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Heterobifunctional chimeric degraders are a class of ligands that recruit target proteins to E3 ubiquitin ligases to drive compound-dependent protein degradation. Advancing from initial chemical tools, protein degraders represent a mechanism of growing interest in drug discovery. Critical to the mechanism of action is the formation of a ternary complex between the target, degrader and E3 ligase to promote ubiquitination and subsequent degradation. However, limited insights into ternary complex structures exist, including a near absence of studies on one of the most widely co-opted E3s, cellular inhibitor of apoptosis 1 (cIAP1). In this work, we use a combination of biochemical, biophysical and structural studies to characterize degrader-mediated ternary complexes of Bruton's tyrosine kinase and cIAP1. Our results reveal new insights from unique ternary complex structures and show that increased ternary complex stability or rigidity need not always correlate with increased degradation efficiency.

The drugable proteome is limited by the number of functional binding sites that can bind small molecules and respond with a therapeutic effect. Orthosteric and allosteric modulators of enzyme function or receptor signaling are well-established mechanisms of drug action. Drugs that perturb protein-protein interactions have only recently been launched. This approach is more difficult due to the extensive contact surfaces that must be perturbed antagonistically. Compounds that promote novel protein-protein interactions promise to dramatically expand opportunities for therapeutic intervention. This approach is precedented with natural products (rapamycin, FK506, sanglifehrin A), synthetic small molecules (thalidomide and IMiD derivatives) and indisulam analogues.

Heterobifunctional chimeric degraders are a class of ligands that recruit target proteins to E3 ubiquitin ligases to drive compound-dependent protein degradation. Advancing from initial chemical tools, protein degraders represent a mechanism of growing interest in drug discovery. Critical to the mechanism of action is the formation of a ternary complex between the target, degrader and E3 ligase to promote ubiquitination and subsequent degradation. However, limited insights into ternary complex structures exist, including a near absence of studies on one of the most widely co-opted E3s, cellular inhibitor of apoptosis 1 (cIAP1). In this work, we use a combination of biochemical, biophysical and structural studies to characterize degrader-mediated ternary complexes of Bruton's tyrosine kinase and cIAP1. Our results reveal new insights from unique ternary complex structures and show that increased ternary complex stability or rigidity need not always correlate with increased degradation efficiency.

Proteolysis targeting chimeras (PROTACs) are heterobifunctional small molecules that simultaneously bind to a target protein and an E3 ligase, thereby leading to ubiquitination and subsequent degradation of the target. They present an exciting opportunity to modulate proteins in a manner independent of enzymatic or signaling activity. As such, they have recently emerged as an attractive mechanism to explore previously “undruggable” targets. Despite this interest, fundamental questions remain regarding the parameters most critical for achieving potency and selectivity. Here we employ a series of biochemical and cellular techniques to investigate requirements for efficient knockdown of Bruton’s tyrosine kinase (BTK), a nonreceptor tyrosine kinase essential for B cell maturation. Members of an 11-compound PROTAC library were investigated for their ability to form binary and ternary complexes with BTK and cereblon (CRBN, an E3 ligase component). Results were extended to measure effects on BTK–CRBN cooperative interactions as well as in vitro and in vivo BTK degradation. Our data show that alleviation of steric clashes between BTK and CRBN by modulating PROTAC linker length within this chemical series allows potent BTK degradation in the absence of thermodynamic cooperativity.

Interest in drugs that covalently modify their target is driven by the desire for enhanced efficacy that can result from the silencing of enzymatic activity until protein resynthesis can occur, along with the potential for increased selectivity by targeting uniquely positioned nucleophilic residues in the protein. However, covalent approaches carry additional risk for toxicities or hypersensitivity reactions that can result from covalent modification of unintended targets. Here we describe methods for measuring the reactivity of covalent reactive groups (CRGs) with a biologically relevant nucleophile, glutathione (GSH), along with kinetic data for a broad array of electrophiles. We also describe a computational method for predicting electrophilic reactivity, which taken together can be applied to the prospective design of thiol-reactive covalent inhibitors.

Herein we describe the structure-aided design and synthesis of a series of pyridone-conjugated monobactam analogues with in vitro antibacterial activity against clinically relevant Gram-negative species including Pseudomonas aeruginosa , Klebsiella pneumoniae , and Escherichia coli . Rat pharmacokinetic studies with compound 17 demonstrate low clearance and low plasma protein binding. In addition, evidence is provided for a number of analogues suggesting that the siderophore receptors PiuA and PirA play a role in drug uptake in P. aeruginosa strain PAO1.

We report novel polymyxin analogues with improved antibacterial in vitro potency against polymyxin resistant recent clinical isolates of Acinetobacter baumannii and Pseudomonas aeruginosa . In addition, a human renal cell in vitro assay (hRPTEC) was used to inform structure-toxicity relationships and further differentiate analogues. Replacement of the Dab-3 residue with a Dap-3 in combination with a relatively polar 6-oxo-1-phenyl-1,6-dihydropyridine-3-carbonyl side chain as a fatty acyl replacement yielded analogue 5x, which demonstrated an improved in vitro antimicrobial and renal cytotoxicity profiles relative to polymyxin B (PMB). However, in vivo PK/PD comparison of 5x and PMB in a murine neutropenic thigh model against P. aeruginosa strains with matched MICs showed that 5x was inferior to PMB in vivo, suggesting a lack of improved therapeutic index in spite of apparent in vitro advantages.

We report novel syntheses of 12-membered macrocyclic templates and a library of 4000 macrocyclic analogs. The key macrocyclization step was performed at up to 100 g scale without resorting to syringe pumps, flow reactors or large volumes of solvent. An interesting observation of considerably different permeability properties was made on diastereomeric analogs due to differences in intramolecular hydrogen bond interactions.

The synthesis and antibacterial activity of heterocyclic methylsulfone hydroxamates is presented. Compounds in this series are potent inhibitors of the LpxC enzyme, a key enzyme involved in the production of lipopolysaccharide (LPS) found in the outer membrane of Gram-negative bacteria. SAR evaluation of compounds in this series revealed analogs with potent antibacterial activity against challenging Gram-negative species such as Pseudomonas aeruginosa and Klebsiella pneumoniae.

Novel siderophore-linked monobactams with in vitro and in vivo anti-microbial activity against MDR Gram-negative pathogens are described.

Linezolid (Zyvox) is the first member of an entirely new class of antibiotics to reach the market in over 35 years; it was approved for use in 2000. A member of the oxazolidinone class of antibiotics, linezolid is highly effective for the treatment of serious Gram-positive infections and has activity that compares favorably with vancomycin for most clinically relevant pathogens. Zyvox is approved for use against serious Gram-positive infections, including those caused by Streptococcus pneumoniae, and the very challenging methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium organisms. Zyvox inhibits bacterial protein synthesis by binding to 23S rRNA in the catalytic site of the 50S ribosome. It can be administered both orally and intravenously and has good tissue distribution. Recent results have demonstrated that oxazolidinone analogs related to linezolid are effective in treating pulmonary tuberculosis caused by resistant Mycobacterium tuberculosis in animal infection models and suggest additional new therapeutic applications for these antibiotics.

The design, synthesis, and biological evaluation of potent inhibitors of the TrkA kinase is presented. A homology model is created to aid in the enhancement of potency and selectivity of isothiazole inhibitors found during a high-throughput screen. Three different syntheses are utilized to make diverse analogs within this series. Aminoheterocycles are found to be good urea surrogates, whereas bicyclic substituents on the C3 thio group were found to be extremely potent TrkA inhibitors in kinase and cell assays.

A series of 3-hydroxy-3-methylpipecolic hydroxamate inhibitors of MMP-13 and aggrecanase was designed based on the observation of increased aggrecanase activity with substitution at the 3-position of the piperidine ring. Potency versus aggrecanase was optimized by modification of the benzyloxyarylsulfonamide group that binds in the S1′ pocket. These compounds also possess markedly improved bioavailability and lower metabolic clearance compared to analogous 3,3-dimethyl-5-hydroxypipecolic hydroxamates. These improvements are attributed to lowered lipophilicity proximal to the metabolically labile hydroxamic acid. Synthesis, structure activity relationships, and in vivo efficacy data are described.

A series of pipecolic hydroxamate inhibitors of MMP-13 and aggrecanase was discovered based on screening known inhibitors of TNF-alpha converting enzyme (TACE). Potency versus aggrecanase was optimized by modification of the benzyloxyarylsulfonamide group. Incorporation of geminal alkyl substitution at the 3-position of the piperidine ring improved metabolic stability, presumably by increasing steric hindrance around the metabolically labile hydroxamic acid. This modification also resulted in dramatic improvement of aggrecanase activity with a slight reduction in selectivity versus MMP-1. Synthesis, structure activity relationships, and strategies to reduce metabolic clearance are described.

N-Hydroxy-3-hydroxy-4-arylsulfonyltetrahydropyranyl-3-carboxamides were designed as novel inhibitors of MMP-13 and aggrecanase based on known endocyclic hydroxamate inhibitors of matrix metalloproteinases. These compounds offer favorable physicochemical properties and low metabolic clearance. Synthesis and structure-activity relationships are reported.

A series of novel MMP-13 and TNF-α converting enzyme inhibitors based on piperazine 2-hydroxamic acid scaffolds are described. The TACE, MMP-1 and MMP-13 activity of these inhibitors as well as the effect of substitution of the piperazine nitrogen and the P-1′ benzyloxy tailpiece is discussed. Moderate in vivo activity is observed with several members of this group.

The modern drug discovery process involves a hypothesis-oriented approach to target selection and medicinal chemistry design. Recent advances in human genetics, systems biology and chemical proteomics enable medicinal chemists to play a significant role in generating and supporting the initial hypothesis underpinning a drug discovery project. Diverse lead seeking strategies from high throughput screening to targeted subset assessment, ligand-based pharmacophore searches, target-based virtual screens and fragment based approaches provide medicinal chemists more control over the source of initial chemical equity. Powerful in silico predictive tools enabling ADME and safety property prediction, coupled with multiparameter optimization techniques, enable a more rational approach to lead optimization using a holistic view of drug properties. Upon selecting a clinical candidate, medicinal chemists become knowledgeable partners in understanding and solving physical form issues, applying new formulation technologies and addressing synthetic scalability. As the drug candidate progresses through preclinical and clinical studies, knowledge gained around safety, pharmacokinetics and efficacy is incorporated into future drug discovery efforts for backup compounds and other related programs. The medicinal chemist's role in conceiving the initial compound design and providing matter that drives drug discovery within a project gives them a prominent role from idea inception to clinical studies.

Tumor necrosis factor-alpha (TNF-alpha) is implicated in inflammatory processes and much effort is being directed at inhibiting the release of TNF-alpha for treatment of inflammatory conditions. In this context, the drug CP-661,631 has been developed to inhibit the TNF-alpha converting enzyme (TACE). However, TACE is also implicated in amyloid precursor protein secretion. Amyloid precursor protein (APP) undergoes constitutive and regulated secretion by alpha-secretase endoproteolytic cleavage within the amyloid beta peptide (Abeta) domain. Alternative cleavage at the N- and C-terminus of the Abeta domain by beta- and gamma-secretases results in the production of Abeta. In many cellular and in vivo animal models, increased secretion of APP results in a concomitant decrease in the production of Abeta suggesting that the two pathways are intricately linked. However, in human primary neuron cultures, increased APP secretion is not associated with a decrease in total Abeta production. To determine if the use of CP-661,631 may enhance amyloidogenic processing in human brain, we have assessed the effect of CP-661,631 on APP metabolism in primary cultures of human neurons. Our results show that CP-661,631 effectively prevents regulated APP secretion but does not increase total Abeta levels in human primary neuron cultures.

The chiral quaternary ammonium salt 1 serves as phase transfer catalyst for the enantioselective conversion of the glycine derivative 2 to a variety of cyclic and acyclic chiral α-amino acids with enantioselectivities as high as 200:1 in alkylation and Michael addition reactions.

The regioselectivity of 1,3-dipolar cycloaddition reactions between mesoionic compounds with singly-tethered substituents is examined. The results with propiolate dipolarophiles are compared with other singly and doubly-tethered examples according to a model using an asynchronous, concerted transition state. The isolation and reaction of a novel, nonaryl substituted mesoionic compound 7 is reported. A regiodirected synthesis starting with N-(2-thiazolinyl)proline gives a complementary dihydropyrroline compared with the reaction between N-formylproline and alkyl propiolates.

This paper presents a critical analysis of two transition state models for the bis-cinchona alkaloid catalyzed enantioselective dihydroxylation of olefins using a broad range of experimental data. In one model (Sharpless) the transition state resembles a metallaoxetane structure formed by [2 + 2] cycloaddition of OsO and CC, and in the other the transition state is a five-membered structure in which one axial and one equatorial oxygen of cinchona bound OsO4 are becoming attached to the olefinic carbons by a [3 + 2] cycloaddition process from an Os−olefin π-complex (CCN model, Figure 1). Data on the enantioselectivity of the asymmetric dihydroxylation of a wide variety of olefinic substrates and on the selectivity of a range of catalyst structures agree well with expectations based on the CCN model, but not the Sharpless model.

The 12 C 13 C kinetic isotope effects for the bis-cinchona-OsO4 catalyzed dihydroxylation of 4-nitrostyrene, 4-methoxystyrene and allyl 4-methoxybenzoate have been measured at the olefinic carbons by the method of Singleton. For each olefin, the 12 C 13 C kinetic isotope values are substantial and similar at the two olefinic carbons. These results accord well with prediction based on a [3+2] cycloaddition pathway but not with expectations for a [2+2] cycloaddition process.

The asymmetric dihydroxylation of p-methoxybenzoate esters of p-methoxyphenyl ethers of 2-hydroxymethyl-1,3-butadienes or 2-hydroxyethyl-1,3-butadienes proceeds with excellent position and enantioselectivity using bis-cinchona alkaloid catalysts. The regioselectivity of these reactions is strongly influenced by binding interactions between the aromatic ether or ester group and the catalyst as predicted from a previously proposed transition state model.

The catalytic dihydroxylation of p-methoxybenzoate esters of various bishomoallylic alcohols proceeds with excellent enantioselectivity and, in the case of diolefins, with imporved regioselectivity using a designed catalyst that incorporates an N-anthracenylmethyl group to enhance catalyst-substrate binding interactions.

The Sharpless enantioselective dihydroxylation of terminal olefins by OsO4 using the catalytic chiral ligand (DHQD)2PYDZ (1) has been shown to follow Michaelis−Menten kinetics, demonstrating fast reversible formation of a complex of olefin, OsO4, and 1 prior to the rate-limiting conversion to the Os(VI) ester intermediate. There is a good correlation between the observed binding constants, Km, and the degree of enantioselectivity of the dihydroxylation indicating that van der Waals binding of the substrate by 1·OsO4 is important to enantioselective rate enhancement. Inhibition of the oxidation by various compounds has been demonstrated kinetically using Dixon analysis of the data, and Ki values have been determined and correlated with inhibitor structure. The strongest inhibitors are compounds with the ability to coordinate to Os(VIII) of the 1·OsO4 complex while simultaneously binding in the pocket formed by the aromatic subunits of the ligand. Parallelism between Km and Ki values and their relationship ...

Summary The mechanistically designed bis-cinchona alkaloid derivative 3 serves as an excellent catalytic ligand in the OsO4-promoted catalytic enantioselective dihydroxylation of the terminal isopropylidene group infamesyl, geranylgeranyl, and solanesyl esters and also squalene, with selectivity as high as 120: 1 with E,E-farnesyl acetate. 1H NMR and X-ray studies support the conformation described by 3 in which the V-shaped catalytic binding pocket is composed of the two 6-(4-heptyloxy)-quinoline units (sides and rear) and the naphthopyridazine linker (bottom).

Summary A simple, highly enantioselective synthesis of sirenin ( 1 ) (bioactive form) has been developed which depends on the intramolecular [2 +1] cycloaddition reaction of diazo ester 5 to form bicyclic ester 6 (95 : 5 enantioselectivity) using a new and remarkably stable monomeric chiral Cu(I) complex ( 2 ) whose structure was proven by X-ray diffraction analysis.

A simple and efficient synthesis of the biologically important vitamin A-derived retinoid (14R)-14-hydroxy-4,14-retro-retinol ( 1 ) from retinyl acetate in four steps is described.

The catalytic dihydroxylation of p-methoxyphenyl ethers of various homoallylic alcohols proceeds with excellent enantioselectivity and in the case of diolefins with regioselectivity due to the favorable influence of the aryl ether moiety, as predicted from a previously proposed transition-state model.

Targeted covalent enzyme inhibition is experiencing resurgence as a medicinal chemistry design strategy. Targeted covalent inhibitors exhibit slow target offset, increased binding efficiency and potency, enhanced selectivity, reduced propensity for target-based drug resistance and prolonged pharmacodynamic effects. These attributes offer the possibility of pursuing small molecule approaches for targets previously considered to be undruggable. New technologies for assessing selectivity at the cellular proteome level, coupled with a better understanding of reversible and irreversible covalent inhibitor design strategies, enable more confident safety risk assessment and higher-quality design. This review covers literature published between 2006 and 2012, classifying inhibitors based on their target nucleophile and reversibility properties, and offers a perspective on future opportunities for covalent inhibitor design strategies.

The electron deficiency of Ti(IV) in complexes with chiral o,o′-bisphenols influences the CArOTi angle which, in turn determines the topology of the most stable (or easily formed) cyclic complex.

On the basis of ideas recently advanced regarding the origin of enantioselectivity in the OsO4-promoted dihydroxylation of olefins catalyzed by bis-cinchona alkaloid derivatives such as 1, specifically strong evidence for reaction via transition state assembly 2, the mono-quinidine derivative 3 was selected as a promising catalytic ligand. The experimental observation of high enantioselectivity promoted by 3 provides additional evidence in favor of transition-state 2.

X-Ray crystallographic analysis on single crystals and 1H NMR studies in solution of various bis-cinchona alkaloid derivatives reveal a general preference for a conformation which possesses a U-shaped binding pocket with favorable dimensions for the inclusion of olefinic substrates and the acceleration of face selective dihydroxylation by a proximate pentacoordinate OsO4.

A series of 1,3-dipolar cycloadditions of munchnones with acetylenic dipolarophiles was studied, wherein factors related to regioselectivity were investigated. The results from munchnones with electronically divergent thioaryl substituents compared with others bearing alkyl substituents suggest that an unsymmetrical transition state structure, rather than FMO perturbation, plays a significant role in regioselection. If eclipsing interactions preclude a highly unsymmetrical transition state however, then minimizing steric interactions becomes important. A pair of complementarily substituted munchnones, differing only in the position of isotopic labels, establishes an inherently symmetrical electronic nature of the mesoionic heterocycle.

This paper describes the synthesis of the chiral tetraol 1, and its conversion with Ti(IV) 1,1,1,3,3,3-hexafluoroisopropoxide to the novel linear trinuclear titanium complex 8 whose structure has been determined by spectroscopic and X-ray crystallographic analysis.

In this paper, we present the synthesis and SAR as well as selectivity, pharmacokinetic, and infection model data for representative analogues of a novel series of potent antibacterial LpxC inhibitors represented by hydroxamic acid 1a.

Linezolid (Zyvox) is the first member of an entirely new class of antibiotics to reach the market in over 35 years; it was approved for use in 2000. A member of the oxazolidinone class of antibiotics, linezolid is highly effective for the treatment of serious Gram-positive infections and has activity that compares favorably with vancomycin for most clinically relevant pathogens. Zyvox is approved for use against serious Gram-positive infections, including those caused by Streptococcus pneumoniae, and the very challenging methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium organisms. Zyvox inhibits bacterial protein synthesis by binding to 23S rRNA in the catalytic site of the 50S ribosome. It can be administered both orally and intravenously and has good tissue distribution. Recent results have demonstrated that oxazolidinone analogs related to linezolid are effective in treating pulmonary tuberculosis caused by resistant Mycobacterium tuberculosis in animal infection models and suggest additional new therapeutic applications for these antibiotics.

To facilitate a drug discovery project, we needed to develop a robust asymmetric synthesis of (2S,5S)-5-substituted-azepane-2-carboxylate derivatives. Two key requirements for the synthesis were flexibility for elaboration at C5 and suitability for large scale preparation. To this end we have successfully developed a scalable asymmetric synthesis of these derivatives that starts with known hydroxy-ketone 8. The key step features an oxidative cleavage of aza-bicyclo[3.2.2]nonene 14, which simultaneously generates the C2 and C5 substituents in a stereoselective manner.

A novel series of monocarbam compounds exhibiting promising antibacterial activity against multidrug resistant Gram-negative microorganisms is reported, along with the synthesis of one such molecule MC-1 (1). Also reported are structure−activity relationships associated with the in vitro and in vivo efficacy of 1 and related analogues in addition to the hydrolytic stability of such compounds and possible implications thereof.

Torsional restriction and a highly unsymmetrical transition state for a 1,3-dipolar cycloaddition divert a portion of the reaction through a stepwise pathway

A very useful synthesis of (3S)-2,3-oxidosqualene from geraniol, farnesol and E-1-bromo-4-chloro-3-methyl-2-butene is described which makes use of enantioselective and catalytic dihydroxylation of geranyl acetate and two E-stereospecific allylic coupling reactions mediated by E-prenylbarium reagents.

X-Ray crystallographic analysis on single crystals and 1H NMR studies in solution of various bis-cinchona alkaloid derivatives reveal a general preference for a conformation which possesses a U-shaped binding pocket with favorable dimensions for the inclusion of olefinic substrates and the acceleration of face selective dihydroxylation by a proximate pentacoordinate OsO4.

Torsional restriction and a highly unsymmetrical transition state for a 1,3-dipolar cycloaddition divert a portion of the reaction through a stepwise pathway