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Article ; Online: A Plasmodium falciparum RING Finger E3 Ubiquitin Ligase Modifies the Roles of PfMDR1 and PfCRT in Parasite Drug Responses.

Singh, Brajesh K / Zhang, Cui / Wu, Jian / Peng, Yu-Chih / He, Xiao / Tumas, Keyla C / Sá, Juliana M / Lane, Kristin D / Eastman, Richard T / Narum, David L / Wellems, Thomas E / Su, Xin-Zhuan

Antimicrobial agents and chemotherapy

2023 Volume 67, Issue 2, Page(s) e0082122

Abstract: Protein ubiquitination is an important posttranslational regulation mechanism that ... ...

Abstract	Protein ubiquitination is an important posttranslational regulation mechanism that mediates
MeSH term(s)	Humans ; Antimalarials/pharmacology ; Chloroquine/pharmacology ; Drug Resistance/genetics ; Malaria, Falciparum/drug therapy ; Membrane Transport Proteins/genetics ; Multidrug Resistance-Associated Proteins/genetics ; Plasmodium falciparum/drug effects ; Plasmodium falciparum/genetics ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
Chemical Substances	Antimalarials ; Chloroquine (886U3H6UFF) ; Membrane Transport Proteins ; Multidrug Resistance-Associated Proteins ; Protozoan Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-01-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/aac.00821-22
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Article ; Online: Novel Transmission-Blocking Antimalarials Identified by High-Throughput Screening of Plasmodium berghei Ookluc.

Calit, Juliana / Araújo, Jessica E / Deng, Bingbing / Miura, Kazutoyo / Gaitán, Xiomara A / Araújo, Maisa da Silva / Medeiros, Jansen F / Long, Carole A / Simeonov, Anton / Eastman, Richard T / Bargieri, Daniel Y

Antimicrobial agents and chemotherapy

2023 Volume 67, Issue 4, Page(s) e0146522

Abstract: Safe and effective malaria transmission-blocking chemotherapeutics would allow a community-level approach to malaria control and eradication efforts by targeting the mosquito sexual stage of the parasite life cycle. However, only a single drug, ... ...

Abstract	Safe and effective malaria transmission-blocking chemotherapeutics would allow a community-level approach to malaria control and eradication efforts by targeting the mosquito sexual stage of the parasite life cycle. However, only a single drug, primaquine, is currently approved for use in reducing transmission, and drug toxicity limits its widespread implementation. To address this limitation in antimalarial chemotherapeutics, we used a recently developed transgenic Plasmodium berghei line, Ookluc, to perform a series of high-throughput
MeSH term(s)	Animals ; Humans ; Antimalarials/pharmacology ; Antimalarials/therapeutic use ; Plasmodium berghei ; High-Throughput Screening Assays ; Malaria/prevention & control ; Primaquine/therapeutic use ; Plasmodium falciparum ; Malaria, Vivax/drug therapy ; Culicidae ; Malaria, Falciparum/drug therapy
Chemical Substances	Antimalarials ; Primaquine (MVR3634GX1)
Language	English
Publishing date	2023-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/aac.01465-22
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Article ; Online: Small molecule antiviral compound collection (SMACC): A comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules.

Martin, Holli-Joi / Melo-Filho, Cleber C / Korn, Daniel / Eastman, Richard T / Rai, Ganesha / Simeonov, Anton / Zakharov, Alexey V / Muratov, Eugene / Tropsha, Alexander

Antiviral research

2023 Volume 217, Page(s) 105620

Abstract: Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential ... ...

Abstract	Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential threat to global human health. By identifying and solving several challenges related to data annotation accuracy, we developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic and target-based assays for these viruses that we dubbed SMACC (Small Molecule Antiviral Compound Collection). The pilot version of the SMACC database contains over 32,500 entries for 13 viruses. By analyzing data in SMACC, we have identified ∼50 compounds with polyviral inhibition profile, mostly covering flavi- and coronaviruses. The SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks. SMACC is publicly available at https://smacc.mml.unc.edu.
MeSH term(s)	Humans ; Antiviral Agents/pharmacology ; Viruses/genetics ; Databases, Factual ; Coronavirus Infections
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2023-05-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2023.105620
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Article ; Online: A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria.

KalantarMotamedi, Yasaman / Eastman, Richard T / Guha, Rajarshi / Bender, Andreas

Malaria journal

2018 Volume 17, Issue 1, Page(s) 160

Abstract: Background: Nearly half of the world's population (3.2 billion people) were at risk of malaria in 2015, and resistance to current therapies is a major concern. While the standard of care includes drug combinations, there is a pressing need to identify ... ...

Abstract	Background: Nearly half of the world's population (3.2 billion people) were at risk of malaria in 2015, and resistance to current therapies is a major concern. While the standard of care includes drug combinations, there is a pressing need to identify new combinations that can bypass current resistance mechanisms. In the work presented here, a combined transcriptional drug repositioning/discovery and machine learning approach is proposed. Methods: The integrated approach utilizes gene expression data from patient-derived samples, in combination with large-scale anti-malarial combination screening data, to predict synergistic compound combinations for three Plasmodium falciparum strains (3D7, DD2 and HB3). Both single compounds and combinations predicted to be active were prospectively tested in experiment. Results: One of the predicted single agents, apicidin, was active with the AC50 values of 74.9, 84.1 and 74.9 nM in 3D7, DD2 and HB3 P. falciparum strains while its maximal safe plasma concentration in human is 547.6 ± 136.6 nM. Apicidin at the safe dose of 500 nM kills on average 97% of the parasite. The synergy prediction algorithm exhibited overall precision and recall of 83.5 and 65.1% for mild-to-strong, 48.8 and 75.5% for moderate-to-strong and 12.0 and 62.7% for strong synergies. Some of the prospectively predicted combinations, such as tacrolimus-hydroxyzine and raloxifene-thioridazine, exhibited significant synergy across the three P. falciparum strains included in the study. Conclusions: Systematic approaches can play an important role in accelerating discovering novel combinational therapies for malaria as it enables selecting novel synergistic compound pairs in a more informed and cost-effective manner.
MeSH term(s)	Antimalarials/pharmacology ; Antimalarials/therapeutic use ; Drug Combinations ; Drug Discovery ; Drug Repositioning ; Drug Synergism ; Humans ; Machine Learning ; Malaria, Falciparum/drug therapy ; Malaria, Falciparum/prevention & control ; Plasmodium falciparum/drug effects ; Plasmodium falciparum/genetics ; Protozoan Proteins/genetics ; Protozoan Proteins/metabolism
Chemical Substances	Antimalarials ; Drug Combinations ; Protozoan Proteins
Language	English
Publishing date	2018-04-11
Publishing country	England
Document type	Journal Article
ISSN	1475-2875
ISSN (online)	1475-2875
DOI	10.1186/s12936-018-2294-5
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Article ; Online: Deep learning identifies synergistic drug combinations for treating COVID-19.

Jin, Wengong / Stokes, Jonathan M / Eastman, Richard T / Itkin, Zina / Zakharov, Alexey V / Collins, James J / Jaakkola, Tommi S / Barzilay, Regina

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 39

Abstract: Effective treatments for COVID-19 are urgently needed. However, discovering single-agent therapies with activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been challenging. Combination therapies play an important role in ... ...

Abstract	Effective treatments for COVID-19 are urgently needed. However, discovering single-agent therapies with activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been challenging. Combination therapies play an important role in antiviral therapies, due to their improved efficacy and reduced toxicity. Recent approaches have applied deep learning to identify synergistic drug combinations for diseases with vast preexisting datasets, but these are not applicable to new diseases with limited combination data, such as COVID-19. Given that drug synergy often occurs through inhibition of discrete biological targets, here we propose a neural network architecture that jointly learns drug-target interaction and drug-drug synergy. The model consists of two parts: a drug-target interaction module and a target-disease association module. This design enables the model to utilize drug-target interaction data and single-agent antiviral activity data, in addition to available drug-drug combination datasets, which may be small in nature. By incorporating additional biological information, our model performs significantly better in synergy prediction accuracy than previous methods with limited drug combination training data. We empirically validated our model predictions and discovered two drug combinations, remdesivir and reserpine as well as remdesivir and IQ-1S, which display strong antiviral SARS-CoV-2 synergy in vitro. Our approach, which was applied here to address the urgent threat of COVID-19, can be readily extended to other diseases for which a dearth of chemical-chemical combination data exists.
MeSH term(s)	Adenosine Monophosphate/analogs & derivatives ; Alanine/analogs & derivatives ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Cell Survival/drug effects ; Deep Learning ; Drug Combinations ; Drug Interactions ; Drug Synergism ; Humans ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Drug Combinations ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2021-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2105070118
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Article: Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2

Eastman, Richard T / Rusinova, Radda / Herold, Karl F / Huang, Xi-Ping / Dranchak, Patricia / Voss, Ty C / Rana, Sandeep / Shrimp, Jonathan H / White, Alex D / Hemmings, Hugh C / Roth, Bryan L / Inglese, James / Andersen, Olaf S / Dahlin, Jayme L

bioRxiv : the preprint server for biology

2023

Abstract: Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the ... ...

Abstract	Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in
Language	English
Publishing date	2023-10-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.23.563088
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Article ; Online: Quantitative Bioactivity Signatures of Dietary Supplements and Natural Products.

Yasgar, Adam / Bougie, Danielle / Eastman, Richard T / Huang, Ruili / Itkin, Misha / Kouznetsova, Jennifer / Lynch, Caitlin / McKnight, Crystal / Miller, Mitch / Ngan, Deborah K / Peryea, Tyler / Shah, Pranav / Shinn, Paul / Xia, Menghang / Xu, Xin / Zakharov, Alexey V / Simeonov, Anton

ACS pharmacology & translational science

2023 Volume 6, Issue 5, Page(s) 683–701

Abstract: Dietary supplements and natural products are often marketed as safe and effective alternatives to conventional drugs, but their safety and efficacy are not well regulated. To address the lack of scientific data in these areas, we assembled a collection ... ...

Abstract	Dietary supplements and natural products are often marketed as safe and effective alternatives to conventional drugs, but their safety and efficacy are not well regulated. To address the lack of scientific data in these areas, we assembled a collection of Dietary Supplements and Natural Products (DSNP), as well as Traditional Chinese Medicinal (TCM) plant extracts. These collections were then profiled in a series of
Language	English
Publishing date	2023-04-14
Publishing country	United States
Document type	Journal Article
ISSN	2575-9108
ISSN (online)	2575-9108
DOI	10.1021/acsptsci.2c00194
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Article ; Online: A platform of assays for the discovery of anti-Zika small-molecules with activity in a 3D-bioprinted outer-blood-retina model.

Dorjsuren, Dorjbal / Eastman, Richard T / Song, Min Jae / Yasgar, Adam / Chen, Yuchi / Bharti, Kapil / Zakharov, Alexey V / Jadhav, Ajit / Ferrer, Marc / Shi, Pei-Yong / Simeonov, Anton

PloS one

2022 Volume 17, Issue 1, Page(s) e0261821

Abstract: The global health emergency posed by the outbreak of Zika virus (ZIKV), an arthropod-borne flavivirus causing severe neonatal neurological conditions, has subsided, but there continues to be transmission of ZIKV in endemic regions. As such, there is ... ...

Abstract	The global health emergency posed by the outbreak of Zika virus (ZIKV), an arthropod-borne flavivirus causing severe neonatal neurological conditions, has subsided, but there continues to be transmission of ZIKV in endemic regions. As such, there is still a medical need for discovering and developing therapeutical interventions against ZIKV. To identify small-molecule compounds that inhibit ZIKV disease and transmission, we screened multiple small-molecule collections, mostly derived from natural products, for their ability to inhibit wild-type ZIKV. As a primary high-throughput screen, we used a viral cytopathic effect (CPE) inhibition assay conducted in Vero cells that was optimized and miniaturized to a 1536-well format. Suitably active compounds identified from the primary screen were tested in a panel of orthogonal assays using recombinant Zika viruses, including a ZIKV Renilla luciferase reporter assay and a ZIKV mCherry reporter system. Compounds that were active in the wild-type ZIKV inhibition and ZIKV reporter assays were further evaluated for their inhibitory effects against other flaviviruses. Lastly, we demonstrated that wild-type ZIKV is able to infect a 3D-bioprinted outer-blood-retina barrier tissue model and disrupt its barrier function, as measured by electrical resistance. One of the identified compounds (3-Acetyl-13-deoxyphomenone, NCGC00380955) was able to prevent the pathological effects of the viral infection on this clinically relevant ZIKV infection model.
MeSH term(s)	Animals ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Chlorocebus aethiops ; Drug Evaluation, Preclinical ; Hep G2 Cells ; Humans ; Models, Biological ; Printing, Three-Dimensional ; Retina/metabolism ; Retina/virology ; Vero Cells ; Virus Replication/drug effects ; Virus Replication/genetics ; Zika Virus/physiology ; Zika Virus Infection/drug therapy ; Zika Virus Infection/genetics ; Zika Virus Infection/metabolism
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2022-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0261821
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Article: Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules.

Martin, Holli-Joi / Melo-Filho, Cleber C / Korn, Daniel / Eastman, Richard T / Rai, Ganesha / Simeonov, Anton / Zakharov, Alexey V / Muratov, Eugene / Tropsha, Alexander

bioRxiv : the preprint server for biology

2022

Abstract: Diseases caused by new viruses costs thousands if not millions of human lives and trillions of dollars in damage to the global economy. Despite the rapid development of vaccines for SARS-CoV-2, the lack of small molecule antiviral drugs that work against ...

Abstract	Diseases caused by new viruses costs thousands if not millions of human lives and trillions of dollars in damage to the global economy. Despite the rapid development of vaccines for SARS-CoV-2, the lack of small molecule antiviral drugs that work against multiple viral families (broad-spectrum antivirals; BSAs) has left the entire worldâ€™s human population vulnerable to the infection between the beginning of the outbreak and the widespread availability of vaccines. Developing BSAs is an attractive, yet challenging, approach that could prevent the next, inevitable, viral outbreak from becoming a global catastrophe. To explore whether historical medicinal chemistry efforts suggest the possibility of discovering novel BSAs, we (i) identified, collected, curated, and integrated all chemical bioactivity data available in ChEMBL for molecules tested in respective assays for 13 emerging viruses that, based on published literature, hold the greatest potential threat to global human health; (ii) identified and solved the challenges related to data annotation accuracy including assay description ambiguity, missing cell or target information, and incorrect BioAssay Ontology (BAO) annotations; (iii) developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic (21,392 entries) and target-based (11,123 entries) assays for these viruses; and (iv) identified a subset of compounds showing BSA activity. For the latter task, we eliminated inconclusive and annotated duplicative entries by checking the concordance between multiple assay results and identified eight compounds active against 3-4 viruses from the phenotypic data, 16 compounds active against two viruses from the target-based data, and 35 compounds active in at least one phenotypic and one target-based assay. The pilot version of our SMACC (Small Molecule Antiviral Compound Collection) database contains over 32,500 entries for 13 viruses. Our analysis indicates that previous research yielded very small number of BSA compounds. We posit that focused and coordinated efforts strategically targeting the discovery of such agents must be established and maintained going forward. The SMACC database publicly available at https://smacc.mml.unc.edu may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks.
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.07.09.499397
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Article: Targeting ACE2-RBD interaction as a platform for COVID19 therapeutics: Development and drug repurposing screen of an AlphaLISA proximity assay.

Hanson, Quinlin M / Wilson, Kelli M / Shen, Min / Itkin, Zina / Eastman, Richard T / Shinn, Paul / Hall, Matthew D

bioRxiv : the preprint server for biology

2020

Abstract: The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor ... ...

Abstract	The COVID-19 pandemic, caused by SARS-CoV-2, is a pressing public health emergency garnering rapid response from scientists across the globe. Host cell invasion is initiated through direct binding of the viral spike protein to the host receptor angiotensin-converting enzyme 2 (ACE2). Disrupting the spike-ACE2 interaction is a potential therapeutic target for treating COVID-19. We have developed a proximity-based AlphaLISA assay to measure binding of SARS-CoV-2 spike protein Receptor Binding Domain (RBD) to ACE2. Utilizing this assay platform, a drug-repurposing screen against 3,384 small molecule drugs and pre-clinical compounds was performed, yielding 25 high-quality, small-molecule hits that can be evaluated in cell-based models. This established AlphaLISA RBD-ACE2 platform can facilitate evaluation of biologics or small molecules that can perturb this essential viral-host interaction to further the development of interventions to address the global health pandemic.
Keywords	covid19
Language	English
Publishing date	2020-06-16
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.06.16.154708
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