CAS: Chemistry: Scholarly Papers

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Perturbation detection through modeling of gene expression on a latent biological pathway network: a Bayesian hierarchical approach
(Taylor & Francis, 2016) Pham, Lisa M.; Carvalho, Luis; Schaus, Scott; Kolaczyk, Eric D.
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell's fate. Here our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge data set. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases.
Targeting the oncogene LSF with either the small molecule inhibitor FQI1 or siRNA causes mitotic delays with unaligned chromosomes, resulting in cell death or senescence
(Springer Science and Business Media LLC, 2020-06-15) Willoughby, Jennifer L.S.; George, Kelly; Roberto, Mark P.; Chin, Hang Gyeong; Stoiber, Patrick; Shin, Hyunjin; Pedamallu, Chandra Sekhar; Schaus, Scott E.; Fitzgerald, Kevin; Shah, Jagesh; Hansen, Ulla
BACKGROUND: The oncogene LSF (encoded by TFCP2) has been proposed as a novel therapeutic target for multiple cancers. LSF overexpression in patient tumors correlates with poor prognosis in particular for both hepatocellular carcinoma and colorectal cancer. The limited treatment outcomes for these diseases and disappointing clinical results, in particular, for hepatocellular carcinoma in molecularly targeted therapies targeting cellular receptors and kinases, underscore the need for molecularly targeting novel mechanisms. LSF small molecule inhibitors, Factor Quinolinone Inhibitors (FQIs), have exhibited robust anti-tumor activity in multiple pre-clinical models, with no observable toxicity. METHODS: To understand how the LSF inhibitors impact cancer cell proliferation, we characterized the cellular phenotypes that result from loss of LSF activity. Cell proliferation and cell cycle progression were analyzed, using HeLa cells as a model cancer cell line responsive to FQI1. Cell cycle progression was studied either by time lapse microscopy or by bulk synchronization of cell populations to ensure accuracy in interpretation of the outcomes. In order to test for biological specificity of targeting LSF by FQI1, results were compared after treatment with either FQI1 or siRNA targeting LSF. RESULTS: Highly similar cellular phenotypes are observed upon treatments with FQI1 and siRNA targeting LSF. Along with similar effects on two cellular biomarkers, inhibition of LSF activity by either mechanism induced a strong delay or arrest prior to metaphase as cells progressed through mitosis, with condensed, but unaligned, chromosomes. This mitotic disruption in both cases resulted in improper cellular division leading to multiple outcomes: multi-nucleation, apoptosis, and cellular senescence. CONCLUSIONS: These data strongly support that cellular phenotypes observed upon FQI1 treatment are due specifically to the loss of LSF activity. Specific inhibition of LSF by either small molecules or siRNA results in severe mitotic defects, leading to cell death or senescence - consequences that are desirable in combating cancer. Taken together, these findings confirm that LSF is a promising target for cancer treatment. Furthermore, this study provides further support for developing FQIs or other LSF inhibitory strategies as treatment for LSF-related cancers with high unmet medical needs.
Factor quinolinone inhibitors alter cell morphology and motility by destabilizing interphase microtubules
(Springer Science and Business Media LLC, 2021-12-07) Stoiber, Patrick; Scribani Rossi, Pietro; Pokharel, Niranjana; Germany, Jean-Luc; York, Emily A.; Schaus, Scott E.; Hansen, Ulla
Factor quinolinone inhibitors are promising anti-cancer compounds, initially characterized as specific inhibitors of the oncogenic transcription factor LSF (TFCP2). These compounds exert anti-proliferative activity at least in part by disrupting mitotic spindles. Herein, we report additional interphase consequences of the initial lead compound, FQI1, in two telomerase immortalized cell lines. Within minutes of FQI1 addition, the microtubule network is disrupted, resulting in a substantial, although not complete, depletion of microtubules as evidenced both by microtubule sedimentation assays and microscopy. Surprisingly, this microtubule breakdown is quickly followed by an increase in tubulin acetylation in the remaining microtubules. The sudden breakdown and partial depolymerization of the microtubule network precedes FQI1-induced morphological changes. These involve rapid reduction of cell spreading of interphase fetal hepatocytes and increase in circularity of retinal pigment epithelial cells. Microtubule depolymerization gives rise to FH-B cell compaction, as pretreatment with taxol prevents this morphological change. Finally, FQI1 decreases the rate and range of locomotion of interphase cells, supporting an impact of FQI1-induced microtubule breakdown on cell motility. Taken together, our results show that FQI1 interferes with microtubule-associated functions in interphase, specifically cell morphology and motility.
Factor quinolinone inhibitors disrupt spindles and multiple LSF (TFCP2)-protein interactions in mitosis, including with microtubule-associated proteins
(Public Library of Science (PLoS), 2022) Yunes, Sarah A.; Willoughby, Jennifer L.S.; Kwan, Julian H.; Biagi, Jessica M.; Pokharel, Niranjana; Chin, Hang Gyeong; York, Emily A.; Su, Kuan-Chung; George, Kelly; Shah, Jagesh V.; Emili, Andrew; Schaus, Scott E.; Hansen, Ulla; Prigent, Claude
Factor quinolinone inhibitors (FQIs), a first-in-class set of small molecule inhibitors targeted to the transcription factor LSF (TFCP2), exhibit promising cancer chemotherapeutic properties. FQI1, the initial lead compound identified, unexpectedly induced a concentration-dependent delay in mitotic progression. Here, we show that FQI1 can rapidly and reversibly lead to mitotic arrest, even when added directly to mitotic cells, implying that FQI1-mediated mitotic defects are not transcriptionally based. Furthermore, treatment with FQIs resulted in a striking, concentration-dependent diminishment of spindle microtubules, accompanied by a concentration-dependent increase in multi-aster formation. Aberrant γ-tubulin localization was also observed. These phenotypes suggest that perturbation of spindle microtubules is the primary event leading to the mitotic delays upon FQI1 treatment. Previously, FQIs were shown to specifically inhibit not only LSF DNA-binding activity, which requires LSF oligomerization to tetramers, but also other specific LSF-protein interactions. Other transcription factors participate in mitosis through non-transcriptional means, and we recently reported that LSF directly binds α-tubulin and is present in purified cellular tubulin preparations. Consistent with a microtubule role for LSF, here we show that LSF enhanced the rate of tubulin polymerization in vitro, and FQI1 inhibited such polymerization. To probe whether the FQI1-mediated spindle abnormalities could result from inhibition of mitotic LSF-protein interactions, mass spectrometry was performed using as bait an inducible, tagged form of LSF that is biotinylated by endogenous enzymes. The global proteomics analysis yielded expected associations for a transcription factor, notably with RNA processing machinery, but also to nontranscriptional components. In particular, and consistent with spindle disruption due to FQI treatment, mitotic, FQI1-sensitive interactions were identified between the biotinylated LSF and microtubule-associated proteins that regulate spindle assembly, positioning, and dynamics, as well as centrosome-associated proteins. Probing the mitotic LSF interactome using small molecule inhibitors therefore supported a non-transcriptional role for LSF in mediating progression through mitosis.
OvoAMtht from Methyloversatilis thermotolerans ovothiol biosynthesis is a bifunction enzyme: thiol oxygenase and sulfoxide synthase activities
(Royal Society of Chemistry (RSC), 2022-03-24) Cheng, Ronghai; Weitz, Andrew C.; Paris, Jared; Tang, Yijie; Zhang, Jingyu; Song, Heng; Naowarojna, Nathchar; Li, Kelin; Qiao, Lu; Lopez, Juan; Grinstaff, Mark W.; Zhang, Lixin; Guo, Yisong; Elliott, Sean; Liu, Pinghua
Mononuclear non-heme iron enzymes are a large class of enzymes catalyzing a wide-range of reactions. In this work, we report that a non-heme iron enzyme in Methyloversatilis thermotolerans, OvoAMtht, has two different activities, as a thiol oxygenase and a sulfoxide synthase. When cysteine is presented as the only substrate, OvoAMtht is a thiol oxygenase. In the presence of both histidine and cysteine as substrates, OvoAMtht catalyzes the oxidative coupling between histidine and cysteine (a sulfoxide synthase). Additionally, we demonstrate that both substrates and the active site iron's secondary coordination shell residues exert exquisite control over the dual activities of OvoAMtht (sulfoxide synthase vs. thiol oxygenase activities). OvoAMtht is an excellent system for future detailed mechanistic investigation on how metal ligands and secondary coordination shell residues fine-tune the iron-center electronic properties to achieve different reactivities.
Dissecting the mechanism of the nonheme iron endoperoxidase FtmOx1 using substrate analogues
(American Chemical Society (ACS), 2022-07-25) Zhu, Guoliang; Yan, Wupeng; Wang, Xinye; Cheng, Ronghai; Naowarojna, Nathchar; Wang, Kun; Wang, Jun; Song, Heng; Wang, Yuyang; Liu, Hairong; Xia, Xuekui; Costello, Catherine E.; Liu, Xueting; Zhang, Lixin; Liu, Pinghua
FtmOx1 is a nonheme iron (NHFe) endoperoxidase, catalyzing three disparate reactions, endoperoxidation, alcohol dehydrogenation, and dealkylation, under in vitro conditions; the diversity complicates its mechanistic studies. In this study, we use two substrate analogues to simplify the FtmOx1-catalyzed reaction to either a dealkylation or an alcohol dehydrogenation reaction for structure-function relationship analysis to address two key FtmOx1 mechanistic questions: (1) Y224 flipping in the proposed COX-like model vs α-ketoglutarate (αKG) rotation proposed in the CarC-like mechanistic model and (2) the involvement of a Y224 radical (COX-like model) or a Y68 radical (CarC-like model) in FtmOx1-catalysis. When 13-oxo-fumitremorgin B (7) is used as the substrate, FtmOx1-catalysis changes from the endoperoxidation to a hydroxylation reaction and leads to dealkylation. In addition, consistent with the dealkylation side-reaction in the COX-like model prediction, the X-ray structure of the FtmOx1•CoII•αKG•7 ternary complex reveals a flip of Y224 to an alternative conformation relative to the FtmOx1•FeII•αKG binary complex. Verruculogen (2) was used as a second substrate analogue to study the alcohol dehydrogenation reaction to examine the involvement of the Y224 radical or Y68 radical in FtmOx1-catalysis, and again, the results from the verruculogen reaction are more consistent with the COX-like model.
Atomically precise binding conformations of adenine and its variants on gold using single molecule conductance signatures
(AIP Publishing, 2022-12-21) Pan, Xiaoyun; Qian, Cheng; Chow, Amber; Wang, Lu; Kamenetska, Maria
We demonstrate single molecule conductance as a sensitive and atomically precise probe of binding configurations of adenine and its biologically relevant variants on gold. By combining experimental measurements and density functional theory (DFT) calculations of single molecule–metal junction structures in aqueous conditions, we determine for the first time that robust binding of adenine occurs in neutral or basic pH when the molecule is deprotonated at the imidazole moiety. The molecule binds through the donation of the electron lone pairs from the imidazole nitrogen atoms, N7 and N9, to the gold electrodes. In addition, the pyrimidine ring nitrogen, N3, can bind concurrently and strengthen the overall metal–molecule interaction. The amine does not participate in binding to gold in contrast to most other amine-terminated molecular wires due to the planar geometry of the nucleobase. DFT calculations reveal the importance of interface charge transfer in stabilizing the experimentally observed binding configurations. We demonstrate that biologically relevant variants of adenine, 6-methyladenine and 2′-deoxyadenosine, have distinct conductance signatures. These results lay the foundation for biosensing on gold using single molecule conductance readout.
Formation and evolution of metallocene single-molecule circuits with direct gold-π links
(American Chemical Society (ACS), 2022-04-13) Lawson, Brent; Zahl, Percy; Hybertsen, Mark S.; Kamenetska, Maria
Single-molecule circuits with group 8 metallocenes are formed without additional linker groups in scanning tunneling microscope-based break junction (STMBJ) measurements at cryogenic and room-temperature conditions with gold (Au) electrodes. We investigate the nature of this direct gold-π binding motif and its effect on molecular conductance and persistence characteristics during junction evolution. The measurement technique under cryogenic conditions tracks molecular plateaus through the full cycle of extension and compression. Analysis reveals that junction persistence when the metal electrodes are pushed together correlates with whether electrodes are locally sharp or blunt, suggesting distinct scenarios for metallocene junction formation and evolution. The top and bottom surfaces of the “barrel”-shaped metallocenes present the electron-rich π system of cyclopentadienyl rings, which interacts with the gold electrodes in two distinct ways. An undercoordinated gold atom on a sharp tip forms a donor–acceptor bond to a specific carbon atom in the ring. However, a small, flat patch on a dull tip can bind more strongly to the ring as a whole through van der Waals interactions. Density functional theory (DFT)-based calculations of model electrode structures provide an atomic-scale picture of these scenarios, demonstrating the role of these bonding motifs during junction evolution and showing that the conductance is relatively independent of tip atomic-scale structure. The nonspecific interaction of the cyclopentadienyl rings with the electrodes enables extended conductance plateaus, a mechanism distinct from that identified for the more commonly studied, rod-shaped organic molecular wires.
Effect of lattice mismatch on film morphology of the quasi-one dimensional conductor K0.3MoO3
(Royal Society of Chemistry (RSC), 2022-02-03) Cao, Yifeng; Russo, Nicholas; Gao, Lei; Ji, Ailing; Doerrer, Linda H.; Lu, Nianpeng; Smith, Kevin E.
High quality epitaxial thin films of the quasi-one dimensional conductor K0.3MoO3 have been successfully grown on SrTiO3(100), SrTiO3(110), and SrTiO3(510) substrates via pulsed laser deposition. Scanning electron microscopy revealed quasi-one dimensional rod-shaped structures parallel to the substrate surface, and the crystal structure was verified by using X-ray diffraction. The temperature dependence of the resistivity for the K0.3MoO3 thin films demonstrates a metal-to-semiconductor transition at about 180 K. Highly anisotropic resistivity was also observed for films grown on SrTiO3(510).
Divergent, C-C bond forming macrocyclizations using modular sulfonylhydrazone and derived substrates
(American Chemical Society (ACS), 2021-12-03) Xu, Wenqing; Brown, Lauren E.; Porco, John A.
A divergent approach to C-C bond forming macrocycle construction is described. Modular sulfonylhydrazone and derived pyridotriazole substrates with three key building blocks have been constructed and cyclized to afford diverse macrocyclic frameworks. Broad substrate scope and functional group tolerance have been demonstrated. In addition, site-selective postfunctionalization allowed for further diversification of macrocyclic cores.
Chemical modifications of proteins and their applications in metalloenzyme studies
(Elsevier BV, 2021-03) Naowarojna, Nathchar; Cheng, Ronghai; Lopez, Juan; Wong, Christina; Qiao, Lu; Liu, Pinghua
Protein chemical modifications are important tools for elucidating chemical and biological functions of proteins. Several strategies have been developed to implement these modifications, including enzymatic tailoring reactions, unnatural amino acid incorporation using the expanded genetic codes, and recognition-driven transformations. These technologies have been applied in metalloenzyme studies, specifically in dissecting their mechanisms, improving their enzymatic activities, and creating artificial enzymes with non-natural activities. Herein, we summarize some of the recent efforts in these areas with an emphasis on a few metalloenzyme case studies.
Implications for an imidazol-2-yl carbene intermediate in the rhodanase-catalyzed C-S bond formation reaction of anaerobic ergothioneine biosynthesis
(2021-03-19) Cheng, Ronghai; Lai, Rui; Peng, Chao; Lopez, Juan; Li, Zhihong; Naowarojna, Nathchar; Li, Kelin; Wong, Christina; Lee, Norman; Whelan, Stephen A.; Qiao, Lu; Grinstaff, Mark W.; Wang, Jiangyun; Cui, Qiang; Liu, Pinghua
In the anaerobic ergothioneine biosynthetic pathway, a rhodanese domain containing enzyme (EanB) activates tne hercynine's sp2 ε-C-H Dona ana replaces it with a C-S bond to produce ergothioneine. The key intermediate for this trans-sulfuration reaction is the Cys412 persulfide. Substitution of the EanB-Cys412 persulfide with a Cys412 perselenide does not yield the selenium analog of ergothioneine, selenoneine. However, in deuterated buffer, the perselenide-modified EanB catalyzes the deuterium exchange between hercynine's sp2 ε-C-H bond and D2O. Results from QM/MM calculations suggest that the reaction involves a carbene intermediate and that Tyr353 plays a key role. We hypothesize that modulating the pKa of Tyr353 will affect the deuterium-exchange rate. Indeed, the 3,5-difluoro tyrosine containing EanB catalyzes the deuterium exchange reaction with k ex of ~10-fold greater than the wild-type EanB (EanBWT). With regards to potential mechanisms, these results support the involvement of a carbene intermediate in EanB-catalysis, rendering EanB as one of the few carbene-intermediate involving enzymatic systems.
Inhibition of translation initiation factor eIF4a inactivates heat shock factor 1 (HSF1) and exerts anti-leukemia activity in AML
(2021-09) Nishida, Yuki; Zhao, Ran; Heese, Lauren E.; Akiyama, Hiroki; Patel, Shreya; Jaeger, Alex M.; Jacamo, Rodrigo O.; Kojima, Kensuke; Ma, Man Chun John; Ruvolo, Vivian R.; Chachad, Dhruv; Devine, William G.; Lindquist, Susan; Davis, R. Eric; Porco Jr, John A.; Whitesell, Luke; Andreeff, Michael; Ishizawa, Jo
Eukaryotic initiation factor 4A (eIF4A), the enzymatic core of the eIF4F complex essential for translation initiation, plays a key role in the oncogenic reprogramming of protein synthesis, and thus is a putative therapeutic target in cancer. As important component of its anticancer activity, inhibition of translation initiation can alleviate oncogenic activation of HSF1, a stress-inducible transcription factor that enables cancer cell growth and survival. Here, we show that primary acute myeloid leukemia (AML) cells exhibit the highest transcript levels of eIF4A1 compared to other cancer types. eIF4A inhibition by the potent and specific compound rohinitib (RHT) inactivated HSF1 in these cells, and exerted pronounced in vitro and in vivo anti-leukemia effects against progenitor and leukemia-initiating cells, especially those with FLT3-internal tandem duplication (ITD). In addition to its own anti-leukemic activity, genetic knockdown of HSF1 also sensitized FLT3-mutant AML cells to clinical FLT3 inhibitors, and this synergy was conserved in FLT3 double-mutant cells carrying both ITD and tyrosine kinase domain mutations. Consistently, the combination of RHT and FLT3 inhibitors was highly synergistic in primary FLT3-mutated AML cells. Our results provide a novel therapeutic rationale for co-targeting eIF4A and FLT3 to address the clinical challenge of treating FLT3-mutant AML.
Targeting oncoprotein translation with rocaglates in MYC-driven lymphoma
(AMER SOC HEMATOLOGY, 2018-11-29) Zhang, Xuan; Bi, Chengfeng; Lu, Ting; Yue, Ting; Zhang, Weiwei; Zhang, Xiaoyan; Cheng, Wang; Tian, Tian; Lunning, Matthew A.; Vose, Julie M.; Pelletier, J.; Porco, John A.; Tao, J.; Fu, Kai
MYC-driven lymphomas, especially those with concurrent MYC and BCL2 dysregulation, are currently a challenge in clinical practice due to rapid disease progression, resistance to standard chemotherapy and high risk of refractory disease. MYC plays a central role by coordinating hyperactive protein synthesis with upregulated transcription in order to support rapid proliferation of tumor cells. Translation initiation inhibitor rocaglates have been identified as the most potent drugs in MYC-driven lymphomas as they efficiently inhibit MYC expression and tumor cell viability. We found that this class of compounds can overcome eIF4A abundance by stabilizing target mRNA-eIF4A interaction that directly prevents translation. Proteome-wide quantification demonstrated selective repression of multiple critical oncoproteins in addition to MYC in B cell lymphoma including NEK2, MCL1, AURKA, PLK1, and several transcription factors that are generally considered undruggable. Finally, (−)-SDS-1–021, the most promising synthetic rocaglate, was confirmed to be highly potent as a single agent, and displayed significant synergy with the BCL2 inhibitor ABT199 in inhibiting tumor growth and survival in primary lymphoma cells in vitro and in patient-derived xenograft mouse models. Overall, our findings support the strategy of using rocaglates to target oncoprotein synthesis in MYC-driven lymphomas.
Eukaryotic translation initiation factor 4AI: a potential novel target in neuroblastoma
(2021-02-02) Skofler, Christina; Kleinegger, Florian; Krassnig, Stefanie; Birkl-Toeglhofer, Anna Maria; Singer, Georg; Till, Holger; Benesch, Martin; Cencic, Regina; Porco, John A.; Pelletier, Jerry; Castellani, Christoph; Raicht, Andrea; Izycka-Swieszewska, Ewa; Czapiewski, Piotr; Haybaeck, Johannes
Neuroblastoma (NB) is the most common extracranial pediatric solid tumor. Children suffering from high-risk and/or metastatic NB often show no response to therapy, and new therapeutic approaches are urgently needed. Malignant tumor development has been shown to be driven by the dysregulation of eukaryotic initiation factors (eIFs) at the translation initiation. Especially the activity of the heterotrimeric eIF4F complex is often altered in malignant cells, since it is the direct connection to key oncogenic signaling pathways such as the PI3K/AKT/mTOR-pathway. A large body of literature exists that demonstrates targeting the translational machinery as a promising anti-neoplastic approach. The objective of this study was to determine whether eIF4F complex members are aberrantly expressed in NB and whether targeting parts of the complex may be a therapeutic strategy against NB. We show that eIF4AI is overexpressed in NB patient tissue using immunohistochemistry, immunoblotting, and RT-qPCR. NB cell lines exhibit decreased viability, increased apoptosis rates as well as changes in cell cycle distribution when treated with the synthetic rocaglate CR-1-31-B, which clamps eIF4A and eIF4F onto mRNA, resulting in a translational block. Additionally, this study reveals that CR-1-31-B is effective against NB cell lines at low nanomolar doses (≤20 nM), which have been shown to not affect non-malignant cells in previous studies. Thus, our study provides information of the expression status on eIF4AI in NB and offers initial promising insight into targeting translation initiation as an anti-tumorigenic approach for NB.
A forward genetic screen identifies modifiers of rocaglate responsiveness
(2021-09-16) Shen, Leo; Pugsley, Lauren; Cencic, Regina; Wang, HanChen; Robert, Francis; Naineni, Sai Kiran; Sahni, Ananya; Morin, Genevieve; Zhang, Wenhan; Nijnik, Anastasia; Porco, John A.; Langlais, David; Huang, Sidong; Pelletier, Jerry
Rocaglates are a class of eukaryotic translation initiation inhibitors that are being explored as chemotherapeutic agents. They function by targeting eukaryotic initiation factor (eIF) 4A, an RNA helicase critical for recruitment of the 40S ribosome (and associated factors) to mRNA templates. Rocaglates perturb eIF4A activity by imparting a gain-of-function activity to eIF4A and mediating clamping to RNA. To appreciate how rocaglates could best be enabled in the clinic, an understanding of resistance mechanisms is important, as this could inform on strategies to bypass such events as well as identify responsive tumor types. Here, we report on the results of a positive selection, ORFeome screen aimed at identifying cDNAs capable of conferring resistance to rocaglates. Two of the most potent modifiers of rocaglate response identified were the transcription factors FOXP3 and NR1I3, both of which have been implicated in ABCB1 regulation-the gene encoding P-glycoprotein (Pgp). Pgp has previously been implicated in conferring resistance to silvestrol, a naturally occurring rocaglate, and we show here that this extends to additional synthetic rocaglate derivatives. In addition, FOXP3 and NR1I3 impart a multi-drug resistant phenotype that is reversed upon inhibition of Pgp, suggesting a potential therapeutic combination strategy.
Synthesis and multiplexed activity profiling of synthetic acylphloroglucinol scaffolds
(2021-01-18) Boyce, Jonathan H.; Reisman, Benjamin J.; Bachmann, Brian O.; Porco, John A.
Reported here are novel formic-acid-mediated rearrangements of dearomatized acylphloroglucinols to access a structurally diverse group of synthetic acylphloroglucinol scaffolds (SASs). Density-functional theory (DFT) optimized orbital and stereochemical analyses shed light on the mechanism of these rearrangements. Products were evaluated by multiplexed activity profiling (MAP), an unbiased platform which assays multiple biological readouts simultaneously at single-cell resolution for markers of cell signaling, and can aid in distinguishing genuine activity from assay interference. MAP identified a number of SASs that suppressed pS6 (Ser235/236), a marker for activation of the mTOR and ERK signaling pathways. These results illustrate how biomimetic synthesis and multiplexed activity profiling can reveal the pharmacological potential of novel chemotypes by diversity-oriented synthesis.
A progesterone biosensor derived from microbial screening
(2020-03-09) Grazon, C.; Baer, R. Cooper; Kuzmanović, U.; Nguyen, T.; Chen, M.; Zamani, M.; Chern, Margaret; Aquino, P.; Zhang, X.; Lecommandoux, S.; Fan, Andy; Cabodi, Mario; Klapperich, Catherine; Grinstaff, Mark W.; Dennis, Allison M.; Galagan, James E.
Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.
Quantum biology revisited
(2020-04) Cao, Jianshu; Cogdell, Richard J.; Coker, David F.; Duan, Hong-Guang; Hauer, Jürgen; Kleinekathöfer, Ulrich; Jansen, Thomas L.C.; Mančal, Tomáš; Miller, R.J. Dwayne; Ogilvie, Jennifer P.; Prokhorenko, Valentyn I.; Renger, Thomas; Tan, Howe-Siang; Tempelaar, Roel; Thorwart, Michael; Thyrhaug, Erling; Westenhoff, Sebastian; Zigmantas, Donatas
Photosynthesis is a highly optimized process from which valuable lessons can be learned about the operating principles in nature. Its primary steps involve energy transport operating near theoretical quantum limits in efficiency. Recently, extensive research was motivated by the hypothesis that nature used quantum coherences to direct energy transfer. This body of work, a cornerstone for the field of quantum biology, rests on the interpretation of small-amplitude oscillations in two-dimensional electronic spectra of photosynthetic complexes. This Review discusses recent work reexamining these claims and demonstrates that interexciton coherences are too short lived to have any functional significance in photosynthetic energy transfer. Instead, the observed long-lived coherences originate from impulsively excited vibrations, generally observed in femtosecond spectroscopy. These efforts, collectively, lead to a more detailed understanding of the quantum aspects of dissipation. Nature, rather than trying to avoid dissipation, exploits it via engineering of exciton-bath interaction to create efficient energy flow.
Surface enhanced Raman spectroscopy of Chlamydia trachomatis and Neisseria gonorrhoeae for diagnostics, and extra-cellular metabolomics and biochemical monitoring
(NATURE PUBLISHING GROUP, 2018-03-26) Chen, Y.; Premasiri, W.R.; Ziegler, L.D.
SERS spectra excited at 785 nm of the bacteria Chlamydia trahomatis (elementary bodies, EB) and Neisseria gonorrheoae, the causative pathogens for the two most common sexually transmitted diseases (STD), chlamydia and gonorrhea, respectively, are reported. Although both are Gram-negative bacteria, the SERS signatures of C. trachomatis and N. gonorrheoae are completely different. N. gonorrheoae SERS spectra are due to the starvation induced nucleotide metabolites adenine and guanine, and the surface associated co-enzyme nicotinamide adenine dinucleotide and are very similar on Au and Ag although the spectrum appears more rapidly on Ag. The C. trachomatis SERS spectrum is dominated by the vibrational features of cell surface proteins. While features attributable to specific residues and the amide backbone characterize the C. trachomatis spectrum on Ag, the corresponding SERS spectrum on Au substrates displays vibrational characteristics of aggregated proteins. The prospects for the development of a SERS based platform for rapid (

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