Biology subjects

Lane, T. R.

Publications and source records attributed to Lane, T. R..

11 recordsLinked to original sources

bioRxiv2026

Human CYP1A2 metabolism of organophosphorus pesticides and nerve agent surrogates

CYP1A2 contributes 13-15% of hepatic CYP450 content and plays a critical role in the metabolism of approximately 10% of pharmaceutical drugs in the human body. CYP1A2 has been previously reported to bioactivate and detoxify both the thion (P=S) and oxon (P=O) forms of organophosphorus (OP) compounds. In this study, we determined the capacity of CYP1A2 to degrade OP compounds using LC-MS/MS, as well as the inhibition of its activity by OP compounds using the previously developed pFluor50 assay. CYP1A2 was selective in metabolizing thions over oxons, and several OP compounds inhibited its activity in a time- and dose-dependent manner. To further investigate the mechanism of CYP1A2-OP interactions, molecular docking studies were performed using a crystal structure of CYP1A2 (PDB ID: 2HI4). Linear correlation analysis between CYP1A2 inhibition at 10 M with 30 minute preincubation and the % OP compound remaining at 2 hours (R = -0.71, P<0.001) showed a moderate but significant correlation. Based on these findings, CYP1A2 was identified as a potential bioscavenger for OP compound metabolism, supporting the future integration of experimental and in silico data for developing artificial intelligence (AI) / machine learning (ML) models for prediction of CYP1A2-mediated metabolism of existing and emerging OP compounds, including those of toxicological and chemical warfare relevance.

pharmacology and toxicology↗

bioRxiv2026

Organophosphorus pesticide and nerve agent surrogate metabolism by human CYP3A4

Of the cytochrome P450 enzymes, CYP3A4 is the most abundant isoform in the human liver, and this enzyme plays a dominant role in the metabolism of a wide range of clinical drugs and xenobiotics. Previous studies have demonstrated that CYP3A4 participates in the oxidative metabolism of several organophosphorus (OP) pesticides involving both thion (P=S) and oxon (P=O) forms. In the present study, we evaluated the capacity of CYP3A4 to metabolize a structurally diverse set of OP compounds using LC-MS/MS methods and assessed their potential to inhibit CYP3A4 activity using previously developed pFlour50 fluorogenic assay. Our results demonstrate that CYP3A4 preferentially metabolizes thions, as compared to oxons, and several OP compounds were also found to inhibit CYP3A4 activity in a time-dependent manner. To gain further mechanistic structural insight into the CYP3A4-OP interactions, molecular docking studies were performed using a crystal structure of CYP3A4 (PDB ID: 3NXU). Linear correlation analysis between in silico parameters like molecular weight or binding energy correlated with experimental data including inhibition data for 10 or 30 minutes or the LC-MS/MS data showing the degradation at 1 or 2 hours showed moderate but significant correlation. Soman surrogate PiMP, and cyclosarin surrogate CMP, were both effectively metabolized by CYP3A4, while docking of these surrogates and authentic agents with CYP3A4 receptor revealed very similar binding poses and interactions. Collectively, these findings highlight the important role of CYP3A4 in OP metabolism and support the potential of integrating experimental and in silico data to predict CYP3A4-mediated metabolism of existing and emerging OP compounds, including those of toxicological and chemical warfare relevance.

pharmacology and toxicology↗

bioRxiv2025

Human CYP2C9 metabolism of organophosphorus pesticides and nerve agent surrogates

Of the Cytochrome P450 enzymes, the CYP2C9 variant is very important and is the cytochrome P450 (CYP) involved in the metabolism of several human drugs where it acts as a natural bioscavenger. Previously, CYP2C9 was demonstrated to remove sulfur from different organophosphorus (OP) pesticides, such as dimethoate, diazinon and parathion. In this study, we have tested the ability of CYP2C9 to degrade other OP compounds. We investigated the metabolism of OP compounds by CYP2C9 using LC-MS/MS approaches as well as the time-dependent inhibition of CYP2C9 by OP compounds using the previously developed pFluor50 fluorogenic assay. We found that CYP2C9 metabolizes thions (P=S) preferentially over oxons (P=O) and there were many OP compounds that inhibited CYP2C9 activity in a time-dependent manner. Additionally, we performed molecular docking based on the Protein Data Bank (PDB)crystal structure (1OG5) of the CYP2C9 receptor in order to gain atomistic insight from the in vitro experimental results. We observed a positive though moderate correlation between the calculated binding energy and the CYP2C9 metabolism of various OP compounds (R = 0.61) as well as the time-dependent changes in inhibition of OPs with binding energy (R = 0.59). Although the R values were modest,59). These in vitro data combined with analysis of additional OP derivatives could be used to develop artificial intelligence (AI)machine learning models to predict the metabolism of specific OP compounds by CYP2C9. This type of approach could be particularly relevant for the prediction of the metabolism of current and emerging chemical warfare agents.

pharmacology and toxicology↗

bioRxiv2023

Development and characterization of pFluor50, a fluorogenic-based kinetic assay system for high-throughput inhibition screening and characterization of time-dependent inhibition and inhibition type for six human CYPs

1Cytochrome P450 enzymes (CYPs) play an integral role in drug and xenobiotic metabolism in humans and thus understanding CYP inhibition or activation by new therapeutic candidates is an important step in the drug development process. Ideally, CYP inhibition/activation assays should be high-throughput, use commercially available components, allow for analysis of metabolism by the majority of human CYPs, and allow for kinetic analysis of inhibition type and time-dependent inhibition. Here, we developed pFluor50, a 384-well microtiter plate-based fluorogenic kinetic enzyme assay system using substrates metabolized by six human CYPs to generate fluorescent products and determined the Michaelis-Menten kinetics constant (KM) and product formation rate (Vmax) for each substrate-CYP pair. The substrate-CYP pairs were as follows: resorufin ethyl ether for CYP1A2 (KM= 0.8 M), CYP2C9 (KM= 0.6 M), and CYP2D6 (KM= 2.7 M); resorufin benzyl ether for CYP2B6 (KM= 46 M); 3-O-methyl fluorescein for CYP2C19 (KM= 3.0 M); and dibenzyl fluorescein for CYP3A4 (KM= 2.9 M). We then validated each assay using known inhibitors: -naphthoflavone for CYP1A2 (IC50= 13.5 nM); sertraline for CYP2B6 (IC50= 410 nM) and CYP2D6 (IC50= 2.4 M); sulfaphenazole for CYP2C9 (IC50= 1 M); ticlopidine for CYP2C19 (IC50= 1.2 M); and CYP3cide for CYP3A4 (IC50= 56 nM). pFluor50 was also used to elucidate inhibition type and time-dependent inhibition for some inhibitors demonstrating its utility for characterizing the observed inhibition, even mechanism-based inhibition. The pFluor50 assay system developed in this study using commercially available components should be very useful for high-throughput screening and further characterization of potential therapeutic candidates for inhibition/activation with the most prevalent human CYPs.

pharmacology and toxicology↗

bioRxiv2021

Strain dependent structural effects and in vivo efficacy of enterovirus-D68 inhibitors

Acute flaccid myelitis (AFM) leads to loss of limb control in young children and is likely due to Enterovirus-D68 (EV-D68), for which there is no current treatment. We have developed a lead isoxazole-3-carboxamide analog of pleconaril (11526092) which displayed potent inhibition of the pleconaril-resistant CVB3-Woodruff (IC50 6-20 nM), EV-D68 (IC50 58 nM), and other enteroviruses. A mouse respiratory model of EV-D68 infection, in which pleconaril is inactive, showed decreased viremia of 3 log units as well as statistically significant 1 log reduction in lung titer reduction at day 5 after treatment with 11526092. A cryo-electron microscopy (cryo-EM) structure of EV-D68 in complex with 11526092 suggests that the increased potency may be due to additional hydrophobic interactions. Cryo-EM structures of 11526092 and pleconaril demonstrate destabilization of EV-D68 (MO strain) compared to the previously described stabilization of EV-D68 (Fermon strain) with pleconaril, illustrating clear strain dependent mechanisms of this molecule. 11526092 represents a more potent inhibitor in vitro with in vivo efficacy providing a potential future treatment for EV-D68 and AFM, suggesting an improvement over pleconaril for further optimization. One-Sentence Summary11526092 demonstrates protein destabilization, improved in vitro potency and in vivo efficacy when compared with pleconaril against EV-D68.

pharmacology and toxicology↗

bioRxiv2021

Pyronaridine Protects Against SARS-CoV-2 in Mouse

There are currently relatively few small-molecule antiviral drugs that are either approved or emergency approved for use against SARS-CoV-2. One of these is remdesivir, which was originally repurposed from its use against Ebola and functions by causing early RNA chain termination. We used this as justification to evaluate three molecules we had previously identified computationally with antiviral activity against Ebola and Marburg. Out of these we previously identified pyronaridine, which inhibited the SARS-CoV-2 replication in A549-ACE2 cells. Herein, the in vivo efficacy of pyronaridine has now been assessed in a K18-hACE transgenic mouse model of COVID-19. Pyronaridine treatment demonstrated a statistically significant reduction of viral load in the lungs of SARS CoV-2 infected mice. Furthermore, the pyronaridine treated group reduced lung pathology, which was also associated with significant reduction in the levels of pro-inflammatory cytokines/chemokine and cell infiltration. Notably, pyronaridine inhibited the viral PLpro activity in vitro (IC50 of 1.8 {micro}M) without any effect on Mpro, indicating a possible molecular mechanism involved in its ability to inhibit SARS-CoV-2 replication. Interestingly, pyronaridine also selectively inhibits the host kinase CAMK1 (IC50 of 2.4 {micro}M). We have also generated several pyronaridine analogs to assist in understanding the structure activity relationship for PLpro inhibition. Our results indicate that pyronaridine is a potential therapeutic candidate for COVID-19. One sentence summaryThere is currently intense interest in discovering small molecules with direct antiviral activity against the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Pyronaridine, an antiviral drug with in vitro activity against Ebola, Marburg and SARS-CoV-2 has now statistically significantly reduced the viral load in mice along with IL-6, TNF-, and IFN-{beta} ultimately demonstrating a protective effect against lung damage by infection to provide a new potential treatment for testing clinically.

pharmacology and toxicology↗

bioRxiv2020

Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In vitro Activity Against SARS-CoV-2 and Potential Mechanisms

SARS-CoV-2 is a newly identified virus that has resulted in over 1.3 M deaths globally and over 59 M cases globally to date. Small molecule inhibitors that reverse disease severity have proven difficult to discover. One of the key approaches that has been widely applied in an effort to speed up the translation of drugs is drug repurposing. A few drugs have shown in vitro activity against Ebola virus and demonstrated activity against SARS-CoV-2 in vivo. Most notably the RNA polymerase targeting remdesivir demonstrated activity in vitro and efficacy in the early stage of the disease in humans. Testing other small molecule drugs that are active against Ebola virus would seem a reasonable strategy to evaluate their potential for SARS-CoV-2. We have previously repurposed pyronaridine, tilorone and quinacrine (from malaria, influenza, and antiprotozoal uses, respectively) as inhibitors of Ebola and Marburg virus in vitro in HeLa cells and of mouse adapted Ebola virus in mouse in vivo. We have now tested these three drugs in various cell lines (VeroE6, Vero76, Caco-2, Calu-3, A549-ACE2, HUH-7 and monocytes) infected with SARS-CoV-2 as well as other viruses (including MHV and HCoV 229E). The compilation of these results indicated considerable variability in antiviral activity observed across cell lines. We found that tilorone and pyronaridine inhibited the virus replication in A549-ACE2 cells with IC50 values of 180 nM and IC50 198 nM, respectively. We have also tested them in a pseudovirus assay and used microscale thermophoresis to test the binding of these molecules to the spike protein. They bind to spike RBD protein with Kd values of 339 nM and 647 nM, respectively. Human Cmax for pyronaridine and quinacrine is greater than the IC50 hence justifying in vivo evaluation. We also provide novel insights into their mechanism which is likely lysosomotropic.

pharmacology and toxicology↗

bioRxiv2020

Machine Learning Models Identify Inhibitors of SARS-CoV-2

With the ongoing SARS-CoV-2 pandemic there is an urgent need for the discovery of a treatment for the coronavirus disease (COVID-19). Drug repurposing is one of the most rapid strategies for addressing this need and numerous compounds have been selected for in vitro testing by several groups already. These have led to a growing database of molecules with in vitro activity against the virus. Machine learning models can assist drug discovery through prediction of the best compounds based on previously published data. Herein we have implemented several machine learning methods to develop predictive models from recent SARS-CoV-2 in vitro inhibition data and used them to prioritize additional FDA approved compounds for in vitro testing selected from our in-house compound library. From the compounds predicted with a Bayesian machine learning model, CPI1062 and CPI1155 showed antiviral activity in HeLa-ACE2 cell-based assays and represent potential repurposing opportunities for COVID-19. This approach can be greatly expanded to exhaustively virtually screen available molecules with predicted activity against this virus as well as a prioritization tool for SARS-CoV-2 antiviral drug discovery programs. The very latest model for SARS-CoV-2 is available at www.assaycentral.org.Competing Interest StatementSE is CEO and owner of Collaborations Pharmaceuticals, Inc. DHF, KMZ, TRL, AP are employees of Collaborations Pharmaceuticals, Inc.View Full Text

pharmacology and toxicology↗

bioRxiv2020

Towards the Target: Tilorone, Quinacrine and Pyronaridine Bind to Ebola Virus Glycoprotein

Pyronaridine, tilorone and quinacrine were recently identified by a machine learning model and demonstrated in vitro and in vivo activity against Ebola virus (EBOV) and represent viable candidates for drug repurposing. These drugs were docked into the crystal structure of the ebola glycoprotein and then experimentally validated in vitro to generate Kd values for tilorone (0.73 μM) pyronaridine (7.34 μM), and quinacrine (7.55 μM). These are more potent than the previously reported toremifene (16 μM).View Full Text

pharmacology and toxicology↗

bioRxiv2020

Repurposing Pyramax for the Treatment of Ebola Virus Disease: Additivity of the Lysosomotropic Pyronaridine and Non-Lysosomotropic Artesunate

We have recently identified three molecules (tilorone, quinacrine and pyronaridine tetraphosphate) which all demonstrated efficacy in the mouse model of infection with mouse-adapted Ebola virus (EBOV) model of disease and had similar in vitro inhibition of an Ebola pseudovirus (VSV-EBOV-GP), suggesting they interfere with viral entry. Using a machine learning model to predict lysosomotropism these compounds were evaluated for their ability to inhibit via a lysosomotropic mechanism in vitro. We now demonstrate in vitro that pyronaridine tetraphosphate is an inhibitor of Lysotracker accumulation in lysosomes (IC50 = 0.56 M). Further, we evaluated synergy between pyronaridine and artesunate (Pyramax(R)), which are used in combination to treat malaria. Artesunate was not found to have lysosomotropic activity in vitro and the combination effect on EBOV inhibition was shown to be additive. Pyramax(R) may represent a unique example of the repurposing of a combination product for another disease.

pharmacology and toxicology↗

bioRxiv2020

Pyronaridine Tetraphosphate Efficacy Against Ebola Virus Infection in Guinea Pig

The recent outbreaks of the Ebola virus (EBOV) in Africa have brought global visibility to the shortage of available therapeutic options to treat patients infected with this or closely related viruses. We have recently computationally identified three molecules which have all demonstrated statistically significant efficacy in the mouse model of infection with mouse adapted Ebola virus (ma-EBOV). One of these molecules is the antimalarial pyronaridine tetraphosphate (IC50 range of 0.82-1.30 {micro}M against three strains of EBOV and IC50 range of 1.01-2.72 {micro}M against two strains of Marburg virus (MARV)) which is an approved drug in the European Union and used in combination with artesunate. To date, no small molecule drugs have shown statistically significant efficacy in the guinea pig model of EBOV infection. Pharmacokinetics and range-finding studies in guinea pigs directed us to a single 300mg/kg or 600mg/kg oral dose of pyronaridine 1hr after infection. Pyronaridine resulted in statistically significant survival of 40% at 300mg/kg and protected from a lethal challenge with EBOV. In comparison, oral favipiravir (300 mg/kg dosed once a day) had 43.5 % survival. The in vitro metabolism and metabolite identification of pyronaridine and another of our EBOV active molecules, tilorone, which suggests significant species differences which may account for the efficacy or lack thereof, respectively in guinea pig. In summary, our studies with pyronaridine demonstrates its utility for repurposing as an antiviral against EBOV and MARV, providing justification for future testing in non-human primates. ImportanceThere is currently no antiviral small molecule drug approved for treating Ebola Virus infection. We have previously used machine learning models to identify new uses for approved drugs and demonstrated their activity against the Ebola virus in vitro and in vivo. We now describe the pharmacokinetic properties of the antimalarial pyronaridine in the guinea pig. In addition, we show that this drug is effective against multiple strains of EBOV and MARV in vitro and in the guinea pig model of Ebola virus infection. These combined efforts indicate the need to further test this molecule in larger animal efficacy studies prior to clinical use in humans. These findings also may be useful for repurposing this drug for use against other viruses in future.

pharmacology and toxicology↗