Our quest to undertaking signaling pathway-based targets is challenging the current thinking of building a chemical toolbox that is traditionally enriched with heterocyclic compounds or compounds, in general, dominated by sp2 bonds. One of the main limitations with the current approaches is that they are biased to search for inhibitors of enzymes (i.e. the luxury of deep and well-defined pockets which is generally not the case for protein-protein interactions (PPIs)). Over the years, natural products from various sources have demonstrated a proven track record to function as the modulators of protein-protein interactions, and, in general, signaling pathways, but often they are hard to placing onto the drug discovery journey. To us, they serve as an excellent source of inspiration in developing novel synthesis approaches allowing us building a chemical toolbox with compounds that can be classified as natural product-like and hybrid natural products. Several features in our design and synthesis program are unique and highly attractive, and, these are: (i) natural product-inspired 3D architectures, (ii) compounds are more close to bioactive natural products with sufficient complexity, (iii) practical methods that utilize modern organic synthesis for obtaining compounds in sufficient amounts and in a timely manner, (iv) functionalized macrocyclic compounds (for mapping a large surface area, in particular for crucial for PPIs), and (v) amenable to developing medicinal chemistry programs on first generation hits. During the past nearly 2 decades, we have developed several methods for obtaining polycyclic and macrocyclic compounds having indole- and tetrahydroquinoline-inspired alkaloids, benzofuran- and benzopuran-inspired polyphenolics. The past few years (see our recent publications), we reported several practical approaches to the fragments of bioactive natural products/compounds such as eribulin, rapamycin, epothilone/ixabepilone, treprostinil, latrunclins and geldanamycin and thoroughly utilized them to building a macrocyclic diversity-based chemical toolbox.
Collaborative Team Members:
The proposed integrated, multidisciplinary research program aims at developing chemical biology approaches to study the trans-differentiation of human mesenchymal stem cells to neurons by novel, natural product-inspired small molecules. Through creating a highly interconnected team culture and working with different skill-sets, we plan enhancing our current understanding of various factors playing key roles in this process. Following the discovery of novel small molecules causing this trans-differentiation, serious efforts will be made to addressing the mechanistic questions involving: genomics studies (i.e. next generation sequencing and single cell genomics), CRISPR-Cas9 studies and small molecule-biotin conjugates (for target identification and validation). To further expand the scope of active compounds identified in differentiation, these novel small molecules will then be thoroughly tested for their ability to function, either as neuroprotective or neurogenesis agents in various neurological disorders (for example, studies related to Huntington and Alzheimers's/dementia). Finally, the lead compounds identified through our deep chemical biology studies will then be subjected to a series of neuro-disease specific, animal model studies for building a solid foundation of the translational research path.
To achieve these objectives, our highly integrated team comprises skills-sets and leadership in (i) modern and stereoselective organic synthesis, (ii) isolation of mesenchymal stem cells from healthy donors (source - umbilical cord tissue and blood) and neuro-patients (source - blood), (iii) development of various cellular assays to study the trans-differentiation of stem cells to neurons, (iv) validation of neuronal cells by electrophysiology studies (v) validation of neuronal cells by specific biomarkers using RT-PCR methods, (vi) validation of biomarkers using genomic tools - next generation sequencing and by the techniques of single cell genomic studies, (vii) target validation and identification by CRISP-Cas9 studies and small molecule-biotin conjugates for pull-down experiments, (viii) evaluation of active small molecules in various neuro-assays specific for Huntington’s and Alzheimer's/dementia and, finally, (ix) the extension of our cellular studies to various neuro-disease-related animal model studies.
The foundation of this comprehensive program was initiated a few years ago where our early work identified several novel natural product-inspired small molecules capable of trans-differentiating human mesenchymal stem cells (from healthy donors) to neurons. These findings were further validated by the formation of neuronal cells by specific biomarkers, such as agrin, nestin and RTN4. The initial results obtained to date have allowed us to file 4 patent applications (Indian patents filed; work is in progress for US patent applications), submit 1 paper for publication (Jan 2017) and prepare 3 more publications that are in progress.
Our early success through working at the interface of modern organic synthesis and human stem cell biology (isolation and development of various cellular assays) has allowed us establishing a solid foundation in this program. Moreover, this further led us providing an excellent opportunity to bring other competencies for taking this program to a different translational level with a strong scientific base. To our knowledge, this has not been achieved to date, even at the international level. No single research group can achieve these objectives, and typically, the lack of integrated deeper research efforts, often results in a fragmented translational output with a little serious impact! The successful outcome of this program is highly likely to play a seminal role for our younger generation to build highly integrated teams for undertaking complex and challenging research problems. Not only will these efforts lead to publishing high quality papers but given the translational research of this program, this will also lead to building a strong IP portfolio, eventually leading to next generation highly innovative spin-outs, that we are all striving for in India!
Collaborative Team Members:
The proposed program aims at utilizing our first generation, novel, natural product-inspired, small molecules identified by our group, as the selective killer (tested by cell viability, toxicology and selectivity) and the promoters of apoptosis (caspase 3 activation assay) in patient-derived brain glioblastoma cells (published work from Arya group, 2016). By using this knowledge and experience, we are now aiming for designing highly selective, next generation natural product-inspired compounds that would go through an extensive cell viability testing, caspase 3 activation assay for apoptosis in 24 different primary cancer cells and tumorspheres (enriched with cancer stem cells) from a panel of patient-derived samples (from Brain, Breast and Head and Neck Cancer) before and after the xenograft studies. In addition to this, we will also be testing our compounds for their cell migration inhibitory properties utilizing these different cell lines. Finally, the highly selective compounds after going through extensive toxicology and selectivity studies, along with the SAR program, will then be subjected to patient-derived tumor xenograft-based, in vivo studies.
Using a diverse panel of patient-derived primary cancer cells, tumorspheres (enriched in cancer stem cells) for three different cancers - Brain, Breast and Head and Neck, and also with primary cells after the tumor xenograft studies, this approach places us in a unique position for exploring the scope of tumor heterogeneity and complexity for the generation of highly efficacious and selective, next-generation, anti-cancer drug candidates.
Our program that brings together (i) modern organic synthesis / medicinal chemistry (expertise with DRILS), (ii) Indian patient-derived various tumor banking with primary cancer cells and tumorspheres (expertise with Transcell Biologics, Hyderabad), (iii) patient-derived xenograft (expertise with Reliance Life Sciences, Mumbai), and finally, (iv) cell biology expertise with a variety of apoptosis and cell migration assays (expertise with Transcell Biologics and DRILS Biology), is unprecedented. Our early work done together as a team, also places us in a highly advantageous situation, for taking these challenges that are hitherto not possible to achieve in a single academic and/or industrial setting. Our early published work (Asian JOC 2016) at the interface of natural product-inspired synthesis and patient-derived screening for cell viability and apoptosis led the identification of a novel small molecule as the highly selective promoter of apoptosis in glioblastoma cells. As an extension to this study, we established a team in India, and are now, aiming to identify novel small molecules as highly selective anti-cancer agents after going through extensive testing (for apoptosis and cell migration) with Indian patient-derived primary cancer cells and tumorspheres for three categories - Brain, Breast and Head and Neck Cancer. In addition, these cell lines will also be utilized in patient-derived tumor xenograft studies which would then allow evaluating a variety of cancer cells that would be obtained from the xenograft work.
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