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Menendez CA, Mohamed A, Perez-Lemus GR, Weiss AM, Rawe BW, Liu G, Crolais AE, Kenna E, Byléhn F, Alvarado W, Mendels D, Rowan SJ, Tay S, de Pablo JJ. Development of Masitinib Derivatives with Enhanced M pro Ligand Efficiency and Reduced Cytotoxicity. Molecules 2023; 28:6643. [PMID: 37764425 PMCID: PMC10536273 DOI: 10.3390/molecules28186643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Recently, a high-throughput screen of 1900 clinically used drugs identified masitinib, an orally bioavailable tyrosine kinase inhibitor, as a potential treatment for COVID-19. Masitinib acts as a broad-spectrum inhibitor for human coronaviruses, including SARS-CoV-2 and several of its variants. In this work, we rely on atomistic molecular dynamics simulations with advanced sampling methods to develop a deeper understanding of masitinib's mechanism of Mpro inhibition. To improve the inhibitory efficiency and to increase the ligand selectivity for the viral target, we determined the minimal portion of the molecule (fragment) that is responsible for most of the interactions that arise within the masitinib-Mpro complex. We found that masitinib forms highly stable and specific H-bond interactions with Mpro through its pyridine and aminothiazole rings. Importantly, the interaction with His163 is a key anchoring point of the inhibitor, and its perturbation leads to ligand unbinding within nanoseconds. Based on these observations, a small library of rationally designed masitinib derivatives (M1-M5) was proposed. Our results show increased inhibitory efficiency and highly reduced cytotoxicity for the M3 and M4 derivatives compared to masitinib.
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Affiliation(s)
- Cintia A. Menendez
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adil Mohamed
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Gustavo R. Perez-Lemus
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Adam M. Weiss
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Benjamin W. Rawe
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Guancen Liu
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Alex E. Crolais
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Fabian Byléhn
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Walter Alvarado
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Dan Mendels
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Stuart J. Rowan
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA (G.L.); (A.E.C.)
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
| | - Juan J. de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA (G.R.P.-L.); (B.W.R.); (S.J.R.); (S.T.)
- Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
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Son M, Wang AG, Kenna E, Tay S. High-throughput co-culture system for analysis of spatiotemporal cell-cell signaling. Biosens Bioelectron 2023; 225:115089. [PMID: 36736159 PMCID: PMC9991101 DOI: 10.1016/j.bios.2023.115089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
Study of spatial and temporal aspects of signaling between individual cells is essential in understanding development, the immune response, and host-pathogen interactions. We present an automated high-throughput microfluidic platform that chemically stimulates immune cells to initiate cytokine secretion, and controls the formation of signal gradients that activate neighboring cell populations. Furthermore, our system enables controlling the cell type and density based on distance, and retrieval of cells from different regions for gene expression analysis. Our device performs these tasks in 192 independent chambers to simultaneously test different co-culture conditions. We demonstrate these capabilities by creating various cellular communication scenarios between macrophages and fibroblasts in vitro. We find that spatial distribution of macrophages and heterogeneity in cytokine secretion determine spatiotemporal gene expression responses. Furthermore, we describe how gene expression dynamics depend on a cell's distance from the signaling source. Our device addresses key challenges in the study of cell-to-cell signaling, and provides high-throughput and automated analysis over a wide range of co-culture conditions.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Medical Scientist Training Program, University of Chicago, Chicago, IL, 60637, USA
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
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Kim J, Rosenberger MG, Chen S, IP CKM, Bahmani A, Chen Q, Shen J, Tang Y, Wang A, Kenna E, Son M, Tay S, Ferguson AL, Esser-Kahn AP. Discovery of New States of Immunomodulation for Vaccine Adjuvants via High Throughput Screening: Expanding Innate Responses to PRRs. ACS Cent Sci 2023; 9:427-439. [PMID: 36968540 PMCID: PMC10037445 DOI: 10.1021/acscentsci.2c01351] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Indexed: 06/18/2023]
Abstract
Stimulation of the innate immune system is crucial in both effective vaccinations and immunotherapies. This is often achieved through adjuvants, molecules that usually activate pattern recognition receptors (PRRs) and stimulate two innate immune signaling pathways: the nuclear factor kappa-light-chain-enhancer of activated B-cells pathway (NF-κB) and the interferon regulatory factors pathway (IRF). Here, we demonstrate the ability to alter and improve adjuvant activity via the addition of small molecule "immunomodulators". By modulating signaling activity instead of receptor binding, these molecules allow the customization of select innate responses. We demonstrate both inhibition and enhancement of the products of the NF-κB and IRF pathways by several orders of magnitude. Some modulators apply generally across many receptors, while others focus specifically on individual receptors. Modulators boost correlates of a protective immune responses in a commercial flu vaccine model and reduced correlates of reactogenicity in a typhoid vaccine model. These modulators have a range of applications: from adjuvanticity in prophylactics to enhancement of immunotherapy.
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Affiliation(s)
| | | | - Siquan Chen
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Carman KM IP
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Azadeh Bahmani
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Qing Chen
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Jinjing Shen
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Yifeng Tang
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrew Wang
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrew L. Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Aaron P. Esser-Kahn
- Pritzker School of Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
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Wang AG, Son M, Kenna E, Thom N, Tay S. NF-κB memory coordinates transcriptional responses to dynamic inflammatory stimuli. Cell Rep 2022; 40:111159. [PMID: 35977475 PMCID: PMC10794069 DOI: 10.1016/j.celrep.2022.111159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022] Open
Abstract
Many scenarios in cellular communication require cells to interpret multiple dynamic signals. It is unclear how exposure to inflammatory stimuli alters transcriptional responses to subsequent stimulus. Using high-throughput microfluidic live-cell analysis, we systematically profile the NF-κB response to different signal sequences in single cells. We find that NF-κB dynamics store the short-term history of received signals: depending on the prior pathogenic or cytokine signal, the NF-κB response to subsequent stimuli varies from no response to full activation. Using information theory, we reveal that these stimulus-dependent changes in the NF-κB response encode and reflect information about the identity and dose of the prior stimulus. Small-molecule inhibition, computational modeling, and gene expression profiling show that this encoding is driven by stimulus-dependent engagement of negative feedback modules. These results provide a model for how signal transduction networks process sequences of inflammatory stimuli to coordinate cellular responses in complex dynamic environments.
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Affiliation(s)
- Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, University of Chicago, Chicago, IL 60637, USA
| | - Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Emma Kenna
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Thom
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.
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Semrau JD, Chistoserdov A, Lebron J, Costello A, Davagnino J, Kenna E, Holmes AJ, Finch R, Murrell JC, Lidstrom ME. Particulate methane monooxygenase genes in methanotrophs. J Bacteriol 1995; 177:3071-9. [PMID: 7768803 PMCID: PMC176995 DOI: 10.1128/jb.177.11.3071-3079.1995] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A 45-kDa membrane polypeptide that is associated with activity of the particulate methane monooxygenase (pMMO) has been purified from three methanotrophic bacteria, and the N-terminal amino acid sequence was found to be identical in 17 of 20 positions for all three polypeptides and identical in 14 of 20 positions for the N terminus of AmoB, the 43-kDa subunit of ammonia monooxygenase. DNA from a variety of methanotrophs was screened with two probes, an oligonucleotide designed from the N-terminal sequence of the 45-kDa polypeptide from Methylococcus capsulatus Bath and an internal fragment of amoA, which encodes the 27-kDa subunit of ammonia monooxygenase. In most cases, two hybridizing fragments were identified with each probe. Three overlapping DNA fragments containing one of the copies of the gene encoding the 45-kDa pMMO polypeptide (pmoB) were cloned from Methylococcus capsulatus Bath. A 2.1-kb region was sequenced and found to contain both pmoB and a second gene, pmoA. The predicted amino acid sequences of these genes revealed high identity with those of the gene products of amoB and amoA, respectively. Further hybridization experiments with DNA from Methylococcus capsulatus Bath and Methylobacter albus BG8 confirmed the presence of two copies of pmoB in both strains. These results suggest that the 45- and 27-kDa pMMO-associated polypeptides of methanotrophs are subunits of the pMMO and are present in duplicate gene copies in methanotrophs.
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Affiliation(s)
- J D Semrau
- California Institute of Technology, Pasadena 91125, USA
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