Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation

Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns

Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation

Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns

Synthesis, Characterization, and Application in HeLa Cells of an NIR Light Responsive Doxorubicin Delivery System Based on NaYF₄:Yb,Tm@SiO₂‑PEG Nanoparticles

Herein, we present a phototriggered drug delivery system based on light responsive nanoparticles, which is able to release doxorubicin upon NIR light illumination. The proposed system is based on upconversion fluorescence nanoparticles of β-NaYF₄:Yb,Tm@SiO₂-PEG with a mean diameter of 52 ± 2.5 nm that absorb the NIR light and emit UV light. The UV radiation causes the degradation of photodegradable <i>ortho</i>-nitrobenzyl alcohol derivates, which are attached on one side to the surface of the nanoparticles and on the other to doxorubicin. This degradation triggers the doxorubicin release. This drug delivery system has been tested “<i>in vitro</i>” with HeLa cells. The results of this study demonstrated that this system caused negligible cytotoxicity when they were not illuminated with NIR light. In contrast, under NIR light illumination, the HeLa cell viability was conspicuously reduced. These results demonstrated the suitability of the proposed system to control the release of doxorubicin via an external NIR light stimulus

Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation

Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns

Aggregated Compound Biological Signatures Facilitate Phenotypic Drug Discovery and Target Elucidation

Predicting the cellular response of compounds is a challenge central to the discovery of new drugs. Compound biological signatures have risen as a way of representing the perturbation produced by a compound in the cell. However, their ability to encode specific phenotypic information and generating tangible predictions remains unknown, mainly because of the inherent noise in such data sets. In this work, we statistically aggregate signals from several compound biological signatures to find compounds that produce a desired phenotype in the cell. We exploit this method in two applications relevant for phenotypic screening in drug discovery programs: target-independent hit expansion and target identification. As a result, we present here (i) novel nanomolar inhibitors of cellular division that reproduce the phenotype and the mode of action of reference natural products and (ii) blockers of the NKCC1 cotransporter for autism spectrum disorders. Our results were confirmed in both cellular and biochemical assays of the respective projects. In addition, these examples provided novel insights on the information content and biological significance of compound biological signatures from HTS, and their applicability to drug discovery in general. For target identification, we show that novel targets can be predicted successfully for drugs by reporting new activities for nimedipine, fluspirilene, and pimozide and providing a rationale for repurposing and side effects. Our results highlight the opportunities of reusing public bioactivity data for prospective drug discovery, including scenarios where the effective target or mode of action of a particular molecule is not known, such as in phenotypic screening campaigns

Design and Synthesis of Pironetin Analogue/Colchicine Hybrids and Study of Their Cytotoxic Activity and Mechanisms of Interaction with Tubulin

We here report the synthesis of a series of 12 hybrid molecules composed of a colchicine moiety and a pironetin analogue fragment. The two fragments are connected through an ester–amide spacer of variable length. The cytotoxic activities of these compounds and their interactions with tubulin have been investigated. Relations between the structure and activity are discussed. Since the spacer is not long enough to permit a simultaneous binding of the hybrid molecules to the colchicine and pironetin sites on tubulin, a further feature investigated was whether these molecules would interact with the latter through the pironetin end (irreversible covalent binding) or through the colchicine end (reversible noncovalent binding). It has been found that binding to tubulin may take place preferentially at either of these ends depending on the length of the connecting spacer

Total Synthesis of Amphidinolide K, a Macrolide That Stabilizes F‑Actin

The total synthesis of (−)-amphidinolide K (<b>1</b>) based on asymmetric addition of allylsilane <b>C1</b>–<b>C8</b> to enal <b>C9</b>–<b>C22</b> is reported. The 1,9,18-tris-<i>O</i>-TBDPS ether was converted into the desired 9,18-dihydroxy acid. Its macrolactonization was accomplished by the Shiina method. Compound <b>1</b> together with some of its stereoisomers and analogues were subjected to evaluation of the possible disruption of the α,β-tubulin–microtubule and/or G-actin–F-actin equilibria. Compound <b>1</b> behaves as a stabilizer of actin filaments (F-actin) in vitro

Structural and Biochemical Characterization of the Interaction of Tubulin with Potent Natural Analogues of Podophyllotoxin

Four natural analogues of podophyllotoxin obtained from the Mexican medicinal plant <i>Bursera fagaroides</i>, namely, acetyl podophyllotoxin (<b>2</b>), 5′-desmethoxy-β-peltatin A methyl ether (<b>3</b>), 7′,8′-dehydro acetyl podophyllotoxin (<b>4</b>), and burseranin (<b>5</b>), have been characterized, and their interactions with tubulin have been investigated. Cytotoxic activity measurements, followed by immunofluorescence microscopy and flow cytometry studies, demonstrated that these compounds disrupt microtubule networks in cells and cause cell cycle arrest in the G2/M phase in the A549 cell line. A tubulin binding assay showed that compounds <b>1</b>–<b>4</b> were potent assembly inhibitors, displaying binding to the colchicine site with <i>K</i>_b values ranging from 11.75 to 185.0 × 10⁵ M^–1. In contrast, burseranin (<b>5</b>) was not able to inhibit tubulin assembly. From the structural perspective, the ligand-binding epitopes of compounds <b>1</b>–<b>3</b> have been mapped using STD-NMR, showing that B and E rings are the major points for interaction with the protein. The obtained results indicate that the inhibition of tubulin assembly of this family of compounds is more effective when there are at least two methoxyl groups at the E ring, along with a <i>trans</i> configuration of the lactone ring in the aryltetralin lignan core

Cyclostreptin Derivatives Specifically Target Cellular Tubulin and Further Map the Paclitaxel Site

Cyclostreptin is the first microtubule-stabilizing agent whose mechanism of action was discovered to involve formation of a covalent bond with tubulin. Treatment of cells with cyclostreptin irreversibly stabilizes their microtubules because cyclostreptin forms a covalent bond to β-tubulin at either the T220 or the N228 residue, located at the microtubule pore or luminal taxoid binding site, respectively. Because of its unique mechanism of action, cyclostreptin overcomes P-glycoprotein-mediated multidrug resistance in tumor cells. We used a series of reactive cyclostreptin analogues, 6-chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and [¹⁴C-<i>acetyl</i>]-8-acetyl-cyclostreptin, to characterize the cellular target of the compound and to map the binding site. The three analogues were cytotoxic and stabilized microtubules in both sensitive and multidrug resistant tumor cells. In both types of cells, we identified β-tubulin as the only or the predominantly labeled cellular protein, indicating that covalent binding to microtubules is sufficient to prevent drug efflux mediated by P-glycoprotein. 6-Chloroacetyl-cyclostreptin, 8-chloroacetyl-cyclostreptin, and 8-acetyl-cyclostreptin labeled both microtubules and unassembled tubulin at a single residue of the same tryptic peptide of β-tubulin as was labeled by cyclostreptin (219-LTTPTYGDLNHLVSATMSGVTTCLR-243), but labeling with the analogues occurred at different positions of the peptide. 8-Acetyl-cyclostreptin reacted with either T220 or N228, as did the natural product, while 8-chloroacetyl-cyclostreptin formed a cross-link to C241. Finally, 6-chloroacetyl-cyclostreptin reacted with any of the three residues, thus labeling the pathway for cyclostreptin-like compounds, leading from the pore where these compounds enter the microtubule to the luminal binding pocket

Synthesis and Antimitotic and Tubulin Interaction Profiles of Novel Pinacol Derivatives of Podophyllotoxins

Several pinacol derivatives of podophyllotoxins bearing different side chains and functions at C-7 were synthesized through reductive cross-coupling of podophyllotoxone and several aldehydes and ketones. While possessing a hydroxylated chain at C-7, the compounds retained their respective hydroxyl group with either the 7α (podo) or 7β (epipodo) configuration. Along with pinacols, some C-7 alkylidene and C-7 alkyl derivatives were also prepared. Cytotoxicities against neoplastic cells followed by cell cycle arrest and cellular microtubule disruption were evaluated and mechanistically characterized through tubulin polymerization inhibition and assays of binding to the colchicine site. Compounds of the epipodopinacol (7β-OH) series behaved similarly to podophyllotoxin in all the assays and proved to be the most potent inhibitors. Significantly, 7α-isopropyl-7-deoxypodophyllotoxin (<b>20</b>), without any hydroxyl function, appeared as a promising lead compound for a novel type of tubulin polymerization inhibitors. Experimental results were in overall agreement with modeling and docking studies performed on representative compounds of each series