Marc Ronald Campitelli

Drug-like Properties: Guiding Principles for the Design of Natural Product Libraries

While natural products or their derivatives and mimics have contributed around 50% of current drugs, there has been no approach allowing front-loading of chemical space compliant with lead- and drug-like properties. The importance of physicochemical properties of molecules in the development of orally bioavailable drugs has been recognized. Classical natural product drug discovery has only been able to undertake this analysis retrospectively after compounds are isolated and structures elucidated. The present approach addresses front-loading of both extracts and subsequent fractions with desired physicochemical properties prior to screening for drug discovery. The physicochemical profiles of natural products active against two neglected disease targets, malaria and African trypanosomiasis, are presented based on this strategy. This approach can ensure timely development of natural product leads at a hitherto unachievable rate.

Capturing nature's diversity.

Natural products are universally recognized to contribute valuable chemical diversity to the design of molecular screening libraries. The analysis undertaken in this work, provides a foundation for the generation of fragment screening libraries that capture the diverse range of molecular recognition building blocks embedded within natural products. Physicochemical properties were used to select fragment-sized natural products from a database of known natural products (Dictionary of Natural Products). PCA analysis was used to illustrate the positioning of the fragment subset within the property space of the non-fragment sized natural products in the dataset. Structural diversity was analysed by three distinct methods: atom function analysis, using pharmacophore fingerprints, atom type analysis, using radial fingerprints, and scaffold analysis. Small pharmacophore triplets, representing the range of chemical features present in natural products that are capable of engaging in molecular interactions with small, contiguous areas of protein binding surfaces, were analysed. We demonstrate that fragment-sized natural products capture more than half of the small pharmacophore triplet diversity observed in non fragment-sized natural product datasets. Atom type analysis using radial fingerprints was represented by a self-organizing map. We examined the structural diversity of non-flat fragment-sized natural product scaffolds, rich in sp3 configured centres. From these results we demonstrate that 2-ring fragment-sized natural products effectively balance the opposing characteristics of minimal complexity and broad structural diversity when compared to the larger, more complex fragment-like natural products. These naturally-derived fragments could be used as the starting point for the generation of a highly diverse library with the scope for further medicinal chemistry elaboration due to their minimal structural complexity. This study highlights the possibility to capture a high proportion of the individual molecular interaction motifs embedded within natural products using a fragment screening library spanning 422 structural clusters and comprised of approximately 2800 natural products.

Euodenine A: A Small-Molecule Agonist of Human TLR4

A small-molecule natural product, euodenine A (1), was identified as an agonist of the human TLR4 receptor. Euodenine A was isolated from the leaves of Euodia asteridula (Rutaceae) found in Papua New Guinea and has an unusual U-shaped structure. It was synthesized along with a series of analogues that exhibit potent and selective agonism of the TLR4 receptor. SAR development around the cyclobutane ring resulted in a 10-fold increase in potency. The natural product demonstrated an extracellular site of action, which requires the extracellular domain of TLR4 to stimulate a NF-κB reporter response. 1 is a human-selective agonist that is CD14-independent, and it requires both TLR4 and MD-2 for full efficacy. Testing for immunomodulation in PBMC cells shows the induction of the cytokines IL-8, IL-10, TNF-α, and IL-12p40 as well as suppression of IL-5 from activated PBMCs, indicating that compounds like 1 could modulate the Th2 immune response without causing lung damage.

Isolation, structure determination and cytotoxicity studies of tryptophan alkaloids from an Australian marine sponge Hyrtios sp.

Mass-guided fractionation of the MeOH extract from a specimen of the Australian marine sponge Hyrtios sp. resulted in the isolation of two new tryptophan alkaloids, 6-oxofascaplysin (2), and secofascaplysic acid (3), in addition to the known metabolites fascaplysin (1) and reticulatate (4). The structures of all molecules were determined following NMR and MS data analysis. Structural ambiguities in 2 were addressed through comparison of experimental and DFT-generated theoretical NMR spectral values. Compounds 1-4 were evaluated for their cytotoxicity against a prostate cancer cell line (LNCaP) and were shown to display IC50 values ranging from 0.54 to 44.9 μM.

Trikentramides A-D, indole alkaloids from the Australian sponge Trikentrion flabelliforme.

Chemical investigations of two specimens of Trikentrion flabelliforme collected from Australian waters have resulted in the identification of four new indole alkaloids, trikentramides A-D (9-12). The planar chemical structures for 9-12 were established following analysis of 1D/2D NMR and MS data. The relative configurations for 9-12 were determined following the comparison of (1)H NMR data with data previously reported for related natural products. The application of a quantum mechanical modeling method, density functional theory, confirmed the relative configurations and also validated the downfield carbon chemical shift observed for one of the quaternary carbons (C-5a) in the cyclopenta[g]indole series. The indole-2,3-dione motif present in trikentramides A-C is rare in nature, and this is the first report of these oxidized indole derivatives from a marine sponge.

Analysis of Physicochemical Properties for Drugs of Natural Origin

The impact of time, therapy area, and route of administration on 13 physicochemical properties calculated for 664 drugs developed from a natural prototype was investigated. The mean values for the majority of properties sampled over five periods from pre-1900 to 2013 were found to change in a statistically significant manner. In contrast, lipophilicity and aromatic ring count remained relatively constant, suggesting that these parameters are the most important for successful prosecution of a natural product drug discovery program if the route of administration is not focused exclusively on oral availability. An examination by therapy area revealed that anti-infective agents had the most differences in physicochemical property profiles compared with other areas, particularly with respect to lipophilicity. However, when this group was removed, the variation between the mean values for lipophilicity and aromatic ring count across the remaining therapy areas was again found not to change in a meaningful manner, further highlighting the importance of these two parameters. The vast majority of drugs with a natural progenitor were formulated for either oral and/or injectable administration. Injectables were, on average, larger and more polar than drugs developed for oral, topical, and inhalation routes.

Front-Loading Natural-Product-Screening Libraries for log P: Background, Development, and Implementation

In the period from January 1981 to December 2010, 1068 small‐molecule new chemical entities (NCEs) were introduced, of which ca. 34% are either a natural product or a close analogue. While this metric reflects the impact natural products have played in delivering new chemical starting points (leads) for the pharmaceutical industry, it does not capture the decline this approach has suffered over the last 20 years as the high‐throughput screening (HTS) of pure compound libraries has become more popular. An impediment to natural‐product drug discovery in the HTS paradigm is the lack of a clear strategy that enables front‐loading of an extract or fractions chemical constituents so that they are compliant with lead‐ and drug‐like chemical space. To address this imbalance, an approach based on lipophilicity, as measured by clog P has been developed that, together with advances being made in isolation and structural elucidation, can afford natural product leads in timelines compatible with pure compound screening.

Formation of an Unusual Four-Membered Nitrogen Ring (Tetrazetidine) Radical Cation

Treatment of triphenylphosphine (Ph(3)P) with an excess of diisopropyl azodicarboxylate at 0-25 °C resulted in the formation of a symmetrical tetraalkyl tetrazetidinetetracarboxylate radical cation, containing the elusive cyclic N(4) ring system. Electron paramagnetic resonance (EPR) spectroscopy revealed a 9-line spectrum, with hyperfine coupling constants indicative of four almost magnetically equivalent nitrogen atoms. The radical species was surprisingly long-lived, and could still be observed several hours after generation and standing at 25 °C. Expansion of the central resonance revealed further splitting into a pentet (hyperfine coupling to the four methine protons). Three mechanistically plausible structures containing the tetrazetidine substructure were proposed based on the 9-line EPR spectrum. Following DFT calculations, the predicted hyperfine coupling constants were used to simulate the EPR spectra for the three candidate structures. The combined calculations and simulations were consistent with a radical cation species, but not a radical anion or radical-carbenoid structure. The lowest energy conformation of the N(4) ring was slightly puckered, with the alkyl carboxylate groups all trans and the four carbonyl groups aligned in a pinwheel arrangement around the ring. Analogous results were obtained with the original Mitsunobu reagents, Ph(3)P and diethyl azodicarboxylate, but not with Ph(3)P and di-tert-butyl azodicarboxylate. A mechanism is proposed based on a radical version of the Rauhut-Currier or Morita-Baylis-Hillman reactions.

Quantitative structure-property relationships (QSPR) for steroidal compounds of environmental importance

A quantitative structure-property relationships (QSPR) study was carried out for 17 steroidal compounds using calculated molecular descriptors and measured properties. The utility of calculated molecular descriptors and properties was evaluated and improved in some instances by subgroup classification of these 17 compounds into estrogens and androgens. The calculated values for the octanol-water partition coefficient (logK(ow)) were found to be in good agreement with the measured values for all 17 compounds, whilst good agreement between the calculated and measured values for aqueous solubility (logS) was found only for the subgroup of androgens. Good linear relationships (R(2)0.782) were found between measured logK(ow) values and three molecular descriptors (logFOSA, hydrophobic component of the total solvent accessible surface area; logFISA, hydrophilic component of the total solvent accessible area and logPSA, Van de Waals surface area of polar nitrogen and oxygen atoms). For the measured logS values, only weak correlations with molecular descriptors were observed (R(2)0.505). The coefficient of logS in the relationship with the hydrophobic parameter (logFOSA) was negative but positive with the hydrophilic parameters (logFISA and logPSA). Conversely with logK(ow) the opposite was found. These observations are in accord with the effects of molecular polarity on aqueous solubility.

Structural investigation on phenyl- and pyridin-2-ylamino(methylene)naphthalen-2(3H)-one. Substituent effects on the NMR chemical shifts

Schiff bases bearing phenyl and pyridyl groups were synthesized by condensation of appropriate amines with 2‐hydroxynaphthaldehyde. These Schiff bases were obtained as colored crystalline solids. The proton NMR spectra of these compounds showed a doublet for the NH protons indicating a keto tautomer for these Schiff bases. The pyridyl‐substituted Schiff bases containing hydroxyl moiety were found to show the most downfield shift for the NH protons in DMSO solvent, and this was rationalized due to the formation of a six‐ and five‐membered ring using hydrogen bonds for these two compounds. Correspondingly, the olefinic proton of the Schiff bases is also found to be a doublet due to coupling to the amine proton. These Schiff bases exhibited thermochromic properties. Detailed NMR spectral analysis for both the phenyl‐ and pyridyl‐substituted Schiff bases is presented. Copyright