Discovery of indoline-based, natural-product-like compounds as probes of focal adhesion kinase signaling pathways.

With the goal of identifying small molecule modulators of protein-protein interactions, we developed a solid-phase synthesis method, which was then successfully utilized in a library generation of 164 aminoindoline-derived, natural-product-like compounds. This library and several other related intermediates synthesized during this project were then subjected to different biological assays in search of small molecule modulators of focal adhesion kinase (FAK)-mediated signaling pathways. This study included (i) an in vitro, full length FAK inhibition assay, (ii) a cell proliferation assay, and (iii) a wound healing assay. In FAK inhibition assay, eight library members (5-12) and three aminoindoline derivatives (13, 14, and 2) were identified as promising candidates. Compounds 13 and 2 inhibited the FAK activity by 25-45% at 10 microM. These two lead compounds also showed activity in a wound healing assay. To our knowledge, these aminoindoline-derived small molecules belong to a new family of FAK inhibitors.

Benzofuran-derived cyclic beta-amino acid scaffold for building a diverse set of flavonoid-like probes and the discovery of a cell motility inhibitor.

We report here a practical, enantioselective synthesis of benzofuran-derived, cyclic trans-beta-amino acid scaffold. In two cases, tricyclic derivatives having six- and eight-membered unsaturated lactams were obtained from this versatile scaffold. To explore the biological applications, these compounds were subjected to cell-based assays, using NIH3T3 mouse cells to examine their potency as cell motility inhibitors and identified 18 as a potent cell motility inhibitor (IC50 approximately 40 microM in chamber cell migration assay).

The discovery of small molecule chemical probes of Bcl-X(L) and Mcl-1.

A tetrahydroaminoquinoline-based library was generated with the goals of finding small molecule modulators of protein-protein interactions. Several library members as well as other related intermediates were tested for their ability to bind to Bcl-X(L) and Mcl-1 by in silico and (15)N NMR studies. The NMR study led to the identification of the tetrahydroaminoquinoline-based nude scaffold, 7 as a weak binder (K(d)=200 microM for Bcl-X(L) and K(d)=300 microM for Mcl-1) to both proteins. Using this scaffold as the starting material, we then synthesized a focused library of only 9 derivatives by applying the principles of a fragment-based approach. All these derivatives were then tested by NMR and this led to the discovery of a novel, small molecule (MIPRALDEN, 17) as a binder to Mcl-1 and Bcl-X(L) (K(D)=25 and 70 microM). This finding is novel because to our knowledge there are not many small molecules known in the literature that bind to Mcl-1.

Building skeletally diverse architectures on the Indoline Scaffold: the discovery of a chemical probe of focal adhesion kinase signaling networks.

Inspired by bioactive indoline alkaloid natural products, here, we report a divergent synthesis approach that led to skeletally diverse indoline alkaloid-inspired compounds. The natural product-inspired compounds obtained were then subjected to a series of in vitro and cellular assays to examine their properties as modulators of focal adhesion kinase (FAK) activity. This study resulted in the identification of a promising lead inhibitor of FAK (42), which also showed activity in a wound healing and cell invasion assay. The in silico study of the lead compound (42) was also undertaken.

Reagent-based, modular, tandem Michael approach for obtaining different indoline alkaloid-inspired polycyclic architectures.

A modular, reagent-based approach to obtain different indoline alkaloid-inspired, tetracyclic architectures is developed. With the use of TBSOTf as a Lewis acid, we report here a tandem Michael-based approach that led to the synthesis of a diastereomeric mixture of tetracyclic derivatives with two additional six-membered rings. By simply changing the Lewis acid to TMSOTf, we were able to obtain a different tetracyclic compound having additional functionalized 5- and 7-membered rings with complete stereocontrol.

Synthesis and biological evaluation of rapamycin-derived, next generation small molecules.

Over the years, rapamycin has attracted serious attention due to its remarkable biological properties and as a potent inhibitor of the mammalian target of rapamycin (mTOR) protein through its binding with FKBP-12. Several efficient strategies that utilize synthetic and biosynthetic approaches have been utilized to develop small molecule rapamycin analogs or for synthesizing hybrid compounds containing a partial rapamycin structure to improve pharmacokinetic properties. Herein, we report selected case studies related to the synthesis of rapamycin-derived compounds and hybrid molecules to explore their biological properties.

Geldanamycin-inspired compounds induce direct trans-differentiation of human mesenchymal stem cells to neurons.

Inspired from geldanamycin, the synthesis of a new series of 20-membered macrocyclic compounds is developed. The key features in our design are (i) retention of the fragment having the precise chiral functional groups of geldanamycin at C10, C11, C12 and C14, and (ii) replacement of an olefin moiety with the ester group, and the quinoid sub-structure with the triazole ring. The southern fragment needed for the macrocyclic ring formation was obtained from Evans' syn aldol as the key reaction and with the use of D-mannitol as the cheap source of a chiral starting material. For the synthesis of the northern fragment, we utilized l-ascorbic acid, which provided the desired chiral functional groups at C6 and C7. Further, the chain extension completed the synthesis of the northern fragment. In our approach, the crucial 20 membered macrocyclic ring was formed employing the click chemistry. When tested for their ability to directly trans-differentiate human mesenchymal stem cells to neurons, two novel compounds (20a and 7) from this series were identified and this was further validated by the presence of specific neuronal biomarkers (i.e. nestin, agrin and RTN4).

A Small-Molecule Inhibitor of Bax and Bak Oligomerization Prevents Genotoxic Cell Death and Promotes Neuroprotection.

Aberrant apoptosis can lead to acute or chronic degenerative diseases. Mitochondrial outer membrane permeabilization (MOMP) triggered by the oligomerization of the Bcl-2 family proteins Bax/Bak is an irreversible step leading to execution of apoptosis. Here, we describe the discovery of small-molecule inhibitors of Bax/Bak oligomerization that prevent MOMP. We demonstrate that these molecules disrupt multiple, but not all, interactions between Bax dimer interfaces thereby interfering with the formation of higher-order oligomers in the MOM, but not recruitment of Bax to the MOM. Small-molecule inhibition of Bax/Bak oligomerization allowed cells to evade apoptotic stimuli and rescued neurons from death after excitotoxicity, demonstrating that oligomerization of Bax is essential for MOMP. Our discovery of small-molecule Bax/Bak inhibitors provides novel tools for the investigation of the mechanisms leading to MOMP and will ultimately facilitate development of compounds inhibiting Bax/Bak in acute and chronic degenerative diseases.

Natural product-like chemical space: search for chemical dissectors of macromolecular interactions.

Macromolecular interactions (i.e. protein-protein or DNA/RNA-protein interactions) play important cellular roles, including cellular communication and programmed cell death. Small-molecule chemical probes are crucial for dissecting these highly organized interactions, for mapping their function at the molecular level and developing new therapeutics. The lack of ideal chemical probes required to understand macromolecular interactions is the missing link in the next step of dissecting such interactions. Unfortunately, the classical combinatorial-chemistry community has not successfully provided the required probes (i.e. natural product inspired chemical probes that are rich in stereochemical and three-dimensional structural diversity) to achieve these goals. The emerging area of diversity-oriented synthesis (DOS) is beginning to provide natural product-like chemical probes that may be useful in this arena.

Exploring new chemical space by stereocontrolled diversity-oriented synthesis.

Natural products that act as highly specific, small-molecule protein-binding agents and as modulators of protein-protein interactions are highly complex and exhibit functional groups with three-dimensional and stereochemical diversity. The complex three-dimensional display of chiral functional groups appears to be crucial for exhibiting specificity in protein binding and in differentiating between closely related proteins. The development of methods that allow a high-throughput access to three-dimensional, skelatally complex, polycyclic compounds having few asymmetric diversity sites is essential and a highly challenging task. In the postgenomic chemical biology age, in which there is a great desire to understand protein-protein interactions and to dissect protein networking-based signaling pathways by small molecules, the need for developing "stereocontrolled, diversity-oriented synthesis" methods to generate natural product-like libraries is of utmost importance.

Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age.

In the age of high-throughput biology, novel genes and proteins are emerging quickly. The need for developing organic synthesis-derived methods that allow rapid access to polyfunctional, complex natural product-like compounds is growing constantly, largely because these small-molecule-based compounds serve as smart, powerful tools both in understanding the roles and functions of emerging biological targets and in validating their biological responses. Developing asymmetric synthesis-derived organic reactions on solid phase allows the synthesis of complex natural product-like compounds in a high-throughput manner. Solid phase organic synthesis is now commonly utilized in the library synthesis of rather simple compounds (i.e., compounds with no multiple stereogenic centers). With few exceptions, the synthesis of complex natural product-like derivatives is still in its infancy. Some recent efforts made in this area indicate opportunities yet to be explored.

Selected hybrid natural products as tubulin modulators.

Modulators of microtubule dynamics have received increasing attention because of their potential to stop cancer growth. Although it belongs to the category of complex protein-protein interactions (PPIs), which are generally considered difficult to modulate through small molecules, the use of microtubule is considered a well-validated target. There are a number of bioactive natural products and related compounds that are currently in use as drugs or in clinical trials as next generation anti-cancer agents. The present review article is focused on two such bioactive natural products, epothilone and halichondrin B, and covers some of the key papers published after 2005 that outline various synthetic approaches to obtain next generation structural analogs as well as the synthesis of hybrid compounds.

Regio- and Stereocontrolled Dieckmann Approach to Treprostinil-Inspired, Polycyclic Scaffold For Building Macrocyclic Diversity.

We developed a regio- and stereocontrolled Dieckmann cyclization approach to the synthesis of a novel, natural-product-like scaffold that was inspired from treprostinil (UT-15). This was further utilized in a diversity-based, 15-membered macrocyclic synthesis of two different sets of hybrid compounds. The amino acid moiety embedded in the macrocyclic skeleton allow exploring various chiral side chain groups within the ring.

Divergent approach to building a latrunculin family derived hybrid macrocyclic toolbox.

A divergent approach to obtain a latrunculin family based hybrid macrocyclic toolbox is developed. A practical, stereoselective synthesis of a common substructure present in latrunculin A and latrunculol A was achieved. This was further utilized in the macrocyclic diversity synthesis. The amino acid moiety embedded in the 15-membered macrocyclic ring allows for the exploration of various chiral side chains as one of the diversity sites.

Practical stereoselective synthesis of eribulin fragment toward building a hybrid macrocyclic toolbox.

A practical stereoselective synthesis to obtain the substituted furan ring as the substructure of eribulin is developed. An asymmetric syn-aldol and intramolecular oxy-Michael were two key steps in our approach. The functionalized furan derivatives were then utilized further to build the 14- and 12-membered macrocyclic diversity as trans- and cis-fused (C-29 and C-30) compounds. This is the first report of building a chemical toolbox with macrocyclic small molecules having trans- or cis-fused 14- or 12-membered rings containing the substructure of eribulin and its diastereomer.

Stereoselective synthesis of rapamycin fragment to build a macrocyclic toolbox.

A stereoselective synthesis of a rapamycin fragment is developed and further utilized toward building a macrocyclic chemical toolbox. The amino alcohol moiety embedded in the 22-membered macrocyclic ring allowed for the addition of a variation in the chiral side chain. The key reactions leading to the synthesis of the rapamycin-derived pyran fragment include the following: (i) Paterson aldol, (ii) stereoselective ß-OH carbonyl reduction, and (iii) regio- and stereoselective intramolecular oxy-Michael reaction. The other piece needed for building the macrocyclic diversity was obtained from the coupling of various amino alcohol moieties with S-pipecolic acid.

High-throughput chemistry toward complex carbohydrates and carbohydrate-like compounds.

In the area of peptide and nucleic acid chemistry and biology, high-throughput synthesis has played an important role in providing useful small-molecule-based chemical probes in understanding the structure and function relationships. The past several years, there has been a constant rise in interest toward understanding the biological roles and functions of another important class of biomolecules, i.e., carbohydrates and carbohydrate conjugates. Although at early stages, in recent years, several groups have developed high-throughput synthetic methods to obtain complex carbohydrates or carbohydrate-like small-molecules. The present review article summarizes some of these developments.

Macrocyclic glycohybrid toolbox identifies novel antiangiogenesis agents from zebrafish assay.

A practical and modular approach to obtain a diverse set of 14-membered macrocyclic compounds from carbohydrates is developed that utilizes functional groups at C-1 and C-5. The evaluation of this toolbox in various zebrafish assays led to the identification of 2.7f as an antiangiogenesis agent.