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  1. Article ; Online: Designing Algorithms To Aid Discovery by Chemical Robots

    Alon B. Henson / Piotr S. Gromski / Leroy Cronin

    ACS Central Science, Vol 4, Iss 7, Pp 793-

    2018  Volume 804

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2018-07-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Discovering New Chemistry with an Autonomous Robotic Platform Driven by a Reactivity-Seeking Neural Network.

    Caramelli, Dario / Granda, Jarosław M / Mehr, S Hessam M / Cambié, Dario / Henson, Alon B / Cronin, Leroy

    ACS central science

    2021  Volume 7, Issue 11, Page(s) 1821–1830

    Abstract: We present a robotic chemical discovery system capable of navigating a chemical space based on a learned general association between molecular structures and reactivity, while incorporating a neural network model that can process data from online ... ...

    Abstract We present a robotic chemical discovery system capable of navigating a chemical space based on a learned general association between molecular structures and reactivity, while incorporating a neural network model that can process data from online analytics and assess reactivity without knowing the identity of the reagents. Working in conjunction with this learned knowledge, our robotic platform is able to autonomously explore a large number of potential reactions and assess the reactivity of mixtures, including unknown chemical spaces, regardless of the identity of the starting materials. Through the system, we identified a range of chemical reactions and products, some of which were well-known, some new but predictable from known pathways, and some unpredictable reactions that yielded new molecules. The validation of the system was done within a budget of 15 inputs combined in 1018 reactions, further analysis of which allowed us to discover not only a new photochemical reaction but also a new reactivity mode for a well-known reagent (
    Language English
    Publishing date 2021-11-11
    Publishing country United States
    Document type Journal Article
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.1c00435
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Designing Algorithms To Aid Discovery by Chemical Robots.

    Henson, Alon B / Gromski, Piotr S / Cronin, Leroy

    ACS central science

    2018  Volume 4, Issue 7, Page(s) 793–804

    Abstract: Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. ... ...

    Abstract Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery.
    Language English
    Publishing date 2018-07-03
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.8b00176
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Discovering New Chemistry with an Autonomous Robotic Platform Driven by a Reactivity-Seeking Neural Network

    Dario Caramelli / Jarosław M. Granda / S. Hessam M. Mehr / Dario Cambié / Alon B. Henson / Leroy Cronin

    ACS Central Science, Vol 7, Iss 11, Pp 1821-

    2021  Volume 1830

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: An autonomous organic reaction search engine for chemical reactivity.

    Dragone, Vincenza / Sans, Victor / Henson, Alon B / Granda, Jaroslaw M / Cronin, Leroy

    Nature communications

    2017  Volume 8, Page(s) 15733

    Abstract: The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical ... ...

    Abstract The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways.
    Language English
    Publishing date 2017-06-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/ncomms15733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An autonomous organic reaction search engine for chemical reactivity

    Vincenza Dragone / Victor Sans / Alon B. Henson / Jaroslaw M. Granda / Leroy Cronin

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Volume 8

    Abstract: While automated reaction systems typically work for the synthesis of pre-defined molecules, automated systems to discover reactivity are more challenging. Here the authors report an autonomous organic reaction search engine that allows discovery of the ... ...

    Abstract While automated reaction systems typically work for the synthesis of pre-defined molecules, automated systems to discover reactivity are more challenging. Here the authors report an autonomous organic reaction search engine that allows discovery of the most reactive pathways in a multi-reagent, multistep reaction system.
    Keywords Science ; Q
    Language English
    Publishing date 2017-06-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Prostate Cancer Cells Are Sensitive to Lysosomotropic Agent Siramesine through Generation Reactive Oxygen Species and in Combination with Tyrosine Kinase Inhibitors.

    Garcia, Emily A / Bhatti, Ilsa / Henson, Elizabeth S / Gibson, Spencer B

    Cancers

    2022  Volume 14, Issue 22

    Abstract: ... family member Mcl-1. Furthermore, lipid peroxidation occurred with siramesine treatment alone or in combination ... siramesine induced cell death alone or in combination with lapatinib. The combination of siramesine and ...

    Abstract Background: Prostate cancer is the most common cancer affecting men often resulting in aggressive tumors with poor prognosis. Even with new treatment strategies, drug resistance often occurs in advanced prostate cancers. The use of lysosomotropic agents offers a new treatment possibility since they disrupt lysosomal membranes and can trigger a series of events leading to cell death. In addition, combining lysosomotropic agents with targeted inhibitors can induce increased cell death in different cancer types, but prostate cancer cells have not been investigated.
    Methods: We treated prostate cancer cells with lysosomotropic agents and determine their cytotoxicity, lysosome membrane permeabilization (LMP), reactive oxygen species (ROS) levels, and mitochondrial dysfunction. In addition, we treated cells with lysosomotropic agent in combination with tyrosine kinase inhibitor, lapatinib, and determined cell death, and the role of ROS in this cell death.
    Results: Herein, we found that siramesine was the most effective lysosomotropic agent at inducing LMP, increasing ROS, and inducing cell death in three different prostate cancer cell lines. Siramesine was also effective at increasing cell death in combination with the tyrosine kinase inhibitor, lapatinib. This increase in cell death was mediated by lysosome membrane permeabilization, an increased in ROS levels, loss of mitochondrial membrane potential and increase in mitochondrial ROS levels. The combination of siramesine and lapatinib induced apoptosis, cleavage of PARP and decreased expression of Bcl-2 family member Mcl-1. Furthermore, lipid peroxidation occurred with siramesine treatment alone or in combination with lapatinib. Treating cells with the lipid peroxidation inhibitor alpha-tocopherol resulted in reduced siramesine induced cell death alone or in combination with lapatinib. The combination of siramesine and lapatinib failed to increase cell death responses in normal prostate epithelial cells.
    Conclusions: This suggests that lysomotropic agents such as siramesine in combination with tyrosine kinase inhibitors induces cell death mediated by ROS and could be an effective treatment strategy in advanced prostate cancer.
    Language English
    Publishing date 2022-11-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers14225478
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Stopping paramagnetic supersonic beams: the advantage of a co-moving magnetic trap decelerator.

    Lavert-Ofir, Etay / David, Liron / Henson, Alon B / Gersten, Sasha / Narevicius, Julia / Narevicius, Edvardas

    Physical chemistry chemical physics : PCCP

    2011  Volume 13, Issue 42, Page(s) 18948–18953

    Abstract: The long standing goal of chemical physics is finding a convenient method to create slow and cold beams intense enough to observe chemical reactions in the temperature range of a few Kelvin. We present an extensive numerical analysis of our moving ... ...

    Abstract The long standing goal of chemical physics is finding a convenient method to create slow and cold beams intense enough to observe chemical reactions in the temperature range of a few Kelvin. We present an extensive numerical analysis of our moving magnetic trap decelerator showing that a 3D confinement throughout the deceleration process enables deceleration of almost all paramagnetic particles within the original supersonic expansion to stopping velocities. We show that the phase space region containing the decelerating species is larger by two orders of magnitude as compared to other available deceleration methods.
    Language English
    Publishing date 2011-11-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c1cp21225g
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Observation of the isotope effect in sub-kelvin reactions.

    Lavert-Ofir, Etay / Shagam, Yuval / Henson, Alon B / Gersten, Sasha / Kłos, Jacek / Zuchowski, Piotr S / Narevicius, Julia / Narevicius, Edvardas

    Nature chemistry

    2014  Volume 6, Issue 4, Page(s) 332–335

    Abstract: Quantum phenomena in the translational motion of reactants, which are usually negligible at room temperature, can dominate reaction dynamics at low temperatures. In such cold conditions, even the weak centrifugal force is enough to create a potential ... ...

    Abstract Quantum phenomena in the translational motion of reactants, which are usually negligible at room temperature, can dominate reaction dynamics at low temperatures. In such cold conditions, even the weak centrifugal force is enough to create a potential barrier that keeps reactants separated. However, reactions may still proceed through tunnelling because, at low temperatures, wave-like properties become important. At certain de Broglie wavelengths, the colliding particles can become trapped in long-lived metastable scattering states, leading to sharp increases in the total reaction rate. Here, we show that these metastable states are responsible for a dramatic, order-of-magnitude-strong, quantum kinetic isotope effect by measuring the absolute Penning ionization reaction rates between hydrogen isotopologues and metastable helium down to 0.01 K. We demonstrate that measurements of a single isotope are insufficient to constrain ab initio calculations, making the kinetic isotope effect in the cold regime necessary to remove ambiguity among possible potential energy surfaces.
    Language English
    Publishing date 2014-02-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2464596-5
    ISSN 1755-4349 ; 1755-4330
    ISSN (online) 1755-4349
    ISSN 1755-4330
    DOI 10.1038/nchem.1857
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Pre-clinical activity of the oral DNA-PK inhibitor, peposertib (M3814), combined with radiation in xenograft models of cervical cancer.

    Gordhandas, Sushmita B / Manning-Geist, Beryl / Henson, Christina / Iyer, Gopa / Gardner, Ginger J / Sonoda, Yukio / Moore, Kathleen N / Aghajanian, Carol / Chui, M Herman / Grisham, Rachel N

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 974

    Abstract: ... into the flank were treated with vehicle alone (n = 3), IR alone (n = 4), and peposertib (M38814) in combination ... with IR (M3814 + IR; n = 4). While IR alone was associated with a trend towards decreased tumor volume ...

    Abstract DNA-dependent protein kinase (DNA-PK) plays a crucial role in repair of DNA double-strand breaks by facilitating non-homologous end-joining. Inhibitors of DNA-PK have the potential to block DNA repair and enhance DNA-damaging agents. Peposertib (M3814) is a DNA-PK inhibitor that has shown preclinical activity in combination with DNA-damaging agents, including ionizing radiation (IR) and topoisomerase II inhibitors. Here we evaluated the activity of peposertib (M3814) in combination with radiation in a mouse xenograft model of HPV-associated cervical cancer. Athymic nude female mice with established tumors derived from HeLa cells injected into the flank were treated with vehicle alone (n = 3), IR alone (n = 4), and peposertib (M38814) in combination with IR (M3814 + IR; n = 4). While IR alone was associated with a trend towards decreased tumor volume compared with untreated, only the M3814 + IR treatment arm was associated with consistent and significant reduction in tumor burden, which correlated with higher levels of γ-H2AX in tumor cells, a marker of double-strand DNA breaks. Our data support further clinical evaluation of the combination of peposertib (M38814) and IR in cervical cancer.
    MeSH term(s) Animals ; Chemoradiotherapy ; DNA-Activated Protein Kinase/antagonists & inhibitors ; Female ; HeLa Cells ; Humans ; Mice ; Pyridazines/pharmacology ; Pyridazines/therapeutic use ; Quinazolines/pharmacology ; Quinazolines/therapeutic use ; Uterine Cervical Neoplasms/drug therapy ; Uterine Cervical Neoplasms/radiotherapy ; Xenograft Model Antitumor Assays
    Chemical Substances Pyridazines ; Quinazolines ; DNA-Activated Protein Kinase (EC 2.7.11.1) ; peposertib (GN429E725A)
    Language English
    Publishing date 2022-01-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-04618-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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