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  1. Article ; Online: Cascading from SARS-CoV-2 to Parkinson's Disease through Protein-Protein Interactions.

    Estrada, Ernesto

    Viruses

    2021  Volume 13, Issue 5

    Abstract: Extensive extrapulmonary damages in a dozen of organs/systems, including the central nervous system (CNS), are reported in patients of the coronavirus disease 2019 (COVID-19). Three cases of Parkinson's disease (PD) have been reported as a direct ... ...

    Abstract Extensive extrapulmonary damages in a dozen of organs/systems, including the central nervous system (CNS), are reported in patients of the coronavirus disease 2019 (COVID-19). Three cases of Parkinson's disease (PD) have been reported as a direct consequence of COVID-19. In spite of the scarce data for establishing a definitive link between COVID-19 and PD, some hypotheses have been proposed to explain the cases reported. They, however, do not fit well with the clinical findings reported for COVID-19 patients, in general, and for the PD cases reported, in particular. Given the importance of this potential connection, we present here a molecular-level mechanistic hypothesis that explains well these findings and will serve to explore the potential CNS damage in COVID-19 patients. The model explaining the cascade effects from COVID-19 to CNS is developed by using bioinformatic tools. It includes the post-translational modification of host proteins in the lungs by viral proteins, the transport of modified host proteins via exosomes out the lungs, and the disruption of protein-protein interaction in the CNS by these modified host proteins. Our hypothesis is supported by finding 44 proteins significantly expressed in the CNS which are associated with PD and whose interactions can be perturbed by 24 host proteins significantly expressed in the lungs. These 24 perturbators are found to interact with viral proteins and to form part of the cargoes of exosomes in human tissues. The joint set of perturbators and PD-vulnerable proteins form a tightly connected network with significantly more connections than expected by selecting a random cluster of proteins of similar size from the human proteome. The molecular-level mechanistic hypothesis presented here provides several routes for the cascading of effects from the lungs of COVID-19 patients to PD. In particular, the disruption of autophagy/ubiquitination processes appears as an important mechanism that triggers the generation of large amounts of exosomes containing perturbators in their cargo, which would insult several PD-vulnerable proteins, potentially triggering Parkinsonism in COVID-19 patients.
    MeSH term(s) COVID-19/complications ; COVID-19/metabolism ; Central Nervous System/virology ; Exosomes/metabolism ; Humans ; Lung/metabolism ; Models, Theoretical ; Parkinson Disease/etiology ; Parkinson Disease/metabolism ; Parkinson Disease/virology ; Parkinson Disease, Secondary/etiology ; Parkinson Disease, Secondary/metabolism ; Parkinson Disease, Secondary/virology ; Protein Interaction Maps ; SARS-CoV-2/pathogenicity ; Viral Proteins/metabolism
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2021-05-12
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13050897
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Topological analysis of SARS CoV-2 main protease.

    Estrada, Ernesto

    Chaos (Woodbury, N.Y.)

    2020  Volume 30, Issue 6, Page(s) 61102

    Abstract: There is an urgent necessity of effective medication against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), which is producing the COVID-19 pandemic across the world. Its main protease ( ... ...

    Abstract There is an urgent necessity of effective medication against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), which is producing the COVID-19 pandemic across the world. Its main protease (M
    MeSH term(s) Amino Acid Sequence ; Betacoronavirus/metabolism ; Binding Sites/drug effects ; COVID-19 ; Catalytic Domain/drug effects ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Crystallography, X-Ray ; Cysteine Endopeptidases/drug effects ; Cysteine Endopeptidases/metabolism ; Drug Design ; Humans ; Pandemics ; Pneumonia, Viral/drug therapy ; Protease Inhibitors/pharmacology ; SARS Virus/metabolism ; SARS-CoV-2 ; Viral Nonstructural Proteins/drug effects ; Viral Nonstructural Proteins/metabolism
    Chemical Substances Protease Inhibitors ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-07-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1472677-4
    ISSN 1089-7682 ; 1054-1500
    ISSN (online) 1089-7682
    ISSN 1054-1500
    DOI 10.1063/5.0013029
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: COVID-19 and SARS-CoV-2. Modeling the present, looking at the future.

    Estrada, Ernesto

    Physics reports

    2020  Volume 869, Page(s) 1–51

    Abstract: Since December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has produced an outbreak of pulmonary disease which has soon become a global pandemic, known as COronaVIrus Disease-19 (COVID-19). The new coronavirus shares about 82% ... ...

    Abstract Since December 2019 the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has produced an outbreak of pulmonary disease which has soon become a global pandemic, known as COronaVIrus Disease-19 (COVID-19). The new coronavirus shares about 82% of its genome with the one which produced the 2003 outbreak (SARS CoV-1). Both coronaviruses also share the same cellular receptor, which is the angiotensin-converting enzyme 2 (ACE2) one. In spite of these similarities, the new coronavirus has expanded more widely, more faster and more lethally than the previous one. Many researchers across the disciplines have used diverse modeling tools to analyze the impact of this pandemic at global and local scales. This includes a wide range of approaches - deterministic, data-driven, stochastic, agent-based, and their combinations - to forecast the progression of the epidemic as well as the effects of non-pharmaceutical interventions to stop or mitigate its impact on the world population. The physical complexities of modern society need to be captured by these models. This includes the many ways of social contacts - (multiplex) social contact networks, (multilayers) transport systems, metapopulations, etc. - that may act as a framework for the virus propagation. But modeling not only plays a fundamental role in analyzing and forecasting epidemiological variables, but it also plays an important role in helping to find cures for the disease and in preventing contagion by means of new vaccines. The necessity for answering swiftly and effectively the questions:
    Keywords covid19
    Language English
    Publishing date 2020-07-28
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 120601-1
    ISSN 0370-1573
    ISSN 0370-1573
    DOI 10.1016/j.physrep.2020.07.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2.

    Estrada, Ernesto

    Chaos (Woodbury, N.Y.)

    2020  Volume 30, Issue 8, Page(s) 81104

    Abstract: The coronavirus 2019 (COVID-19) respiratory disease is caused by the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which uses the enzyme ACE2 to enter human cells. This disease is characterized by important damage at a ... ...

    Abstract The coronavirus 2019 (COVID-19) respiratory disease is caused by the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which uses the enzyme ACE2 to enter human cells. This disease is characterized by important damage at a multi-organ level, partially due to the abundant expression of ACE2 in practically all human tissues. However, not every organ in which ACE2 is abundant is affected by SARS-CoV-2, which suggests the existence of other multi-organ routes for transmitting the perturbations produced by the virus. We consider here diffusive processes through the protein-protein interaction (PPI) network of proteins targeted by SARS-CoV-2 as an alternative route. We found a subdiffusive regime that allows the propagation of virus perturbations through the PPI network at a significant rate. By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19.
    MeSH term(s) Betacoronavirus ; Biomarkers/metabolism ; COVID-19 ; Coronavirus Infections/metabolism ; Coronavirus Infections/physiopathology ; Diffusion ; Humans ; Models, Biological ; Pandemics ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/physiopathology ; Protein Interaction Mapping ; Protein Interaction Maps ; Proteome ; SARS-CoV-2 ; Time Factors
    Chemical Substances Biomarkers ; Proteome
    Keywords covid19
    Language English
    Publishing date 2020-08-31
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1472677-4
    ISSN 1089-7682 ; 1054-1500
    ISSN (online) 1089-7682
    ISSN 1054-1500
    DOI 10.1063/5.0015626
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Protein-driven mechanism of multiorgan damage in COVID-19.

    Estrada, Ernesto

    Medicine in drug discovery

    2020  , Page(s) 100069

    Abstract: We propose a new plausible mechanism by mean of which SARS-CoV-2 produces extrapulmonary damages in severe COVID-19 patients. The mechanism consist on the existence of vulnerable proteins (VPs), which are (i) mainly expressed outside the lungs; (ii) ... ...

    Abstract We propose a new plausible mechanism by mean of which SARS-CoV-2 produces extrapulmonary damages in severe COVID-19 patients. The mechanism consist on the existence of vulnerable proteins (VPs), which are (i) mainly expressed outside the lungs; (ii) their perturbations is known to produce human diseases; and (iii) can be perturbed directly or indirectly by SARS-CoV-2 proteins. These VPs are perturbed by other proteins, which are: (i) mainly expressed in the lungs, (ii) are targeted directly by SARS-CoV-2 proteins, (iii) can navigate outside the lungs as cargo of extracellular vesicles (EVs); and (iv) can activate VPs via subdiffusive processes inside the target organ. Using bioinformatic tools and mathematical modeling we identifies 26 VPs and their 38 perturbators, which predict extracellular damages in the immunologic endocrine, cardiovascular, circulatory, lymphatic, musculoskeletal, neurologic, dermatologic, hepatic, gastrointestinal, and metabolic systems, as well as in the eyes. The identification of these VPs and their perturbators allow us to identify 27 existing drugs which are candidates to be repurposed for treating extrapulmonary damage in severe COVID-19 patients. After removal of drugs having undesirable drug-drug interactions we select 7 drugs and one natural product: apabetalone, romidepsin, silmitasertib, ozanezumab, procaine, azacitidine, amlexanox, volociximab, and ellagic acid, whose combinations can palliate the organs and systems found to be damaged by COVID-19. We found that at least 4 drugs are needed to treat all the multiorgan damages, for instance: the combination of romidepsin, silmitasertib, apabetalone and azacitidine.
    Keywords covid19
    Language English
    Publishing date 2020-10-20
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2590-0986
    ISSN (online) 2590-0986
    DOI 10.1016/j.medidd.2020.100069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: What Is in a Simplicial Complex? A Metaplex-Based Approach to Its Structure and Dynamics.

    Miranda, Manuel / Estrada-Rodriguez, Gissell / Estrada, Ernesto

    Entropy (Basel, Switzerland)

    2023  Volume 25, Issue 12

    Abstract: Geometric realization of simplicial complexes makes them a unique representation of complex systems. The existence of local continuous spaces at the simplices level with global discrete connectivity between simplices makes the analysis of dynamical ... ...

    Abstract Geometric realization of simplicial complexes makes them a unique representation of complex systems. The existence of local continuous spaces at the simplices level with global discrete connectivity between simplices makes the analysis of dynamical systems on simplicial complexes a challenging problem. In this work, we provide some examples of complex systems in which this representation would be a more appropriate model of real-world phenomena. Here, we generalize the concept of metaplexes to embrace that of geometric simplicial complexes, which also includes the definition of dynamical systems on them. A metaplex is formed by regions of a continuous space of any dimension interconnected by sinks and sources that works controlled by discrete (graph) operators. The definition of simplicial metaplexes given here allows the description of the diffusion dynamics of this system in a way that solves the existing problems with previous models. We make a detailed analysis of the generalities and possible extensions of this model beyond simplicial complexes, e.g., from polytopal and cell complexes to manifold complexes, and apply it to a real-world simplicial complex representing the visual cortex of a macaque.
    Language English
    Publishing date 2023-11-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e25121599
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Protein-Driven Mechanism of Multiorgan Damage in COVID-19

    Estrada, Ernesto

    Medicine in Drug Discovery

    2020  , Page(s) 100069

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ISSN 2590-0986
    DOI 10.1016/j.medidd.2020.100069
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Cascading from SARS-CoV-2 to Parkinson’s Disease through Protein-Protein Interactions

    Estrada, Ernesto

    Viruses. 2021 May 12, v. 13, no. 5

    2021  

    Abstract: Extensive extrapulmonary damages in a dozen of organs/systems, including the central nervous system (CNS), are reported in patients of the coronavirus disease 2019 (COVID-19). Three cases of Parkinson’s disease (PD) have been reported as a direct ... ...

    Abstract Extensive extrapulmonary damages in a dozen of organs/systems, including the central nervous system (CNS), are reported in patients of the coronavirus disease 2019 (COVID-19). Three cases of Parkinson’s disease (PD) have been reported as a direct consequence of COVID-19. In spite of the scarce data for establishing a definitive link between COVID-19 and PD, some hypotheses have been proposed to explain the cases reported. They, however, do not fit well with the clinical findings reported for COVID-19 patients, in general, and for the PD cases reported, in particular. Given the importance of this potential connection, we present here a molecular-level mechanistic hypothesis that explains well these findings and will serve to explore the potential CNS damage in COVID-19 patients. The model explaining the cascade effects from COVID-19 to CNS is developed by using bioinformatic tools. It includes the post-translational modification of host proteins in the lungs by viral proteins, the transport of modified host proteins via exosomes out the lungs, and the disruption of protein-protein interaction in the CNS by these modified host proteins. Our hypothesis is supported by finding 44 proteins significantly expressed in the CNS which are associated with PD and whose interactions can be perturbed by 24 host proteins significantly expressed in the lungs. These 24 perturbators are found to interact with viral proteins and to form part of the cargoes of exosomes in human tissues. The joint set of perturbators and PD-vulnerable proteins form a tightly connected network with significantly more connections than expected by selecting a random cluster of proteins of similar size from the human proteome. The molecular-level mechanistic hypothesis presented here provides several routes for the cascading of effects from the lungs of COVID-19 patients to PD. In particular, the disruption of autophagy/ubiquitination processes appears as an important mechanism that triggers the generation of large amounts of exosomes containing perturbators in their cargo, which would insult several PD-vulnerable proteins, potentially triggering Parkinsonism in COVID-19 patients.
    Keywords COVID-19 infection ; Parkinson disease ; Severe acute respiratory syndrome coronavirus 2 ; autophagy ; bioinformatics ; central nervous system ; exosomes ; humans ; models ; protein-protein interactions ; proteome ; ubiquitination
    Language English
    Dates of publication 2021-0512
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13050897
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: What Is in a Simplicial Complex? A Metaplex-Based Approach to Its Structure and Dynamics

    Manuel Miranda / Gissell Estrada-Rodriguez / Ernesto Estrada

    Entropy, Vol 25, Iss 12, p

    2023  Volume 1599

    Abstract: Geometric realization of simplicial complexes makes them a unique representation of complex systems. The existence of local continuous spaces at the simplices level with global discrete connectivity between simplices makes the analysis of dynamical ... ...

    Abstract Geometric realization of simplicial complexes makes them a unique representation of complex systems. The existence of local continuous spaces at the simplices level with global discrete connectivity between simplices makes the analysis of dynamical systems on simplicial complexes a challenging problem. In this work, we provide some examples of complex systems in which this representation would be a more appropriate model of real-world phenomena. Here, we generalize the concept of metaplexes to embrace that of geometric simplicial complexes, which also includes the definition of dynamical systems on them. A metaplex is formed by regions of a continuous space of any dimension interconnected by sinks and sources that works controlled by discrete (graph) operators. The definition of simplicial metaplexes given here allows the description of the diffusion dynamics of this system in a way that solves the existing problems with previous models. We make a detailed analysis of the generalities and possible extensions of this model beyond simplicial complexes, e.g., from polytopal and cell complexes to manifold complexes, and apply it to a real-world simplicial complex representing the visual cortex of a macaque.
    Keywords simplicial complex ; geometric realization ; metaplexes ; diffusion ; brain networks ; higher-order networks ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
    Subject code 514
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: COVID-19 and SARS-CoV-2. Modeling the present, looking at the future

    Estrada, Ernesto

    Physics Reports

    2020  Volume 869, Page(s) 1–51

    Keywords General Physics and Astronomy ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 120601-1
    ISSN 0370-1573
    ISSN 0370-1573
    DOI 10.1016/j.physrep.2020.07.005
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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