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COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning

, Hagit Achdout, Anthony Aimon, Elad Bar-David, Haim Barr, Amir Ben-Shmuel, James Bennett, Melissa Bobby, Juliane Brun, BVNBS Sarma, Mark Calmiano, Anna Carbery, Emma Cattermole, John Chodera, Austin Clyde, Joseph Coffland, Galit Cohen, Jason Cole, Alessandro Contini, Lisa Cox, Milan Cvitkovic, Alex Dias, Alice Douangamath, Shirly Duberstein, Tim Dudgeon, Louise Dunnett, Peter Eastman, Noam Erez, Michael Fairhead, Daren Fearon, Oleg Fedorov, Matteo Ferla, Holly Foster, Richard Foster, Ronen Gabizon, Paul Gehrtz, Carina Gileadi, Charline Giroud, William Glass, Robert Glen, Itai Glinert, Marian Gorichko, Tyler Gorrie-Stone, Edward Griffen, Jag Heer, Michelle Hill, Sam Horrell, Matthew F.D. Hurley, Tomer Israely, Andrew Jajack, Eric Jnoff, Tobias John, Anastassia Kantsadi, Peter Kenny, John Kiappes, Lizbe Koekemoer, Boris Kovar, Tobias Krojer, Alpha Albert Lee, Bruce Lefker, Haim Levy, Nir London, Petra Lukacik, Hannah Bruce Macdonald, Beth MacLean, Tika Malla, Tatiana Matviiuk, Willam McCorkindale, Sharon Melamed, Oleg Michurin, Halina Mikolajek, Aaron Morris, Garrett Morris, Melody Jane Morwitzer, Demetri Moustakas, Jose Brandao Neto, Vladas Oleinikovas, Gijs Overheul, David Owen, Ruby Pai, Jin Pan, Nir Paran, Benjamin Perry, Maneesh Pingle, Jakir Pinjari, Boaz Politi, Ailsa Powell, Vladimir Psenak, Reut Puni, Victor Rangel, Rambabu Reddi, St Patrick Reid, Efrat Resnick, Matthew Robinson, Ralph Robinson, Dominic Rufa, Christopher Schofield, Aarif Shaikh, Jiye Shi, Khriesto Shurrush, Assa Sittner, Rachael Skyner, Adam Smalley, Mihaela Smilova, John Spencer, Claire Strain-Damerell, Vishwanath Swamy, Hadas Tamir, Rachael Tennant, Andrew Thompson, Warren Thompson, Susana Tomasio, Anthony Tumber, Ioannis Vakonakis, Ronald van Rij, Finny Varghese, Mariana Vaschetto, Einat Vitner, Vincent Voelz, Annette von Delft, Frank von Delft, Martin Walsh, Walter Ward, Charlie Weatherall, Shay Weiss, Conor Francis Wild, Matthew Wittmann, Nathan Wright, Yfat Yahalom-Ronen, Daniel Zaidmann, Hadeer Zidane, Nicole Zitzmann,

Abstract Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. Our approach uniquely combines crowdsourced medicinal chemistry insights with high throughput crystallography, exascale computational chemistry infrastructure for simulations, and machine learning in triaging designs ... Read more >>

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Hippocampal plasticity may drive cocaine relapse.

Vanessa E Lehmann, Paul J Kenny,

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2020, :]

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SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations

Craig Richmond, Arick Sabin, Dean Jobe, Steven Lovrich, Paraic Kenny,

ABSTRACT College reopening decisions during the SARS-CoV-2 pandemic represent a trade-off between competing risks to students, faculty and staff, and college finances. Additionally, risks taken in reopening colleges can impose significant burdens on individuals living in surrounding communities. Many colleges that reopened for in-person instruction have reported frequent SARS-CoV-2 outbreaks. ... Read more >>

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Assessing the Attitudes, Awareness, and Behavioral Alterations of Patients Awaiting Total Hip Arthroplasty During the COVID-19 Crisis.

Stephen Fahy, Joss Moore, Michael Kelly, Shane Irwin, Paddy Kenny,

Background:COVID-19 has placed a huge burden on healthcare systems which has led to widespread cancellation elective surgical care. Ireland is recovering from the first wave of COVID-19 and as such the expeditious return of elective surgical care is important. This is the first study to examine the attitudes of patients ... Read more >>

Geriatr Orthop Surg Rehabil (Geriatric orthopaedic surgery & rehabilitation)
[2020, 11:2151459320969377]

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Negative feedback control of neuronal activity by microglia.

Ana Badimon, Hayley J Strasburger, Pinar Ayata, Xinhong Chen, Aditya Nair, Ako Ikegami, Philip Hwang, Andrew T Chan, Steven M Graves, Joseph O Uweru, Carola Ledderose, Munir Gunes Kutlu, Michael A Wheeler, Anat Kahan, Masago Ishikawa, Ying-Chih Wang, Yong-Hwee E Loh, Jean X Jiang, D James Surmeier, Simon C Robson, Wolfgang G Junger, Robert Sebra, Erin S Calipari, Paul J Kenny, Ukpong B Eyo, Marco Colonna, Francisco J Quintana, Hiroaki Wake, Viviana Gradinaru, Anne Schaefer,

Microglia, the brain's resident macrophages, help to regulate brain function by removing dying neurons, pruning non-functional synapses, and producing ligands that support neuronal survival1. Here we show that microglia are also critical modulators of neuronal activity and associated behavioural responses in mice. Microglia respond to neuronal activation by suppressing neuronal ... Read more >>

Nature (Nature)
[2020, 586(7829):417-423]

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Evaluation of optimised 3D turbo spin echo and gradient echo MR pulse sequences of the knee at 3T and 1.5T.

O M Abdulaal, L Rainford, P J MacMahon, P Kenny, F Carty, M Galligan, A Cradock, F H Alhazmi, A McGee,

INTRODUCTION:To investigate the impact of parameter optimisation for novel three-dimensional 3D sequences at 1.5T and 3T on resultant image quality. METHODS:Following institutional review board approval and acquisition of informed consent, MR phantom and knee joint imaging on healthy volunteers (n = 16) was performed with 1.5 and 3T MRI scanners, respectively incorporating ... Read more >>

Radiography (Lond) (Radiography (London, England : 1995))
[2020, :]

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Habenular TCF7L2 links nicotine addiction to diabetes: the broad significance.

Stephanie P B Caligiuri, Paul J Kenny,

Neuropsychopharmacology (Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology)
[2020, :]

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Crystal structure of Leishmania mexicana cysteine protease B in complex with a high-affinity azadipeptide nitrile inhibitor.

Jean F R Ribeiro, Lorenzo Cianni, Chan Li, Thomas G Warwick, Daniela de Vita, Fabiana Rosini, Fernanda Dos Reis Rocho, Felipe C P Martins, Peter W Kenny, Jeronimo Lameira, Andrei Leitão, Jonas Emsley, Carlos A Montanari,

Leishmania mexicana is an obligate intracellular protozoan parasite that causes the cutaneous form of leishmaniasis affecting South America and Mexico. The cysteine protease LmCPB is essential for the virulence of the parasite and therefore, it is an appealing target for antiparasitic therapy. A library of nitrile-based cysteine protease inhibitors was ... Read more >>

Bioorg Med Chem (Bioorganic & medicinal chemistry)
[2020, 28(22):115743]

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The Persistent Challenge of Developing Addiction Pharmacotherapies.

Sarah E Swinford-Jackson, Charles P O'Brien, Paul J Kenny, Louk J M J Vanderschuren, Ellen M Unterwald, R Christopher Pierce,

There are currently effective Food and Drug Administration (FDA)-approved therapies for alcohol, nicotine, and opioid use disorders. This article will review the development of eight compounds used in the treatment of drug addiction with an emphasis on pharmacological mechanisms and the utility of preclinical animal models of addiction in therapeutic ... Read more >>

Cold Spring Harb Perspect Med (Cold Spring Harbor perspectives in medicine)
[2020, :]

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Air Quality and Its Association with Cardiovascular and Respiratory Hospital Admissions in Ireland.

K I Quintyne, A Sheridan, P Kenny, M O'Dwyer,

Aim Cardiovascular (CVD) and respiratory (RSD) diseases are leading causes of morbidity and mortality in Ireland. Clear links have been demonstrated in the literature between poor air quality and these diseases. This study aimed to use routinely available data to examine the relationship between air quality index for health (AQIH) ... Read more >>

Ir Med J (Irish medical journal)
[2020, 113(6):92]

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Prelimbic-amygdala overexcitability mediates trait vulnerability in a novel mouse model of acute social defeat stress

Yael Grossman, Clementine Fillinger, Alessia Manganaro, George Voren, Rachel Waldman, Tiffany Zou, William Janssen, Paul Kenny, Dani Dumitriu,

BACKGROUND Depression is a debilitating neuropsychiatric disorder with 20% lifetime prevalence in the developed world but only approximately half of afflicted individuals respond to currently available therapies. While there is growing understanding of the neurobiological underpinnings of the depressed brain, much less is known about the preexisting circuitry leading to ... Read more >>

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Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa

Craig Richmond, Arick Sabin, Dean Jobe, Steven Lovrich, Paraic Kenny,

SARS-CoV-2 spread has proven to be especially difficult to mitigate in high risk settings, including nursing homes, cruises, prisons and various industrial settings. Among industrial settings, meat processing facilities in the United States have experienced particularly challenging outbreaks. We have sequenced SARS-CoV-2 whole viral genomes from individuals testing positive in ... Read more >>

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Musculoskeletal Infection in Orthopaedic Trauma: Assessment of the 2018 International Consensus Meeting on Musculoskeletal Infection.

William T Obremskey, Willem-Jan Metsemakers, Daniel R Schlatterer, Kevin Tetsworth, Kenneth Egol, Stephen Kates, Martin McNally, ,

Fracture-related infections (FRIs) are among the most common complications following fracture fixation, and they have a huge economic and functional impact on patients. Because consensus guidelines with respect to prevention, diagnosis, and treatment of this major complication are scarce, delegates from different countries gathered in Philadelphia in July 2018 as ... Read more >>

J Bone Joint Surg Am (The Journal of bone and joint surgery. American volume)
[2020, 102(10):e44]

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Mechanisms of Nicotine Addiction.

Marina R Picciotto, Paul J Kenny,

Tobacco smoking results in more than five million deaths each year and accounts for ∼90% of all deaths from lung cancer. 3 Nicotine, the major reinforcing component of tobacco smoke, acts in the brain through the neuronal nicotinic acetylcholine receptors (nAChRs). The nAChRs are allosterically regulated, ligand-gated ion channels consisting ... Read more >>

Cold Spring Harb Perspect Med (Cold Spring Harbor perspectives in medicine)
[2020, :]

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Current concepts and outcomes in cemented femoral stem design and cementation techniques: the argument for a new classification system.

Adrian J Cassar-Gheiti, Rosie McColgan, Martin Kelly, Theresa M Cassar-Gheiti, Paddy Kenny, Colin G Murphy,

Cemented implant fixation design principles have evolved since the 1950s, and various femoral stem designs are currently in use to provide a stable construct between the implant-cement and cement-bone interfaces.Cemented stems have classically been classified into two broad categories: taper slip or force closed, and composite beams or shaped closed ... Read more >>

EFORT Open Rev (EFORT open reviews)
[2020, 5(4):241-252]

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Dopaminylation of histone H3 in ventral tegmental area regulates cocaine seeking.

Ashley E Lepack, Craig T Werner, Andrew F Stewart, Sasha L Fulton, Ping Zhong, Lorna A Farrelly, Alexander C W Smith, Aarthi Ramakrishnan, Yang Lyu, Ryan M Bastle, Jennifer A Martin, Swarup Mitra, Richard M O'Connor, Zi-Jun Wang, Henrik Molina, Gustavo Turecki, Li Shen, Zhen Yan, Erin S Calipari, David M Dietz, Paul J Kenny, Ian Maze,

Vulnerability to relapse during periods of attempted abstinence from cocaine use is hypothesized to result from the rewiring of brain reward circuitries, particularly ventral tegmental area (VTA) dopamine neurons. How cocaine exposures act on midbrain dopamine neurons to precipitate addiction-relevant changes in gene expression is unclear. We found that histone ... Read more >>

Science (Science (New York, N.Y.))
[2020, 368(6487):197-201]

Cited: 2 times

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Acquisition of Cabozantinib-Sensitive MET D1228N Mutation During Progression on Crizotinib in MET-Amplified Triple-Negative Breast Cancer.

Benjamin M Parsons, David R Meier, Craig S Richmond, Grzegorz T Gurda, Kristopher A Lofgren, Mark E Burkard, Dustin A Deming, Paraic A Kenny,

BACKGROUND:Targeting of somatic MET mutations using crizotinib has led to strong clinical responses, most frequently in patients with lung cancer, raising the possibility of adopting similar treatment strategies in patients with MET alterations in other cancer types. PATIENT AND METHODS:We describe a patient with advanced triple-negative breast cancer with a ... Read more >>

Clin Breast Cancer (Clinical breast cancer)
[2020, 20(4):e433-e438]

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A novel quantitative measure of image quality in fluoroscopy.

Patrick Kenny, David Costello, Dean McCarthy, Emer Kenny,

Assessment of fluoroscopic image quality has not kept pace with technological developments in interventional imaging equipment. Access to 'for presentation' data on these systems has motivated this investigation into a novel quantitative method of measuring image quality. We have developed a statistical algorithm as an alternative to subjective assessment using ... Read more >>

Phys Med (Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB))
[2020, 71:150-160]

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Bypass: an integrated hip fracture care pathway.

Nicholas O'Keeffe, Martin Kelly, Ara Francis, Jacinta Shields, Peter Keogh, Paddy Kenny,

BACKGROUND:The incidence of hip fractures is expected to increase over the coming years, placing a greater burden on limited resources. A high volume of patients is brought to hospitals that do not have the resources necessary to provide definitive care. Optimal care involves a coordinated and integrated system of trauma ... Read more >>

Ir J Med Sci (Irish journal of medical science)
[2020, 189(4):1159-1162]

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Amphiregulin deletion strongly attenuates the development of estrogen receptor-positive tumors in p53 mutant mice.

David R Meier, Megan A Girtman, Kristopher A Lofgren, Paraic A Kenny,

PURPOSE:The epidermal growth factor receptor ligand, Amphiregulin, is a transcriptional target of estrogen receptor alpha and is required for pubertal mammary gland development. Previous studies using immortalized human breast cancer cell line xenografts have suggested that Amphiregulin may be an important effector of estrogen receptor alpha during breast cancer development, ... Read more >>

Breast Cancer Res Treat (Breast cancer research and treatment)
[2020, 179(3):653-660]

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Transcriptional mechanisms of drug addiction
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Purva Bali, Paul J Kenny,

Drugs of abuse can modify gene expression in brain reward and motivation centers, which contribute to the structural and functional remodeling of these circuits that impacts the emergence of a state of addiction. Our understanding of how addictive drugs induce transcriptomic plasticity in addiction-relevant brain regions, particularly in the striatum, ... Read more >>

Dialogues Clin Neurosci (Dialogues in clinical neuroscience)
[2019, 21(4):379-387]

Cited: 1 time

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Connolly Hospital Trauma Assessment Clinic (TAC): a virtual solution to patient flow.

Martin Kelly, Nicholas O'Keeffe, Ara Francis, Conor Moran, Karen Gantley, Fintan Doyle, Paddy Kenny,

BACKGROUND:Trauma Assessment Clinics (TAC) were pioneered by the Glasgow Royal Infirmary Group. Patients deemed for non-operative management are referred to the TAC for review by an orthopaedic consultant with multidisciplinary team (MDT) support. Connolly Hospital launched a TAC on 11 September 2018. AIMS:The goal of this study was to evaluate ... Read more >>

Ir J Med Sci (Irish journal of medical science)
[2020, 189(2):425-429]

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Habenular TCF7L2 links nicotine addiction to diabetes.

Alexander Duncan, Mary P Heyer, Masago Ishikawa, Stephanie P B Caligiuri, Xin-An Liu, Zuxin Chen, Maria Vittoria Micioni Di Bonaventura, Karim S Elayouby, Jessica L Ables, William M Howe, Purva Bali, Clementine Fillinger, Maya Williams, Richard M O'Connor, Zichen Wang, Qun Lu, Theodore M Kamenecka, Avi Ma'ayan, Heidi C O'Neill, Ines Ibanez-Tallon, Aron M Geurts, Paul J Kenny,

Diabetes is far more prevalent in smokers than non-smokers, but the underlying mechanisms of vulnerability are unknown. Here we show that the diabetes-associated gene Tcf7l2 is densely expressed in the medial habenula (mHb) region of the rodent brain, where it regulates the function of nicotinic acetylcholine receptors. Inhibition of TCF7L2 ... Read more >>

Nature (Nature)
[2019, 574(7778):372-377]

Cited: 6 times

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InferAMP, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports

Paraic Kenny,

As somatic next-generation sequencing gene panel analysis in advanced cancer patients is becoming more routine, oncologists are frequently presented with reports containing lists of genes with increased copy number. Distinguishing which of these amplified genes, if any, might be driving tumor growth and might thus be worth considering targeting can ... Read more >>

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Synthesis and structure-activity relationship of nitrile-based cruzain inhibitors incorporating a trifluoroethylamine-based P2 amide replacement.

Juliana C Gomes, Lorenzo Cianni, Jean Ribeiro, Fernanda Dos Reis Rocho, Samelyn da Costa Martins Silva, Pedro Henrique Jatai Batista, Carolina Borsoi Moraes, Caio Haddad Franco, Lucio H G Freitas-Junior, Peter W Kenny, Andrei Leitão, Antonio C B Burtoloso, Daniela de Vita, Carlos A Montanari,

The structure-activity relationship for nitrile-based cruzain inhibitors incorporating a P2 amide replacement based on trifluoroethylamine was explored by deconstruction of a published series of inhibitors. It was demonstrated that the P3 biphenyl substituent present in the published inhibitor structures could be truncated to phenyl with only a small loss of ... Read more >>

Bioorg. Med. Chem. (Bioorganic & medicinal chemistry)
[2019, 27(22):115083]

Cited: 1 time

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