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Henry SP, Liosi ME, Ippolito JA, Menges F, Newton AS, Schlessinger J, Jorgensen WL. Covalent Modification of the JH2 Domain of Janus Kinase 2. ACS Med Chem Lett 2022; 13:1819-1826. [PMID: 36385940 PMCID: PMC9661697 DOI: 10.1021/acsmedchemlett.2c00414] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Probe molecules that covalently modify the JAK2 pseudokinase domain (JH2) are reported. Selective targeting of JH2 domains over the kinase (JH1) domains is a necessary feature for ligands intended to evaluate JH2 domains as therapeutic targets. The JH2 domains of three Janus kinases (JAK1, JAK2, and TYK2) possess a cysteine residue in the catalytic loop that does not occur in their JH1 domains. Starting from a non-selective kinase binding molecule, computer-aided design directed attachment of substituents terminating in acrylamide warheads to modify Cys675 of JAK2 JH2. Successful covalent attachment was demonstrated first through observation of enhanced binding with increasing incubation time in fluorescence polarization experiments. Covalent binding also increased selectivity to as much as ca. 30-fold for binding the JAK2 JH2 domain over the JH1 domain after a 20-h incubation. Covalency was confirmed through HPLC electrospray quadrupole time-of-flight HRMS experiments, which revealed the expected mass shifts.
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Affiliation(s)
- Sean P. Henry
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maria-Elena Liosi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Fabian Menges
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana S. Newton
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph Schlessinger
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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2
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Liosi ME, Ippolito JA, Henry SP, Krimmer SG, Newton AS, Cutrona KJ, Olivarez RA, Mohanty J, Schlessinger J, Jorgensen WL. Insights on JAK2 Modulation by Potent, Selective, and Cell-Permeable Pseudokinase-Domain Ligands. J Med Chem 2022; 65:8380-8400. [PMID: 35653642 PMCID: PMC9939005 DOI: 10.1021/acs.jmedchem.2c00283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
JAK2 is a non-receptor tyrosine kinase that regulates hematopoiesis through the JAK-STAT pathway. The pseudokinase domain (JH2) is an important regulator of the activity of the kinase domain (JH1). V617F mutation in JH2 has been associated with the pathogenesis of various myeloproliferative neoplasms, but JAK2 JH2 has been poorly explored as a pharmacological target. In light of this, we aimed to develop JAK2 JH2 binders that could selectively target JH2 over JH1 and test their capacity to modulate JAK2 activity in cells. Toward this goal, we optimized a diaminotriazole lead compound into potent, selective, and cell-permeable JH2 binders leveraging computational design, synthesis, binding affinity measurements for the JH1, JH2 WT, and JH2 V617F domains, permeability measurements, crystallography, and cell assays. Optimized diaminotriazoles are capable of inhibiting STAT5 phosphorylation in both WT and V617F JAK2 in cells.
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Affiliation(s)
- Maria-Elena Liosi
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | | | - Sean P. Henry
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Stefan G. Krimmer
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Ana S. Newton
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Kara J. Cutrona
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Rene A. Olivarez
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Jyotidarsini Mohanty
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA,Corresponding author. William L. Jorgensen.
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3
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Henry SP, Liosi ME, Ippolito JA, Cutrona KJ, Krimmer SG, Newton AS, Schlessinger J, Jorgensen WL. Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies. ACS Med Chem Lett 2022; 13:819-826. [PMID: 35586418 PMCID: PMC9109162 DOI: 10.1021/acsmedchemlett.2c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
The Janus kinase 2 (JAK2) pseudokinase domain (JH2) is an ATP-binding domain that regulates the activity of the catalytic tyrosine kinase domain (JH1). Dysregulation of JAK2 JH1 signaling caused by the V617F mutation in JH2 is implicated in various myeloproliferative neoplasms. To explore if JAK2 activity can be modulated by a small molecule binding to the ATP site in JH2, we have developed several ligand series aimed at selectively targeting the JAK2 JH2 domain. We report here the evolution of a false virtual screen hit into a new JAK2 JH2 series. Optimization guided by computational modeling has yielded analogues with nanomolar affinity for the JAK2 JH2 domain and >100-fold selectivity for the JH2 domain over the JH1 domain. A crystal structure for one of the potent compounds bound to JAK2 JH2 clarifies the origins of the strong binding and selectivity. The compounds expand the platform for seeking molecules to regulate JAK2 signaling, including V617F JAK2 hyperactivation.
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Affiliation(s)
- Sean P. Henry
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maria-Elena Liosi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kara J. Cutrona
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Stefan G. Krimmer
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Ana S. Newton
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph Schlessinger
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
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4
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Zhang CH, Spasov KA, Reilly RA, Hollander K, Stone EA, Ippolito JA, Liosi ME, Deshmukh MG, Tirado-Rives J, Zhang S, Liang Z, Miller SJ, Isaacs F, Lindenbach BD, Anderson KS, Jorgensen WL. Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency. ACS Med Chem Lett 2021; 12:1325-1332. [PMID: 34408808 PMCID: PMC8291137 DOI: 10.1021/acsmedchemlett.1c00326] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Non-covalent inhibitors of the main protease (Mpro) of SARS-CoV-2 having a pyridinone core were previously reported with IC50 values as low as 0.018 μM for inhibition of enzymatic activity and EC50 values as low as 0.8 μM for inhibition of viral replication in Vero E6 cells. The series has now been further advanced by consideration of placement of substituted five-membered-ring heterocycles in the S4 pocket of Mpro and N-methylation of a uracil ring. Free energy perturbation calculations provided guidance on the choice of the heterocycles, and protein crystallography confirmed the desired S4 placement. Here we report inhibitors with EC50 values as low as 0.080 μM, while remdesivir yields values of 0.5-2 μM in side-by-side testing with infectious SARS-CoV-2. A key factor in the improvement is enhanced cell permeability, as reflected in PAMPA measurements. Compounds 19 and 21 are particularly promising as potential therapies for COVID-19, featuring IC50 values of 0.044-0.061 μM, EC50 values of ca. 0.1 μM, good aqueous solubility, and no cytotoxicity.
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Affiliation(s)
- Chun-Hui Zhang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krasimir A. Spasov
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Raquel A. Reilly
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Klarissa Hollander
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Elizabeth A. Stone
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Joseph A. Ippolito
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maria-Elena Liosi
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Maya G. Deshmukh
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- M.D.−Ph.D.
Program, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Julian Tirado-Rives
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Shuo Zhang
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Zhuobin Liang
- Department
of Molecular, Cellular, and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Farren Isaacs
- Department
of Molecular, Cellular, and Developmental Biology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Brett D. Lindenbach
- Department
of Microbial Pathogenesis, Yale University
School of Medicine, New Haven, Connecticut 06536-0812, United States
| | - Karen S. Anderson
- Department
of Pharmacology, Yale University School
of Medicine, New Haven, Connecticut 06520-8066, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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5
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Newton AS, Liosi ME, Henry SP, Deiana L, Faver JC, Krimmer SG, Puleo DE, Schlessinger J, Jorgensen WL. Indoloxytriazines as binding molecules for the JAK2 JH2 pseudokinase domain and its V617F variant. Tetrahedron Lett 2021; 77. [PMID: 34393283 DOI: 10.1016/j.tetlet.2021.153248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Small molecules that selectively bind to the pseudokinase JH2 domain over the JH1 kinase domain of JAK2 kinase are sought. Virtual screening led to the purchase of 17 compounds among which 9 were found to bind to V617F JAK2 JH2 with affinities of 40 - 300 μM in a fluorogenic assay. Ten analogues were then purchased yielding 9 additional active compounds. Aminoanilinyltriazine 22 was particularly notable as it shows no detectable binding to JAK2 JH1, and it has a 65-μM dissociation constant K d with V617F JAK2 JH2. A crystal structure for 22 in complex with wild-type JAK2 JH2 was obtained to elucidate the binding mode. Additional de novo design led to the synthesis of 19 analogues of 22 with the most potent being 33n with K d values of 2-3 μM for WT and V617F JAK2 JH2, and with 16-fold selectivity relative to binding with WT JAK2 JH1.
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Affiliation(s)
- Ana S Newton
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Maria-Elena Liosi
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Sean P Henry
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Luca Deiana
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - John C Faver
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Stefan G Krimmer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
| | - David E Puleo
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
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6
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Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, Cabeza de Vaca I, Liosi ME, Anderson KS, Jorgensen WL. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. ACS Med Chem Lett 2020; 11:2526-2533. [PMID: 33324471 PMCID: PMC7605328 DOI: 10.1021/acsmedchemlett.0c00521] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
![]()
A consensus virtual screening protocol has been applied to ca.
2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 42
drugs emerged as top candidates, and after visual analyses of the
predicted structures of their complexes with Mpro, 17 were
chosen for evaluation in a kinetic assay for Mpro inhibition.
Remarkably 14 of the compounds at 100-μM concentration were
found to reduce the enzymatic activity and 5 provided IC50 values below 40 μM: manidipine (4.8 μM), boceprevir
(5.4 μM), lercanidipine (16.2 μM), bedaquiline (18.7 μM),
and efonidipine (38.5 μM). Structural analyses reveal a common
cloverleaf pattern for the binding of the active compounds to the
P1, P1′, and P2 pockets of Mpro. Further study of
the most active compounds in the context of COVID-19 therapy is warranted,
while all of the active compounds may provide a foundation for lead
optimization to deliver valuable chemotherapeutics to combat the pandemic.
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Affiliation(s)
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Maya Deshmukh
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States and
| | - Joseph A. Ippolito
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States and
| | - Chun-Hui Zhang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Israel Cabeza de Vaca
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Maria-Elena Liosi
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States and
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States,
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7
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Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, de Vaca IC, Liosi ME, Anderson KS, Jorgensen WL. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. bioRxiv 2020. [PMID: 32869018 DOI: 10.1101/2020.08.28.271957] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19. 42 drugs emerged as top candidates, and after visual analyses of the predicted structures of their complexes with M pro , 17 were chosen for evaluation in a kinetic assay for M pro inhibition. Remarkably 14 of the compounds at 100-μM concentration were found to reduce the enzymatic activity and 5 provided IC 50 values below 40 μM: manidipine (4.8 μM), boceprevir (5.4 μM), lercanidipine (16.2 μM), bedaquiline (18.7 μM), and efonidipine (38.5 μM). Structural analyses reveal a common cloverleaf pattern for the binding of the active compounds to the P1, P1', and P2 pockets of M pro . Further study of the most active compounds in the context of COVID-19 therapy is warranted, while all of the active compounds may provide a foundation for lead optimization to deliver valuable chemotherapeutics to combat the pandemic.
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8
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Liosi ME, Krimmer SG, Newton AS, Dawson TK, Puleo DE, Cutrona KJ, Suzuki Y, Schlessinger J, Jorgensen WL. Selective Janus Kinase 2 (JAK2) Pseudokinase Ligands with a Diaminotriazole Core. J Med Chem 2020; 63:5324-5340. [PMID: 32329617 DOI: 10.1021/acs.jmedchem.0c00192] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Janus kinases (JAKs) are non-receptor tyrosine kinases that are essential components of the JAK-STAT signaling pathway. Associated aberrant signaling is responsible for many forms of cancer and disorders of the immune system. The present focus is on the discovery of molecules that may regulate the activity of JAK2 by selective binding to the JAK2 pseudokinase domain, JH2. Specifically, the Val617Phe mutation in JH2 stimulates the activity of the adjacent kinase domain (JH1) resulting in myeloproliferative disorders. Starting from a non-selective screening hit, we have achieved the goal of discovering molecules that preferentially bind to the ATP binding site in JH2 instead of JH1. We report the design and synthesis of the compounds and binding results for the JH1, JH2, and JH2 V617F domains, as well as five crystal structures for JH2 complexes. Testing with a selective and non-selective JH2 binder on the autophosphorylation of wild-type and V617F JAK2 is also contrasted.
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Affiliation(s)
- Maria-Elena Liosi
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Stefan G Krimmer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Ana S Newton
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Thomas K Dawson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - David E Puleo
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Kara J Cutrona
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Yoshihisa Suzuki
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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