Assembly of an in silico model of the platelet interactome and in vitro validation of IPP complex interactions of human platelets

Abstract Background A missense mutation, CACNA1C-E1115K, located in the cardiac L-type calcium channel (LTCC), was recently reported to be associated with diverse arrhythmias. Several studies reported in-vivo and in-vitro modeling of this mutation, but actual mechanism and target drug of this disease has not been clarified due to its complex ion-mechanisms. Objective To reveal the mechanism of this diverse arrhythmogenic phenotype using combination of in-vitro and in-silico model. Methods and results Cell-Engineering Phase: We generated human induced pluripotent stem cell (hiPSC) from a patient carrying heterozygous CACNA1C-E1115K and differentiated into cardiomyocytes. Spontaneous APs were recorded from spontaneously beating single cardiomyocytes by using the perforated patch-clamp technique. Mathematical-Modeling Phase: We newly developed ICaL-mutation mathematical model, fitted into experimental data, including its impaired ion selectivity. Furthermore, we installed this mathematical model into hiPSC-CM simulation model. Collaboration Phase: Mutant in-silico model showed APD prolongation and frequent early afterdepolarization (EAD), which are same as in-vitro model. In-silico model revealed this EAD was mostly related to robust late-mode of sodium current occurred by Na+ overload and suggested that mexiletine is capable of reducing arrhythmia. Afterward, we applicated mexiletine onto hiPSC-CMs mutant model and found mexiletine suppress EADs. Conclusions Precise in-silico disease model can elucidate complicated ion currents and contribute predicting result of drug-testing. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists

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Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00460 ◽

2019 ◽

Vol 59 (11) ◽

pp. 4893-4905 ◽

Cited By ~ 7

Author(s):

Sebastian Schneckener ◽

Sergio Grimbs ◽

Jessica Hey ◽

Stephan Menz ◽

Maren Osmers ◽

...

Keyword(s):

Machine Learning ◽

Oral Bioavailability ◽

In Silico ◽

Chemical Structure ◽

Structure Parameters ◽

Learning Models ◽

In Silico Model ◽

Machine Learning Models

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The Pseudomonas Quorum-Sensing Regulator RsaL Belongs to the Tetrahelical Superclass of H-T-H Proteins

Journal of Bacteriology ◽

10.1128/jb.01552-06 ◽

2006 ◽

Vol 189 (5) ◽

pp. 1922-1930 ◽

Cited By ~ 32

Author(s):

Giordano Rampioni ◽

Fabio Polticelli ◽

Iris Bertani ◽

Karima Righetti ◽

Vittorio Venturi ◽

...

Keyword(s):

Dna Binding ◽

Quorum Sensing ◽

In Silico ◽

Mobility Shift ◽

Specific Domain ◽

Signal Molecule ◽

In Silico Model ◽

Opportunistic Human Pathogen

ABSTRACT In the opportunistic human pathogen Pseudomonas aeruginosa, quorum sensing (QS) is crucial for virulence. The RsaL protein directly represses the transcription of lasI, the synthase gene of the main QS signal molecule. On the basis of sequence homology, RsaL cannot be predicted to belong to any class of characterized DNA-binding proteins. In this study, an in silico model of the RsaL structure was inferred showing that RsaL belongs to the tetrahelical superclass of helix-turn-helix proteins. The overall structure of RsaL is very similar to the N-terminal domain of the lambda cI repressor and to the POU-specific domain of the mammalian transcription factor Oct-1 (Oct-1 POUs). Moreover, residues of Oct-1 POUs important for structural stability and/or DNA binding are conserved in the same positions in RsaL and in its homologs found in GenBank. These residues were independently replaced with Ala, and the activities of the mutated variants of RsaL were compared to that of the wild-type counterpart in vivo by complementation assays and in vitro by electrophoretic mobility shift assays. The results validated the RsaL in silico model and showed that residues Arg 20, Gln 38, Ser 42, Arg 43, and Glu 45 are important for RsaL function. Our data indicate that RsaL could be the founding member of a new protein family within the tetrahelical superclass of helix-turn-helix proteins. Finally, the minimum DNA sequence required for RsaL binding on the lasI promoter was determined, and our data support the hypothesis that RsaL binds DNA as a dimer.

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An in vitro, in utero and in silico framework of oxygen diffusion in intricate vascular networks of the placenta

10.1101/2021.12.01.470714 ◽

2021 ◽

Author(s):

Nikhilesh Bappoo ◽

Lachlan J Kelsey ◽

Yutthapong Tongpob ◽

Kirk W Feindel ◽

Harrison Caddy ◽

...

Keyword(s):

In Silico ◽

Oxygen Diffusion ◽

In Utero ◽

Growth Restriction ◽

Vascular Networks ◽

Placental Perfusion ◽

In Silico Model ◽

Flow Deceleration ◽

Function Relationship

The placenta is a temporary and complex organ critical for fetal development through its subtle but convoluted harmonization of endocrine, vascular, haemodynamic and exchange adaptations. Yet, due to experimental, technological and ethical constraints, this unique organ remains poorly understood. In silico tools are emerging as a powerful means to overcome these challenges and have the potential to actualize novel breakthroughs. Here, we present an interdisciplinary framework combining in vitro experiments used to develop an elegant and scalable in silico model of oxygen diffusion. We then use in utero imaging of placental perfusion and oxygenation in both control and growth-restricted rodent placentas for validation of our in silico model. Our framework revealed the structure-function relationship in the feto-placental vasculature; oxygen diffusion is impaired in growth-restricted placentas, due to the diminished arborization of growth-restricted feto-placental vasculature and the lack of decelerated flow for adequate oxygen diffusion and exchange. We highlight the mechanisms of impairment in a rat model of growth restriction, underpinned by placental vascular impairment. Our framework reports and validates the prediction of blood flow deceleration impairment in growth restricted placentas with the placenta's oxygen transfer capability being significantly impaired, both globally and locally. Key words: Placenta; fetal growth restriction; oxygen diffusion; computational fluid dynamics; MRI

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Structure based virtual screening identifies novel competitive inhibitors for the sialoglycan binding protein Hsa

10.1101/2020.03.27.006247 ◽

2020 ◽

Author(s):

Rupesh Agarwal ◽

Barbara A. Bensing ◽

Dehui Mi ◽

Paige N. Vinson ◽

Jerome Baudry ◽

...

Keyword(s):

Virtual Screening ◽

In Silico ◽

Critical Role ◽

Human Platelets ◽

Screening Strategy ◽

T Antigen ◽

Bacterial Attachment ◽

Bacterial Surface ◽

Adhesin Protein

AbstractInfective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that a serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialyated glycans displayed on human platelets. Despite its important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel inhibitors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. In silico cross screening against the glycan binding domains of closely related SRR proteins from five other S. gordonii or S. sanguinis strains was also performed to further reduce false positives. Using our in silico screening strategy we successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to adhesin protein Hsa (∼20% hit rate).

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Exploration of the Mixing Phenomena during Interaction of Internal and External Circulations (EMPACs): Developing an in-vitro and in-silico Model of the Human Circulation

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0036-1571485 ◽

2016 ◽

Vol 64 (S 01) ◽

Author(s):

P. Grieshaber ◽

J. Gehron ◽

M. Bongert ◽

S. Schäfer ◽

M. Fiebich ◽

...

Keyword(s):

In Silico ◽

In Silico Model

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Monosubstituted Coumarins Inhibit Epinephrine-Induced Platelet Aggregation Antiplatelet Effect of Monosubstituted Coumarins

Cardiovascular & Hematological Agents in Medicinal Chemistry ◽

10.2174/1871525719666210427132808 ◽

2021 ◽

Vol 19 ◽

Author(s):

Fausto Alejandro Jiménez-Orozco ◽

Sergio Galicia-Zapatero ◽

Edgar López-López ◽

José L. Medina-Franco ◽

Fernando León Cedeño ◽

...

Keyword(s):

Platelet Aggregation ◽

In Silico ◽

Drug Targets ◽

Platelet Reactivity ◽

Antiplatelet Agents ◽

Human Platelets ◽

In Silico Studies ◽

Vitro Effect ◽

Induced Aggregation

Aim: Evaluate the in vitro effect of coumarin and 15 monosubstituted derivatives on the inhibition of human platelet aggregation induced by various pro-aggregatory agonists, particularly by epinephrine. Background: The emergence of residual platelet reactivity during the use of conventional antiplatelet agents (acetylsalicylic acid and clopidogrel) is one of the main causes of double therapy´s therapeutic failure. Platelet adrenoceptors participate in residual platelet reactivity. Therefore, it is necessary to develop new antiplatelet agents that inhibit epinephrine-induced platelet aggregation as a new therapeutic strategy. Information on the antiplatelet activity of coumarins in inhibiting epinephrine-induced aggregation is limited. Objective: Establish the structure-activity relationship (SAR) of coumarin derivatives with hydroxy, methoxy, and acetoxy groups in different positions of the coumarin nucleus to identify the most active molecules. Using in silico studies, suggest potential drug targets to which the molecules bind to produce antiplatelet effects. Methods: The platelet aggregation was performed using a Lumi-aggregometer; the inhibitory activity of 16 compounds were evaluated by inducing the aggregation of human platelets (250 × 103/μl) with epinephrine (10 µM), collagen (2 µg / ml) or ADP (10 µM). The aggregation of controls platelets was considered 100% of the response for each pro-aggregatory agonists. Results: Eleven molecules inhibited epinephrine-induced aggregation, with 3-acetoxycoumarin and 7-methoxycoumarin being the most active. Only coumarin inhibited collagen-induced platelet aggregation, but no molecule showed activity when using ADP as an inducer. Conclusions : In silico studies suggest that most active molecules might have antagonistic interactions in the adrenoceptors α2 and β2. The antiplatelet actions of these coumarins have the potential to reduce residual platelet reactivity and thus contribute to the development of future treatments for patients who do not respond adequately to conventional agents.

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