Macrocycles are of increasing interest as chemical probes and drugs for intractable targets like protein-protein interactions, but the determinants of their cell permeability and oral absorption are poorly understood. To enable rational design of cell-permeable macrocycles, we generated an extensive data set under consistent experimental conditions for more than 200 non-peptidic, de novo-designed macrocycles from the Broad Institute's diversity-oriented screening collection. This revealed how specific functional groups, substituents and molecular properties impact cell permeability. Analysis of energy-minimized structures for stereo- and regioisomeric sets provided fundamental insight into how dynamic, intramolecular interactions in the 3D conformations of macrocycles may be linked to physicochemical properties and permeability. Combined use of quantitative structure-permeability modeling and the procedure for conformational analysis now, for the first time, provides chemists with a rational approach to design cell-permeable non-peptidic macrocycles with potential for oral absorption.

An aldol-based ‘build/couple/pair’ (B/C/P) strategy was applied to generate a collection of stereochemically and skeletally diverse small molecules. In the build phase, a series of asymmetric syn- and anti- aldol reactions were performed to produce four stereoisomers of a Boc protected γ-amino acid. In addition both stereoisomers of O-PMB-protected alaninol were generated to provide a chiral amine coupling partner. In the couple step, eight stereoisomeric amides were synthesized by coupling the chiral acid and amine building blocks. The amides were subsequently reduced to generate the corresponding secondary amines. In the pair phase, three different reactions were employed to enable intramolecular ring-forming processes, namely: nucleophilic aromatic substitution (SNAr), Huisgen [3+2] cycloaddition and ring-closing metathesis (RCM). Despite some stereochemical dependencies, the ring-forming reactions were optimized to proceed with good to excellent yields providing a variety of skeletons ranging in size from 8- to 14-membered rings. Scaffolds resulting from the RCM pairing reaction were diversified on solid-phase to yield a 14,400-membered library of macrolactams. Screening of this library led to the discovery of a novel class of histone deacetylase inhibitors, which display mixed enzyme inhibition and led to increased levels of acetylation in a primary mouse neuron culture. The development of stereo-structure/activity relationships (SSAR) was made possible by screening all 16 stereoisomers of the macrolactams produced through the aldol-based B/C/P strategy.

The synthesis and diversification of a densely functionalized azetidine ring system to gain access to a wide variety of fused, bridged and spirocyclic ring systems is described. The in vitro physicochemical and pharmacokinetic properties of representative library members are measured in order to evaluate the use of these scaffolds for the generation of lead-like molecules to be used in targeting the central nervous system. The solid-phase synthesis of 1976-membered library of a spirocyclic azetidines is also described.

Profiling of eight stereoisomeric T. cruzi growth inhibitors revealed vastly different in vitro properties such as solubility, lipophilicity, pKa, and cell permeability for two sets of four stereoisomers. Using computational chemistry and NMR spectroscopy, we identified the formation of an intramolecular NH→NR3 hydrogen bond in the set of stereoisomers displaying lower solubility, higher lipophilicity, and higher cell permeability. The intramolecular hydrogen bond resulted in a significant pKa difference that accounts for the other structure–property relationships. Application of this knowledge could be of particular value to maintain the delicate balance of size, solubility, and lipophilicity required for cell penetration and oral administration for chemical probes or therapeutics with properties at, or beyond, Lipinski’s rule of 5.

A unified strategy for the high-throughput synthesis of multigram quantities of the eta(3)-oxopyranyl- and eta(3)-oxopyridinylmolybdenum complexes TpMo(CO)(2)(eta(3)-oxopyranyl) and TpMo(CO)(2)(eta(3)-oxopyridinyl) is described (Tp = hydridotrispyrazolylborato). The strategy uses the oxa- and aza-Achmatowicz reaction for the preparation of these organometallic enantiomeric scaffolds, in both racemic and high enantiopurity versions.

In 2013, the Centers for Disease Control highlighted Clostridium difficile as an urgent threat for antibiotic-resistant infections, in part due to the emergence of highly virulent fluoroquinolone-resistant strains. Limited therapeutic options currently exist, many of which result in disease relapse. We sought to identify molecules specifically targeting C. difficile in high-throughput screens of our diversity-oriented synthesis compound collection. We identified two scaffolds with apparently novel mechanisms of action that selectively target C. difficile while having little to no activity against other intestinal anaerobes; preliminary evidence suggests that compounds from one of these scaffolds target the glutamate racemase. In vivo efficacy data suggest that both compound series may provide lead optimization candidates.

A diversity-oriented synthesis (DOS) strategy was developed for the synthesis of stereochemically diverse fused-ring systems containing a pyran moiety. Each scaffold contains an amine and methyl ester for future diversification via amine capping and amide coupling. Scaffold diversity was evaluated in comparison to previously prepared scaffolds via a shape-based principal moments of inertia (PMI) analysis.

All stereoisomers of a highly functionalized 2,3-unsaturated C-glycoside can be accessed in 10-100 g quantities from readily available starting materials and reagents in 3-7 steps. These chiral scaffolds contain three stereogenic centers along with orthogonally protected functional groups for downstream reactivity.Due to their synthetic versatility and high level of stereochemical diversity carbohydrates have served as useful starting points for generating molecular diversity. 1 Carbohydratederived glycals in particular have been employed in multiple diversity-oriented synthesis (DOS) pathways. 2 Of interest to us was the utility of C-alkyl pseudoglycals for developing new build/couple/pair pathways in the context of library development. 3 In the present study, we focused on the synthesis of 2,3-unsaturated C-glycosides 1-4 ( Figure 1) which incorporate four chemical handles: (1) an ester, (2) an alkene, (3) a primary alcohol and (4) a secondary alcohol/primary amine, thereby, providing a range of options for subsequent modifications and/or functional group pairing reactions. 4 As part of our design strategy we sought to develop methods for the preparation of all eight stereoisomers of the C-glycoside template to enable the development of stereo/structure-activity relationships. 3b,5 Herein we describe the preparation of C-glycosides 1-4 on large (>50 g) scale.In order to introduce the ester functionality at C-1 we explored a type I Ferrier rearrangement 6 of tri-O-acetyl-D-and L-glucal to access C-glycosides 1-4. We elected to focus solely on optimizing the large-scale Ferrier reaction for the glucal series with the intention of accessing the galactal-derived material (2) via Mitsunobu inversion of the C-4 allylic alcohol. 7,8 Since we discovered that the α-and β-glycosides could be easily separated by silica gel chromatography and we required access to equal quantities of both anomers, we elected to develop reaction conditions that would achieve a closer to 1:1 α/β ratio.As shown in Table 1, we evaluated the Ferrier reaction of tri-O-acetyl-D-glucal with 5 under a range of conditions, mainly focused on varying the nature of the Lewis acid and solvent. Use of BF 3 ·Et 2 O as the Lewis acid in CH 2 Cl 2 led to the formation of C-glycoside 6 in 45% yield as a 1:2 mixture of anomers favoring the β-anomer (entry 1). Changing the Lewis acid to TMSOTf led to a higher isolated yield (73%) and a more favorable ratio of anomers 1:1.5 (entry 2). Using TMSOTf we next investigated the effect of solvent on reaction selectivity. When employing CH 3 CN as a solvent the formation of the α-anomer was slightly favored (α/β ratio = 1.5:1) and a lower yield was obtained (65%, entry 3). The yield of the glycosidation reaction could be improved to 77% on large scale (200 g), using CH 2 Cl 2 as a co-solvent (entries 4 and 5), providing a 1.2:1 mixture of anomers. The α/β isomers could be easily separated by silica gel chromatography to provide 42% of the α-anomer (α-D-6) and 35% of the β-anomer (β-D-6). 14 Deacetylation an...