluoroethanol or with added pyridine (2.0 equiv) and NaPF6 (5.0 equiv). The dibromocyclopropane precursors were made through cyclopropanation with in situ-generated dibromocarbene. The trans-fused lactones are potentially useful building blocks for pseudoguaianolide, guaianolide, and xanthanolide total synthesis. A computational study on the conformational preferences of these systems indicates that the trans-fused bicyclic [5.3.0] butyrolactones are lower in energy than the corresponding cis-fused lactones at the B3LYP/cc-pVTZ level of theory.

Lanthanide(III)-Catalyzed Synthesis of trans-Diaminocyclopentenones from Substituted Furfurals and Secondary Amines via a Domino Ring-Opening/4π-Electrocyclization Pathway.

A strategy toward the synthesis of trans-4,5-diaminocyclopent-2-enones is described. This core motif is embedded in the marine sponge derived alkaloids agelamadin B and nagelamide J. A variety of 2-substituted trans-4,5-diaminocyclopent-2-enones were synthesized in good to quantitative yields using lanthanide(III) catalysis. The products were formed exclusively as the trans-diastereomers via a mechanism in which the C4-C5 bond formation occurs through a 4π-conrotatory electrocyclization. The precursor 3-substituted furfurals can be readily accessed using palladium(0)-catalyzed cross-coupling between 3-bromofurfural and boronic acids, trifluoroborate salts, or alkynes.

Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death.

Acyldepsipeptides (ADEPs) are potential antibiotics that dysregulate the activity of the highly conserved tetradecameric bacterial ClpP protease, leading to bacterial cell death. Here, we identified ADEP analogs that are potent dysregulators of the human mitochondrial ClpP (HsClpP). These ADEPs interact tightly with HsClpP, causing the protease to non-specifically degrade model substrates. Dysregulation of HsClpP activity by ADEP was found to induce cytotoxic effects via activation of the intrinsic, caspase-dependent apoptosis. ADEP-HsClpP co-crystal structure was solved for one of the analogs revealing a highly complementary binding interface formed by two HsClpP neighboring subunits but, unexpectedly, with HsClpP in the compact conformation. Given that HsClpP is highly expressed in multiple cancers and has important roles in cell metastasis, our findings suggest a therapeutic potential for ADEPs in cancer treatment.

Total Synthesis of (+)-Prunustatin A: Utility of Organotrifluoroborate-Mediated Prenylation and Shiina MNBA Esterification and Macrolactonization To Avoid a Competing Thorpe-Ingold Effect Accelerated Transesterification.

A convergent total synthesis of (+)-prunustatin A is described through the assembly of two key fragments and a macrolactonization. Shiina MNBA couplings were used for the formation of each of the four ester bonds in the tetralactone ring, including the key macrocyclization which was essential to minimize competing Thorpe-Ingold accelerated transesterification. Other key steps included an organoboron-based prenylation using potassium prenyltrifluoroborate and a carbonyldiimidazole-mediated coupling to form the salicylamide.

The Role of ClpP Protease in Bacterial Pathogenesis and Human Diseases.

In prokaryotic cells and eukaryotic organelles, the ClpP protease plays an important role in proteostasis. The disruption of the ClpP function has been shown to influence the infectivity and virulence of a number of bacterial pathogens. More recently, ClpP has been found to be involved in various forms of carcinomas and in Perrault syndrome, which is an inherited condition characterized by hearing loss in males and females and by ovarian abnormalities in females. Hence, targeting ClpP is a potentially viable, attractive option for the treatment of different ailments. Herein, the biochemical and cellular activities of ClpP are discussed along with the mechanisms by which ClpP affects bacterial pathogenesis and various human diseases. In addition, a comprehensive overview is given of the new classes of compounds in development that target ClpP. Many of these compounds are currently primarily aimed at treating bacterial infections. Some of these compounds inhibit ClpP activity, while others activate the protease and lead to its dysregulation. The ClpP activators are remarkable examples of small molecules that inhibit protein-protein interactions but also result in a gain of function.

An Alumino-Mannich Reaction of Organoaluminum Reagents, Silylated Amines, and Aldehydes.

A multi-component coupling using organoaluminum reagents, silylated amines, and aldehydes results in the formation of tertiary amines. Both alkenyl- and alkylaluminum reagents undergo reaction with iminium ion substrates for which the corresponding Petasis borono-Mannich reactions are unsuccessful.

DABO Boronate Promoted Conjugate Allylation of α,ß-Unsaturated Aldehydes Using Copper(II) Catalysis.

The first catalytic method for the selective 1,4-conjugate allylation of α,ß-unsaturated aldehydes is reported. The method employs an air-stable diethanolamine-complexed boronic acid (DABO boronate) as the allyl transfer reagent and promotes conjugate addition over 1,2-addition. A variety of aryl- and alkyl-substituted enals are tolerated, providing δ,ε-unsaturated aldehyde products in good yields and selectivities under mild conditions.

Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity.

The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.