Assessing the potential of small molecules of natural origin in emerging biological targets

Natural products are a vast reservoir of complex and highly structurally diverse chemical compounds which play a key role in the discovery of novel bioactive molecules (lead compounds) with therapeutic benefit, and/or structures that could be used as chemical probes for understanding unknown biological processes. Recent advances in our understanding of intra-/inter-cellular processes and interaction mechanisms has led to the discovery of new biological targets for drug discovery. Moreover, technological advances in extraction and screening as well as for characterisation of natural products and biological targets open new possibilities for natural products in areas of biochemistry and drug discovery. In the present study four emerging biological targets (assays) were used to explore new small molecules which: [1] inhibit the complex formation between CUGn-RNA and MBNL1 which was identified as an important target for the treatment of myotonic dystrophy type 1 (DM1); [2] inhibit the expression of a protein named coronin-1, which was proposed as a new target for the treatment of tuberculosis (TB); [3] promote lymphatic endothelial cell (LEC) growth, which is of relevance in the treatment of lymphedema or chronic skin inflammation; and [4] inhibit thrombin-induced [Ca2+] influx which leads to a reduction in endothelial hyperpermeability, since this was found to be an underlying mechanism of action for the commercialised Crataegus WS 1442 extract which is used as a therapy for mild chronic heart failure (CHF). The first three projects (i.e., DM1, TB and Lymphatic) started with the screening of an extract library; whereas the last project (CHF) focused on Crataegus WS 1442 extract. In each of these projects, an approach known as HPLC-based activity profiling was utilised to track activity and characterise selected natural products that exhibited an interaction with the biological target.
In the DM1 project, harmine (from Peganum harmala), 1,2-dihydrotanshinquinone I and methylenetanshinquinone (from Salvia miltiorrhiza), and berberine (from an alkaloid library screening) were identified as the most active compounds in inhibiting CUGn-RNA and MBNL1 complex formation. Accordingly, these hit compounds may have a potential for drug discovery in RNA-mediated diseases. In overall, compounds with planar scaffolds and in particular those containing nitrogen proved to be most active in inhibiting the complex formation and restoring MBNL1 function.
In the TB project, two extracts that lead to the inhibition of coronin-1 expression, namely EtOAc extract of Dorstenia contrajerva and MeOH extract of Pancratium littorale, were prioritised for further investigation. A compound isolated from D. contrajerva EtOAc extract, known as dorstenin, only exhibited activity at a very high concentration. Therefore, it is postulated that the activity of D. contrajerva EtOAc extract was in fact due to minor constituents which act in a synergistic manner. Correlation of activity and toxicity data with structural information for alkaloids from P. littorale MeOH extract showed that molecules with secondary amines and/or methylenedioxy groups exhibited higher toxicity, whereas molecules which contained a hemiacetal ring and acetyl groups were more active. These results were found while using GFP assay. However, further analysis on the active alkaloids with western blotting did not confirm coronin-1 inhibition at the protein level. Accordingly, further investigations are needed to understand the interaction mechanisms of these compounds with the biological assay (GFP).
In the Lymphatic project, DCM extract of Daphne giraldii was identified as an active extract in inducing LEC growth. Consecutive fractionation and assaying of this extract showed that activity was consistently localised in lipophilic regions of the extract. Further analysis on the active micro-fractions showed that each contained trace amounts of potent bioactive constituents. Various correlative analysis techniques suggested that daphnetoxin and some derivatives thereof were the main contributing factors for the observed activity.
In the CHF project, fractions of Crataegus WS 1442 extract were tested in a calcium imaging assay. After further fractionation, one active sub-fraction was obtained that exhibited a strong reduction in endothelial hyperpermeability. The sub-fraction consisted mainly of fatty acids (40%) including stearic and palmitic acids, and triterpenes such as hyptatic acid (50%). However, none of these constituents in a purified state were found to inhibit thrombin-induced calcium influx. Accordingly, it is postulated that the activity of Crataegus WS 1442 extract is possibly induced by either a minor constituent with potent activity, or constituents which act synergistically.
Each of these projects was among the first to assess the interaction of natural products with the four emerging biological targets which are highlighted above. Also, considering the lack of effective agents on the market to treat the corresponding diseases, this study made significant contributions to the discovery of new drugs in therapeutically unmet areas, via: (a) providing new hit compounds; (b) identifying constituents of potently active fractions; (c) correlating structural features with bioactivity as well as (d) identifying challenges and providing recommendations for further investigations.