24 results on '"Allu SR"'
Search Results
2. Direct Measurements of FLASH-Induced Changes in Intracellular Oxygenation.
- Author
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El Khatib M, Motlagh AO, Beyer JN, Troxler T, Allu SR, Sun Q, Burslem GM, and Vinogradov SA
- Subjects
- Humans, Oxygen, Electroporation, Radiation, Ionizing, Radiopharmaceuticals, Radiotherapy Dosage, Hypoxia, Radiation Protection
- Abstract
Purpose: The goal of our study was to characterize the dynamics of intracellular oxygen during application of radiation at conventional (CONV) and FLASH dose rates and obtain evidence for or against the oxygen depletion hypothesis as a mechanism of the FLASH effect., Methods and Materials: The measurements were performed by the phosphorescence quenching method using probe Oxyphor PtG4, which was delivered into the cellular cytosol by electroporation., Results: Intracellular radiochemical oxygen depletion (ROD) g-value for a dose rate of 100 Gy/s in the normoxic range was found to be 0.58 ± 0.03 μM/Gy. Intracellular ROD g-values for FLASH and CONV dose rates in the normoxic range were found to be nearly equal. As in solution-based studies, intracellular ROD was found to exhibit strong dependence on oxygen concentration in the range of 0 to ∼40 μM [O
2 ]., Conclusions: Depletion of oxygen in cells in vitro by a clinical dose of proton radiation delivered as FLASH is unable to produce a transient state of hypoxia and, therefore, unable to induce radioprotection. The difference between ROD g-values for FLASH and CONV dose rates, detected previously in solutions-based experiments, disappears when measurements are conducted inside cells. Understanding this phenomenon should provide additional insight into the role of oxygen in FLASH radiation therapy and help to decipher the mechanism of the FLASH effect., (Copyright © 2023 Elsevier Inc. All rights reserved.)- Published
- 2024
- Full Text
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3. Therapies for the Treatment of Advanced/Metastatic Estrogen Receptor-Positive Breast Cancer: Current Situation and Future Directions.
- Author
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Rej RK, Roy J, and Allu SR
- Abstract
The hormone receptor-positive (HR+) type is the most frequently identified subtype of breast cancer. HR+ breast cancer has a more positive prognosis when compared to other subtypes, such as human epidermal growth factor protein 2-positive disorder and triple-negative disease. The advancement in treatment outcomes for advanced HR+ breast cancer has been considerably elevated due to the discovery of cyclin-dependent kinase 4/6 inhibitors and their combination effects with endocrine therapy. However, despite the considerable effectiveness of tamoxifen, a selective estrogen receptor modulator (SERMs), and aromatase inhibitors (AI), the issue of treatment resistance still presents a significant challenge for HR+ breast cancer. As a result, there is a focus on exploring new therapeutic strategies such as targeted protein degradation and covalent inhibition for targeting ERα. This article discusses the latest progress in treatments like oral selective ER degraders (SERDs), complete estrogen receptor antagonists (CERANs), selective estrogen receptor covalent antagonists (SERCAs), proteolysis targeting chimera (PROTAC) degraders, and combinations of CDK4/6 inhibitors with endocrine therapy. The focus is specifically on those compounds that have transitioned into phases of clinical development.
- Published
- 2024
- Full Text
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4. Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome.
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Zong W, Friedman ES, Allu SR, Firrman J, Tu V, Daniel SG, Bittinger K, Liu L, Vinogradov SA, and Wu GD
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- Animals, Humans, Mice, Feces microbiology, Mice, Inbred C57BL, Dextran Sulfate, Colon microbiology, Colon metabolism, Male, Gastrointestinal Microbiome, Colitis microbiology, Colitis chemically induced, Colitis metabolism, Oxygen metabolism, Bacteria metabolism, Bacteria classification, Bacteria isolation & purification, Bacteria genetics, Intestinal Mucosa metabolism, Intestinal Mucosa microbiology
- Abstract
The juxtaposition of well-oxygenated intestinal colonic tissue with an anerobic luminal environment supports a fundamentally important relationship that is altered in the setting of intestinal injury, a process likely to be relevant to diseases such as inflammatory bowel disease. Herein, using two-color phosphorometry to non-invasively quantify both intestinal tissue and luminal oxygenation in real time, we show that intestinal injury induced by DSS colitis reduces intestinal tissue oxygenation in a spatially defined manner and increases the flux of oxygen from the tissue into the gut lumen. By characterizing the composition of the microbiome in both DSS colitis-affected gut and in a bioreactor containing a stable human fecal community exposed to microaerobic conditions, we provide evidence that the increased flux of oxygen into the gut lumen augments glycan degrading bacterial taxa rich in glycoside hydrolases which are known to inhabit gut mucosal surface. Continued disruption of the intestinal mucus barrier through such a mechanism may play a role in the perpetuation of the intestinal inflammatory process.
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- 2024
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5. CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.
- Author
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Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, and Eberwine J
- Subjects
- Humans, DNA genetics, DNA-Binding Proteins metabolism, Genomics, DNA Replication, DNA, Single-Stranded genetics, DNA Repair
- Abstract
Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe "CHEX-seq" which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3'-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA., (© 2023. The Author(s).)
- Published
- 2023
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6. Aerobic exercise reverses aging-induced depth-dependent decline in cerebral microcirculation.
- Author
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Shin P, Pian Q, Ishikawa H, Hamanaka G, Mandeville ET, Guo S, Fu B, Alfadhel M, Allu SR, Şencan-Eğilmez I, Li B, Ran C, Vinogradov SA, Ayata C, Lo E, Arai K, Devor A, and Sakadžić S
- Subjects
- Animals, Mice, Microcirculation, Aging physiology, Cognition, Cerebral Cortex, Cognitive Dysfunction prevention & control, White Matter physiology
- Abstract
Aging is a major risk factor for cognitive impairment. Aerobic exercise benefits brain function and may promote cognitive health in older adults. However, underlying biological mechanisms across cerebral gray and white matter are poorly understood. Selective vulnerability of the white matter to small vessel disease and a link between white matter health and cognitive function suggests a potential role for responses in deep cerebral microcirculation. Here, we tested whether aerobic exercise modulates cerebral microcirculatory changes induced by aging. To this end, we carried out a comprehensive quantitative examination of changes in cerebral microvascular physiology in cortical gray and subcortical white matter in mice (3-6 vs. 19-21 months old), and asked whether and how exercise may rescue age-induced deficits. In the sedentary group, aging caused a more severe decline in cerebral microvascular perfusion and oxygenation in deep (infragranular) cortical layers and subcortical white matter compared with superficial (supragranular) cortical layers. Five months of voluntary aerobic exercise partly renormalized microvascular perfusion and oxygenation in aged mice in a depth-dependent manner, and brought these spatial distributions closer to those of young adult sedentary mice. These microcirculatory effects were accompanied by an improvement in cognitive function. Our work demonstrates the selective vulnerability of the deep cortex and subcortical white matter to aging-induced decline in microcirculation, as well as the responsiveness of these regions to aerobic exercise., Competing Interests: PS, QP, HI, GH, EM, SG, BF, MA, SA, IŞ, BL, CR, SV, CA, EL, KA, AD, SS No competing interests declared, (© 2023, Shin et al.)
- Published
- 2023
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7. Measurements of cerebral microvascular blood flow, oxygenation, and morphology in a mouse model of whole-brain irradiation-induced cognitive impairment by two-photon microscopy and optical coherence tomography: evidence for microvascular injury in the cerebral white matter.
- Author
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Li B, Yabluchanskiy A, Tarantini S, Allu SR, Şencan-Eğilmez I, Leng J, Alfadhel MAH, Porter JE, Fu B, Ran C, Erdener SE, Boas DA, Vinogradov SA, Sonntag WE, Csiszar A, Ungvari Z, and Sakadžić S
- Subjects
- Mice, Male, Animals, Microcirculation, Microscopy, Cerebrovascular Circulation physiology, Tomography, Optical Coherence, Quality of Life, Cranial Irradiation, Mice, Inbred C57BL, Brain blood supply, Disease Models, Animal, Oxygen, White Matter diagnostic imaging, Brain Neoplasms, Cognitive Dysfunction
- Abstract
Whole-brain irradiation (WBI, also known as whole-brain radiation therapy) is a mainstay treatment modality for patients with multiple brain metastases. It is also used as a prophylactic treatment for microscopic tumors that cannot be detected by magnetic resonance imaging. WBI induces a progressive cognitive decline in ~ 50% of the patients surviving over 6 months, significantly compromising the quality of life. There is increasing preclinical evidence that radiation-induced injury to the cerebral microvasculature and accelerated neurovascular senescence plays a central role in this side effect of WBI. To better understand this side effect, male C57BL/6 mice were first subjected to a clinically relevant protocol of fractionated WBI (5 Gy, two doses per week, for 4 weeks). Nine months post the WBI treatment, we applied two-photon microscopy and Doppler optical coherence tomography to measure capillary red-blood-cell (RBC) flux, capillary morphology, and microvascular oxygen partial pressure (PO
2 ) in the cerebral somatosensory cortex in the awake, head-restrained, WPI-treated mice and their age-matched controls, through a cover-glass-sealed chronic cranial window. Thanks to the extended penetration depth with the fluorophore - Alexa680, measurements of capillary blood flow properties (e.g., RBC flux, speed, and linear density) in the cerebral subcortical white matter were enabled. We found that the WBI-treated mice exhibited a significantly decreased capillary RBC flux in the white matter. WBI also caused a significant reduction in capillary diameter, as well as a large (although insignificant) reduction in segment density at the deeper cortical layers (e.g., 600-700 μm), while the other morphological properties (e.g., segment length and tortuosity) were not obviously affected. In addition, we found that PO2 measured in the arterioles and venules, as well as the calculated oxygen saturation and oxygen extraction fraction, were not obviously affected by WBI. Lastly, WBI was associated with a significant increase in the erythrocyte-associated transients of PO2 , while the changes of other cerebral capillary PO2 properties (e.g., capillary mean-PO2 , RBC-PO2 , and InterRBC-PO2 ) were not significant. Collectively, our findings support the notion that WBI results in persistent cerebral white matter microvascular impairment, which likely contributes to the WBI-induced brain injury and cognitive decline. Further studies are warranted to assess the WBI-induced changes in brain tissue oxygenation and malfunction of the white matter microvasculature as well., (© 2023. The Author(s), under exclusive licence to American Aging Association.)- Published
- 2023
- Full Text
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8. Aerobic exercise reverses aging-induced depth-dependent decline in cerebral microcirculation.
- Author
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Shin P, Pian Q, Ishikawa H, Hamanaka G, Mandeville ET, Shuzhen G, Buyin F, Alfadhel M, Allu SR, Şencan-Eğilmez I, Li B, Ran C, Vinogradov SA, Ayata C, Lo EH, Arai K, Devor A, and Sakadžić S
- Abstract
Aging is a major risk factor for cognitive impairment. Aerobic exercise benefits brain function and may promote cognitive health in older adults. However, underlying biological mechanisms across cerebral gray and white matter are poorly understood. Selective vulnerability of the white matter to small vessel disease and a link between white matter health and cognitive function suggests a potential role for responses in deep cerebral microcirculation. Here, we tested whether aerobic exercise modulates cerebral microcirculatory changes induced by aging. To this end, we carried out a comprehensive quantitative examination of changes in cerebral microvascular physiology in cortical gray and subcortical white matter in mice (3-6 vs. 19-21 months old), and asked whether and how exercise may rescue age-induced deficits. In the sedentary group, aging caused a more severe decline in cerebral microvascular perfusion and oxygenation in deep (infragranular) cortical layers and subcortical white matter compared with superficial (supragranular) cortical layers. Five months of voluntary aerobic exercise partly renormalized microvascular perfusion and oxygenation in aged mice in a depth-dependent manner, and brought these spatial distributions closer to those of young adult sedentary mice. These microcirculatory effects were accompanied by an improvement in cognitive function. Our work demonstrates the selective vulnerability of the deep cortex and subcortical white matter to aging-induced decline in microcirculation, as well as the responsiveness of these regions to aerobic exercise.
- Published
- 2023
- Full Text
- View/download PDF
9. Real-time tracking of brain oxygen gradients and blood flow during functional activation.
- Author
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Chong SH, Ong YH, El Khatib M, Allu SR, Parthasarathy AB, Greenberg JH, Yodh AG, and Vinogradov SA
- Abstract
Significance: Cerebral metabolic rate of oxygen ( CMRO 2 ) consumption is a key physiological variable that characterizes brain metabolism in a steady state and during functional activation., Aim: We aim to develop a minimally invasive optical technique for real-time measurement of CMRO 2 concurrently with cerebral blood flow (CBF)., Approach: We used a pair of macromolecular phosphorescent probes with nonoverlapping optical spectra, which were localized in the intra- and extravascular compartments of the brain tissue, thus providing a readout of oxygen gradients between these two compartments. In parallel, we measured CBF using laser speckle contrast imaging., Results: The method enables computation and tracking of CMRO 2 during functional activation with high temporal resolution ( ∼ 7 Hz ). In contrast to other approaches, our assessment of CMRO 2 does not require measurements of CBF or hemoglobin oxygen saturation., Conclusions: The independent records of intravascular and extravascular partial pressures of oxygen, CBF, and CMRO 2 provide information about the physiological events that accompany neuronal activation, creating opportunities for dynamic quantification of brain metabolism., (© 2022 The Authors.)
- Published
- 2022
- Full Text
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10. Ultrafast Tracking of Oxygen Dynamics During Proton FLASH.
- Author
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El Khatib M, Van Slyke AL, Velalopoulou A, Kim MM, Shoniyozov K, Allu SR, Diffenderfer EE, Busch TM, Wiersma RD, Koch CJ, and Vinogradov SA
- Subjects
- Humans, Lung, Oxygen, Radiobiology, Radiotherapy Dosage, Proton Therapy methods, Protons
- Abstract
Purpose: Radiation therapy delivered at ultrafast dose rates, known as FLASH RT, has been shown to provide a therapeutic advantage compared with conventional radiation therapy by selectively protecting normal tissues. Radiochemical depletion of oxygen has been proposed to underpin the FLASH effect; however, experimental validation of this hypothesis has been lacking, in part owing to the inability to measure oxygenation at rates compatible with FLASH., Methods and Materials: We present a new variant of the phosphorescence quenching method for tracking oxygen dynamics with rates reaching up to ∼3.3 kHz. Using soluble Oxyphor probes we were able to resolve, both in vitro and in vivo, oxygen dynamics during the time of delivery of proton FLASH., Results: In vitro in solutions containing bovine serum albumin the O
2 depletion g values (moles/L of O2 depleted per radiation dose, eg, µM/Gy) are higher for conventional irradiation (by ∼13% at 75 µM [O2 ]) than for FLASH, and in the low-oxygen region (<25 µM [O2 ]) they decrease with oxygen concentration. In vivo, depletion of oxygen by a single FLASH is insufficient to achieve severe hypoxia in initially well-oxygenated tissue, and the g values measured appear to correlate with baseline oxygen levels., Conclusions: The developed method should be instrumental in radiobiological studies, such as studies aimed at unraveling the mechanism of the FLASH effect. The FLASH effect could in part originate from the difference in the oxygen dependencies of the oxygen consumption g values for conventional versus FLASH RT., (Copyright © 2022 Elsevier Inc. All rights reserved.)- Published
- 2022
- Full Text
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11. Neurophotonic tools for microscopic measurements and manipulation: status report.
- Author
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, and Zhao Y
- Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics ' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions., (© 2022 The Authors.)
- Published
- 2022
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12. Quantification of Oxygen Depletion During FLASH Irradiation In Vitro and In Vivo.
- Author
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Cao X, Zhang R, Esipova TV, Allu SR, Ashraf R, Rahman M, Gunn JR, Bruza P, Gladstone DJ, Williams BB, Swartz HM, Hoopes PJ, Vinogradov SA, and Pogue BW
- Subjects
- Animals, Mice, Neoplasms, Experimental metabolism, Oxygen Consumption, Radiotherapy Dosage, Neoplasms, Experimental radiotherapy, Oxygen analysis
- Abstract
Purpose: Delivery of radiation at ultrahigh dose rates (UHDRs), known as FLASH, has recently been shown to preferentially spare normal tissues from radiation damage compared with tumor tissues. However, the underlying mechanism of this phenomenon remains unknown, with one of the most widely considered hypotheses being that the effect is related to substantial oxygen depletion upon FLASH, thereby altering the radiochemical damage during irradiation, leading to different radiation responses of normal and tumor cells. Testing of this hypothesis would be advanced by direct measurement of tissue oxygen in vivo during and after FLASH irradiation., Methods and Materials: Oxygen measurements were performed in vitro and in vivo using the phosphorescence quenching method and a water-soluble molecular probe Oxyphor 2P. The changes in oxygen per unit dose (G-values) were quantified in response to irradiation by 10 MeV electron beam at either UHDR reaching 300 Gy/s or conventional radiation therapy dose rates of 0.1 Gy/s., Results: In vitro experiments with 5% bovine serum albumin solutions at 23°C resulted in G-values for oxygen consumption of 0.19 to 0.21 mm Hg/Gy (0.34-0.37 μM/Gy) for conventional irradiation and 0.16 to 0.17 mm Hg/Gy (0.28-0.30 μM/Gy) for UHDR irradiation. In vivo, the total decrease in oxygen after a single fraction of 20 Gy FLASH irradiation was 2.3 ± 0.3 mm Hg in normal tissue and 1.0 ± 0.2 mm Hg in tumor tissue (P < .00001), whereas no decrease in oxygen was observed from a single fraction of 20 Gy applied in conventional mode., Conclusions: Our observations suggest that oxygen depletion to radiologically relevant levels of hypoxia is unlikely to occur in bulk tissue under FLASH irradiation. For the same dose, FLASH irradiation induces less oxygen consumption than conventional irradiation in vitro, which may be related to the FLASH sparing effect. However, the difference in oxygen depletion between FLASH and conventional irradiation could not be quantified in vivo because measurements of oxygen depletion under conventional irradiation are hampered by resupply of oxygen from the blood., (Published by Elsevier Inc.)
- Published
- 2021
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13. syn -Diarylphthalimidoporphyrins: Effects of Symmetry Breaking on Two-Photon Absorption and Linear Photophysical Properties.
- Author
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Allu SR, Ravotto L, Troxler T, and Vinogradov SA
- Abstract
Aromatically π-extended porphyrins possess exceptionally intense one-photon (1P) and sometimes two-photon (2P) absorption bands, presenting interest for construction of optical imaging probes and photodynamic agents. Here we investigated how breaking the molecular symmetry affects linear and 2PA properties of π-extended porphyrins. First, we developed the synthesis of porphyrins fused with two phthalimide fragments, termed syn -diarylphthalimidoporphyrins (DAPIP). Second, the photophysical properties of H
2 , Zn, Pd, and Pt DAPIP were measured and compared to those of fully symmetric tetraarylphthalimidoporphyrins (TAPIP). The data were interpreted using DFT/TDDFT calculations and sum-over-states (SOS) formalism. Overall, the picture of 2PA in DAPIP was found to resemble that in centrosymmetric porphyrins, indicating that symmetry breaking, even as significant as by syn -phthalimido-fusion, induces a relatively small perturbation to the porphyrin electronic structure. Collectively, the compact size, versatile synthesis, high 1PA and 2PA cross sections, and bright luminescence make DAPIP valuable chromophores for construction of imaging probes and other bioapplications.- Published
- 2021
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14. Herboxidiene Features That Mediate Conformation-Dependent SF3B1 Interactions to Inhibit Splicing.
- Author
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Gamboa Lopez A, Allu SR, Mendez P, Chandrashekar Reddy G, Maul-Newby HM, Ghosh AK, and Jurica MS
- Subjects
- Adenosine Triphosphate chemistry, Base Sequence, Binding Sites, Fatty Alcohols metabolism, HeLa Cells, Humans, Models, Molecular, Protein Binding, Protein Conformation, Pyrans metabolism, RNA, Messenger chemistry, Ribonucleoprotein, U2 Small Nuclear metabolism, Spliceosomes metabolism, Structure-Activity Relationship, Temperature, Fatty Alcohols chemistry, Phosphoproteins agonists, Phosphoproteins antagonists & inhibitors, Pyrans chemistry, RNA Splicing drug effects, RNA Splicing Factors agonists, RNA Splicing Factors antagonists & inhibitors, Ribonucleoprotein, U2 Small Nuclear chemistry, Spliceosomes chemistry
- Abstract
Small molecules that target the spliceosome SF3B complex are potent inhibitors of cancer cell growth. The compounds affect an early stage of spliceosome assembly when U2 snRNP first engages the branch point sequence of an intron. Employing an inactive herboxidiene analog (iHB) as a competitor, we investigated factors that influence inhibitor interactions with SF3B to interfere with pre-mRNA splicing in vitro . Order-of-addition experiments show that inhibitor interactions are long lasting and affected by both temperature and the presence of ATP. Our data are also consistent with the model that not all SF3B conformations observed in structural studies are conducive to productive inhibitor interactions. Notably, SF3B inhibitors do not impact an ATP-dependent rearrangement in U2 snRNP that exposes the branch binding sequence for base pairing. We also report extended structure-activity relationship analysis of the splicing inhibitor herboxidiene. We identified features of the tetrahydropyran ring that mediate its interactions with SF3B and its ability to interfere with splicing. In the context of recent structures of SF3B bound to inhibitor, our results lead us to extend the model for early spliceosome assembly and inhibitor mechanism. We postulate that interactions between a carboxylic acid substituent of herboxidiene and positively charged SF3B1 side chains in the inhibitor binding channel are needed to maintain inhibitor occupancy while counteracting the SF3B transition to a closed state that is required for stable U2 snRNP interactions with the intron.
- Published
- 2021
- Full Text
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15. Design and synthesis of herboxidiene derivatives that potently inhibit in vitro splicing.
- Author
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Ghosh AK, Allu SR, Reddy GC, Lopez AG, Mendez P, and Jurica MS
- Subjects
- Antineoplastic Agents chemical synthesis, Fatty Alcohols chemical synthesis, HeLa Cells, Humans, Pyrans chemical synthesis, Spliceosomes drug effects, Stereoisomerism, Antineoplastic Agents pharmacology, Fatty Alcohols pharmacology, Pyrans pharmacology, RNA Splicing drug effects
- Abstract
Herboxidiene is a potent antitumor agent that targets the SF3B subunit of the spliceosome. Herboxidiene possesses a complex structural architecture with nine stereocenters and design of potent less complex structures would be of interest as a drug lead as well as a tool for studying SF3B1 function in splicing. We investigated a number of C-6 modified herboxidiene derivatives in an effort to eliminate this stereocenter and, also to understand the importance of this functionality. The syntheses of structural variants involved a Suzuki-Miyaura cross-coupling reaction as the key step. The functionalized tetrahydrofuran core has been constructed from commercially available optically active tri-O-acetyl-d-glucal. We investigated the effect of these derivatives on splicing chemistry. The C-6 alkene derivative showed very potent splicing inhibitory activity similar to herboxidiene. Furthermore, the C-6 gem-dimethyl derivative also exhibited very potent in vitro splicing inhibitory activity comparable to herboxidiene.
- Published
- 2021
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16. High-Resolution pO 2 Imaging Improves Quantification of the Hypoxic Fraction in Tumors During Radiation Therapy.
- Author
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Cao X, Allu SR, Jiang S, Gunn Bs JR, Yao PhD C, Xin PhD J, Bruza PhD P, Gladstone ScD DJ, Jarvis Md PhD LA, Tian PhD J, Swartz Md Msph PhD HM, Vinogradov PhD SA, and Pogue PhD BW
- Subjects
- Animals, Cell Line, Tumor, Cell Transformation, Neoplastic, Humans, Luminescence, Mice, Optical Imaging, Oxygen metabolism, Signal-To-Noise Ratio, Tumor Hypoxia radiation effects
- Abstract
Purpose: The extreme microscopic heterogeneity of tumors makes it difficult to characterize tumor hypoxia. We evaluated how changes in the spatial resolution of oxygen imaging could alter measures of tumor hypoxia and their correlation to radiation therapy response., Methods and Materials: Cherenkov-Excited Luminescence Imaging in combination with an oxygen probe, Oxyphor PtG4 was used to directly image tumor pO
2 distributions with 0.2 mm spatial resolution at the time of radiation delivery. These pO2 images were analyzed with variations of reduced spatial resolution from 0.2 mm to 5 mm, to investigate the influence of how reduced imaging spatial resolution would affect the observed tumor hypoxia. As an in vivo validation test, mice bearing tumor xenografts were imaged for hypoxic fraction and median pO2 to examine the predictive link with tumor response to radiation therapy, while accounting for spatial resolution., Results: In transitioning from voxel sizes of 200 μm to 3 mm, the median pO2 values increased by a few mm Hg, and the hypoxic fraction decreased by more than 50%. When looking at radiation-responsive tumors, the median pO2 values changed just a few mm Hg as a result of treatment, and the hypoxic fractions changed by as much as 50%. This latter change, however, could only be seen when sampling was performed with high spatial resolution. Median pO2 or similar quantities obtained from low resolution measurements are commonly used in clinical practice, however these parameters are much less sensitive to changes in the tumor microenvironment than the tumor hypoxic fraction obtained from high-resolution oxygen images., Conclusions: This study supports the hypothesis that for adequate measurements of the tumor response to radiation therapy, oxygen imaging with high spatial resolution is required to accurately characterize the hypoxic fraction., (Copyright © 2020 Elsevier Inc. All rights reserved.)- Published
- 2021
- Full Text
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17. A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
- Author
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Hattori SI, Higashi-Kuwata N, Hayashi H, Allu SR, Raghavaiah J, Bulut H, Das D, Anson BJ, Lendy EK, Takamatsu Y, Takamune N, Kishimoto N, Murayama K, Hasegawa K, Li M, Davis DA, Kodama EN, Yarchoan R, Wlodawer A, Misumi S, Mesecar AD, Ghosh AK, and Mitsuya H
- Subjects
- Adenosine Monophosphate analogs & derivatives, Adenosine Monophosphate pharmacology, Alanine analogs & derivatives, Alanine pharmacology, Animals, Antiviral Agents pharmacology, Cell Line, Chlorocebus aethiops, Humans, Indoles pharmacology, Pyridines pharmacology, Vero Cells, Viral Proteases metabolism, Coronavirus Protease Inhibitors pharmacology, SARS-CoV-2 drug effects, Viral Proteases drug effects, COVID-19 Drug Treatment
- Abstract
Except remdesivir, no specific antivirals for SARS-CoV-2 infection are currently available. Here, we characterize two small-molecule-compounds, named GRL-1720 and 5h, containing an indoline and indole moiety, respectively, which target the SARS-CoV-2 main protease (M
pro ). We use VeroE6 cell-based assays with RNA-qPCR, cytopathic assays, and immunocytochemistry and show both compounds to block the infectivity of SARS-CoV-2 with EC50 values of 15 ± 4 and 4.2 ± 0.7 μM for GRL-1720 and 5h, respectively. Remdesivir permitted viral breakthrough at high concentrations; however, compound 5h completely blocks SARS-CoV-2 infection in vitro without viral breakthrough or detectable cytotoxicity. Combination of 5h and remdesivir exhibits synergism against SARS-CoV-2. Additional X-ray structural analysis show that 5h forms a covalent bond with Mpro and makes polar interactions with multiple active site amino acid residues. The present data suggest that 5h might serve as a lead Mpro inhibitor for the development of therapeutics for SARS-CoV-2 infection.- Published
- 2021
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18. Implantable sensor for local Cherenkov-excited luminescence imaging of tumor pO2 during radiotherapy.
- Author
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Cao X, Gunn JR, Allu SR, Bruza P, Jiang S, Vinogradov SA, and Pogue BW
- Subjects
- Animals, Humans, Optical Imaging, Oxygen, Phantoms, Imaging, Luminescence, Neoplasms
- Abstract
Significance: The necessity to use exogenous probes for optical oxygen measurements in radiotherapy poses challenges for clinical applications. Options for implantable probe biotechnology need to be improved to alleviate toxicity concerns in human use and facilitate translation to clinical trial use., Aim: To develop an implantable oxygen sensor containing a phosphorescent oxygen probe such that the overall administered dose of the probe would be below the Federal Drug Administration (FDA)-prescribed microdose level, and the sensor would provide local high-intensity signal for longitudinal measurements of tissue pO2., Approach: PtG4, an oxygen quenched dendritic molecule, was mixed into an agarose matrix at 100 μM concentration, allowing for local injection into tumors at the total dose of 10 nmol per animal, forming a gel at the site of injection. Cherenkov-excited luminescence imaging (CELI) was used to acquire the phosphorescence and provide intratumoral pO2., Results: Although PtG4 does not form covalent bonds with agarose and gradually leaches out into the surrounding tissue, its retention time within the gel was sufficiently long to demonstrate the capability to measure intratumoral pO2 with the implantable gel sensors. The sensor's performance was first evaluated in vitro in tissue simulation phantoms, and then the sensor was used to measure changes in oxygen in MDA-MB-231 tumors during hypofractionated radiotherapy., Conclusions: Our study demonstrates that implantable oxygen sensors in combination with CELI present a promising approach for quantifying oxygen changes during the course of radiation therapy and thus for evaluating the tumor response to radiation. By improving the design of the gel-probe composition in order to prevent leaching of the probe into the tissue, biosensors can be created that should allow longitudinal oxygen measurements in tumors by means of CELI while using FDA-compliant microdose levels of the probe and thus lowering toxicity concerns.
- Published
- 2020
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19. Endothermic and Exothermic Energy Transfer Made Equally Efficient for Triplet-Triplet Annihilation Upconversion.
- Author
-
Isokuortti J, Allu SR, Efimov A, Vuorimaa-Laukkanen E, Tkachenko NV, Vinogradov SA, Laaksonen T, and Durandin NA
- Abstract
Expanding the anti-Stokes shift for triplet-triplet annihilation upconversion (TTA-UC) systems with high quantum yields without compromising power density thresholds ( I
th ) remains a critical challenge in photonics. Our studies reveal that such expansion is possible by using a highly endothermic TTA-UC pair with an enthalpy difference of +80 meV even in a polymer matrix 1000 times more viscous than toluene. Carrying out efficient endothermic triplet-triplet energy transfer (TET) requires suppression of the reverse annihilator-to-sensitizer TET, which was achieved by using sensitizers with high molar extinction coefficients and long triplet state lifetimes as well as optimized annihilator concentrations. Under these conditions, the sensitizer-to-annihilator forward TET becomes effectively entropy driven, yielding upconversion quantum yields comparable to those achieved with the exothermic TTA-UC pair but with larger anti-Stokes shifts and even lower Ith , a previously unattained achievement.- Published
- 2020
- Full Text
- View/download PDF
20. A Unified Synthetic Approach to Optically Pure Curvularin-Type Metabolites.
- Author
-
Allu SR, Banne S, Jiang J, Qi N, Guo J, and He Y
- Subjects
- Molecular Structure, Optical Phenomena, Zearalenone chemical synthesis, Zearalenone chemistry, Zearalenone metabolism, Zearalenone analogs & derivatives
- Abstract
A unified and concise approach to the synthesis of nine curvularin-type metabolites and two analogues has been developed with few steps and high yields. Among them, sumalactones A-D were synthesized for the first time. The key steps in this approach included esterification, Friedel-Crafts acylation, and ring-closing metathesis (or cross metathesis).
- Published
- 2019
- Full Text
- View/download PDF
21. Total Syntheses of Anti-HIV Cyclodepsipeptides Aetheramides A and B.
- Author
-
Qi N, Wang Z, Allu SR, Liu Q, Guo J, and He Y
- Subjects
- Anti-HIV Agents chemistry, Anti-HIV Agents pharmacology, Carbon-13 Magnetic Resonance Spectroscopy, Cyclization, Depsipeptides chemistry, Depsipeptides pharmacology, Methylation, Proton Magnetic Resonance Spectroscopy, Spectrometry, Mass, Electrospray Ionization, Anti-HIV Agents chemical synthesis, Depsipeptides chemical synthesis
- Abstract
A concise total synthesis of aetheramide A in an overall yield of 4.7% with a longest linear sequence of 15 steps is described. This synthetic strategy features macrocyclization via an intramolecular trapping of acylketene generated from dioxinone precursor, and stereoselective late-stage methylation of β-ketoamide. Aetheramide B could be synthesized via the ester migration of aetheramide A.
- Published
- 2016
- Full Text
- View/download PDF
22. Insertion of Arynes into P-O Bonds: One-Step Simultaneous Construction of C-P and C-O Bonds.
- Author
-
Qi N, Zhang N, Allu SR, Gao J, Guo J, and He Y
- Abstract
The insertion of arynes into P-O bonds for the preparation of o-hydroxy-substituted arylphosphine oxides, -phosphinates, and -phosphonates is described. This novel reaction leads to the simultaneous formation of C-P and C-O bonds in one step with good yields and regioselectivities under mild and transition-metal-free conditions. The easy follow-up transformations of the resulting o-hydroxyl group extend these reactions to the facile construction of other ortho-substituted arylphosphorus compounds.
- Published
- 2016
- Full Text
- View/download PDF
23. Asymmetric Total Syntheses of Aetheramides and Their Stereoisomers: Stereochemical Assignment of Aetheramides.
- Author
-
Qi N, Allu SR, Wang Z, Liu Q, Guo J, and He Y
- Abstract
The concise total syntheses of the potent HIV inhibitors aetheramides A and B (IC50 values of 15 and 18 nM), as well as three pairs of their stereoisomers, were achieved, which allowed the complete stereochemical assignment of aetheramides for the first time. With a longest linear sequence of 15 steps, the convergent, fully stereocontrolled route provided aetheramides A and B in 5.3% and 3.6% yields, respectively. The synthetic strategy features efficient Stille coupling for macrocyclization, asymmetric aldol reactions to establish the ambiguous stereochemistries at C-17 and C-26, and implementation of mild conditions to avoid the epimerization of the sensitive polyketide moiety and the migration of the labile lactone.
- Published
- 2016
- Full Text
- View/download PDF
24. A platform for the discovery of new macrolide antibiotics.
- Author
-
Seiple IB, Zhang Z, Jakubec P, Langlois-Mercier A, Wright PM, Hog DT, Yabu K, Allu SR, Fukuzaki T, Carlsen PN, Kitamura Y, Zhou X, Condakes ML, Szczypiński FT, Green WD, and Myers AG
- Subjects
- Amino Sugars chemical synthesis, Amino Sugars chemistry, Amino Sugars pharmacology, Anti-Bacterial Agents chemistry, Bacteria drug effects, Humans, Ketolides chemical synthesis, Ketolides chemistry, Macrolides chemistry, Microbial Sensitivity Tests, Molecular Structure, Small Molecule Libraries chemical synthesis, Small Molecule Libraries chemistry, Triazoles chemical synthesis, Triazoles chemistry, Triazoles pharmacology, Anti-Bacterial Agents chemical synthesis, Anti-Bacterial Agents pharmacology, Drug Discovery methods, Macrolides chemical synthesis, Macrolides pharmacology
- Abstract
The chemical modification of structurally complex fermentation products, a process known as semisynthesis, has been an important tool in the discovery and manufacture of antibiotics for the treatment of various infectious diseases. However, many of the therapeutics obtained in this way are no longer effective, because bacterial resistance to these compounds has developed. Here we present a practical, fully synthetic route to macrolide antibiotics by the convergent assembly of simple chemical building blocks, enabling the synthesis of diverse structures not accessible by traditional semisynthetic approaches. More than 300 new macrolide antibiotic candidates, as well as the clinical candidate solithromycin, have been synthesized using our convergent approach. Evaluation of these compounds against a panel of pathogenic bacteria revealed that the majority of these structures had antibiotic activity, some efficacious against strains resistant to macrolides in current use. The chemistry we describe here provides a platform for the discovery of new macrolide antibiotics and may also serve as the basis for their manufacture.
- Published
- 2016
- Full Text
- View/download PDF
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