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Shukri A, Carroll AC, Collins R, Charih F, Wong A, Biggar KK. Systematic in vitro optimization of antimicrobial peptides against Escherichia coli. JAC Antimicrob Resist 2024; 6:dlae096. [PMID: 38966332 PMCID: PMC11220656 DOI: 10.1093/jacamr/dlae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/21/2024] [Indexed: 07/06/2024] Open
Abstract
Objectives Antimicrobial resistance is a growing concern and claims over 1 million lives per year. The discovery of new antimicrobial drugs is expensive and often generates low profitability, with very low success rates. One way to combat this is by the improvement of known antimicrobials, such as antimicrobial peptides (AMPs). The aim of this study was to improve the antimicrobial activities of two known AMPs, UyCT3 and indolicidin, with the use of peptide libraries and growth curves. Methods Peptide permutation libraries were synthesized for two AMPs, indolicidin and UyCT3, which included 520 peptides. These peptides were subsequently tested against MG1655-K12, to which subsequent peptide design was performed, then tested against three clinically Gram-negative relevant drug-resistant isolates. Best-performing candidates were subjected to a haemolysis assay for toxicity validation. Results Single amino acid permutations of UyCT3 and indolicidin were sufficient to inhibit growth of MG1655-K12, and subsequent generations of peptide design were able to inhibit growth of clinical isolates at concentrations as low as 5 µM. Our best-performing AMP, UyCT3I5A, W6Y, K10I, F13I, was not seen to be toxic towards sheep RBCs. Conclusions The efficacy of the AMPs improved with the use of our peptide library technology, whereby an AMP was found that inhibited bacterial growth of clinical Gram-negative isolates 4-fold better than its WT counterpart.
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Affiliation(s)
- Ali Shukri
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Amanda C Carroll
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Ryan Collins
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Francois Charih
- Department of Systems and Computer Engineering, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Alex Wong
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
| | - Kyle K Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
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2
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The Multitasker Protein: A Look at the Multiple Capabilities of NUMB. Cells 2023; 12:cells12020333. [PMID: 36672267 PMCID: PMC9856935 DOI: 10.3390/cells12020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
NUMB, a plasma membrane-associated protein originally described in Drosophila, is involved in determining cell function and fate during early stages of development. It is secreted asymmetrically in dividing cells, with one daughter cell inheriting NUMB and the other inheriting its antagonist, NOTCH. NUMB has been proposed as a polarizing agent and has multiple functions, including endocytosis and serving as an adaptor in various cellular pathways such as NOTCH, Hedgehog, and the P53-MDM2 axis. Due to its role in maintaining cellular homeostasis, it has been suggested that NUMB may be involved in various human pathologies such as cancer and Alzheimer's disease. Further research on NUMB could aid in understanding disease mechanisms and advancing the field of personalized medicine and the development of new therapies.
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Chopra A, Shukri AH, Adhikary H, Lukinović V, Hoekstra M, Cowpland M, Biggar KK. A peptide array pipeline for the development of Spike-ACE2 interaction inhibitors. Peptides 2022; 158:170898. [PMID: 36279985 PMCID: PMC9585897 DOI: 10.1016/j.peptides.2022.170898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/27/2022]
Abstract
In humans, coronaviruses are the cause of endemic illness and have been the causative agents of more severe epidemics. Most recently, SARS-CoV-2 was the causative agent of the COVID19 pandemic. Thus, there is a high interest in developing therapeutic agents targeting various stages of the coronavirus viral life cycle to disrupt viral propagation. Besides the development of small-molecule therapeutics that target viral proteases, there is also interest molecular tools to inhibit the initial event of viral attachment of the SARS-CoV-2 Spike protein to host ACE2 surface receptor. Here, we leveraged known structural information and peptide arrays to develop an in vitro peptide inhibitor of the Spike-ACE2 interaction. First, from previous co-crystal structures of the Spike-ACE2 complex, we identified an initial 24-residue long region (sequence: STIEEQAKTFLDKFNHEAEDLFYQ) on the ACE2 sequence that encompasses most of the known contact residues. Next, we scanned this 24-mer window along the ACE2 N-terminal helix and found that maximal binding to the SARS-CoV-2 receptor binding domain (CoV2-RBD) was increased when this window was shifted nine residues in the N-terminal direction. Further, by systematic permutation of this shifted ACE2-derived peptide we identified mutations to the wildtype sequence that confer increased binding of the CoV2-RBD. Among these peptides, we identified binding peptide 19 (referred to as BP19; sequence: SLVAVTAAQSTIEEQAKTFLDKFI) as an in vitro inhibitor of the Spike-ACE2 interaction with an IC50 of 2.08 ± 0.38 μM. Overall, BP19 adds to the arsenal of Spike-ACE2 inhibitors, and this study highlights the utility of systematic peptide arrays as a platform for the development of coronavirus protein inhibitors.
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Affiliation(s)
- Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Ali H Shukri
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Hemanta Adhikary
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Valentina Lukinović
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Matthew Hoekstra
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Michael Cowpland
- NuvoBio Corporation, 150 Isabella Street, Suite 150, Ottawa, ON, K1S 1V7, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; Department of Biology, Carleton University, Ottawa, ON, Canada.
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4
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Hoekstra M, Chopra A, Willmore WG, Biggar KK. Evaluation of Jumonji C lysine demethylase substrate preference to guide identification of in vitro substrates. STAR Protoc 2022; 3:101271. [PMID: 35378885 PMCID: PMC8976124 DOI: 10.1016/j.xpro.2022.101271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Within the realm of lysine methylation, the discovery of lysine methyltransferase (KMTs) substrates has been burgeoning because of established systematic substrate screening protocols. Here, we describe a protocol enabling the systematic identification of JmjC KDM substrate preference and in vitro substrates. Systematically designed peptide libraries containing methylated lysine residues are used to characterize enzyme-substrate preference and identify new candidate substrates in vitro. For complete details on the use and execution of this protocol, please refer to Hoekstra and Biggar (2021). Use of a permutated substrate library to define JmjC KDM recognition motifs JmjC KDM activity is measured via luminescent detection of succinate Recognition motifs enable prediction of novel in vitro substrates of JmjC KDMs
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Affiliation(s)
- Matthew Hoekstra
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Anand Chopra
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - William G. Willmore
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Kyle K. Biggar
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
- Corresponding author
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5
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Chopra A, Willmore WG, Biggar KK. Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A. Biomolecules 2022; 12:biom12050641. [PMID: 35625569 PMCID: PMC9139010 DOI: 10.3390/biom12050641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 02/07/2023] Open
Abstract
Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the removal of methyl (-CH3) groups from modified lysyl residues. Several JmjC KDMs promote cancerous properties and these findings have primarily been in relation to histone demethylation. However, the biological roles of these enzymes are increasingly being shown to also be attributed to non-histone demethylation. Notably, KDM3A has become relevant to tumour progression due to recent findings of this enzyme's role in promoting cancerous phenotypes, such as enhanced glucose consumption and upregulated mechanisms of chemoresistance. To aid in uncovering the mechanism(s) by which KDM3A imparts its oncogenic function(s), this study aimed to unravel KDM3A substrate specificity to predict high-confidence substrates. Firstly, substrate specificity was assessed by monitoring activity towards a peptide permutation library of histone H3 di-methylated at lysine-9 (i.e., H3K9me2). From this, the KDM3A recognition motif was established and used to define a set of high-confidence predictions of demethylation sites from within the KDM3A interactome. Notably, this led to the identification of three in vitro substrates (MLL1, p300, and KDM6B), which are relevant to the field of cancer progression. This preliminary data may be exploited in further tissue culture experiments to decipher the avenues by which KDM3A imparts cancerous phenotypes.
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Affiliation(s)
- Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - William G. Willmore
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence: (W.G.W.); (K.K.B.)
| | - Kyle K. Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada;
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Correspondence: (W.G.W.); (K.K.B.)
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6
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McKenna M, Balasuriya N, Zhong S, Li SSC, O'Donoghue P. Phospho-Form Specific Substrates of Protein Kinase B (AKT1). Front Bioeng Biotechnol 2021; 8:619252. [PMID: 33614606 PMCID: PMC7886700 DOI: 10.3389/fbioe.2020.619252] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022] Open
Abstract
Protein kinase B (AKT1) is hyper-activated in diverse human tumors. AKT1 is activated by phosphorylation at two key regulatory sites, Thr308 and Ser473. Active AKT1 phosphorylates many, perhaps hundreds, of downstream cellular targets in the cytosol and nucleus. AKT1 is well-known for phosphorylating proteins that regulate cell survival and apoptosis, however, the full catalog of AKT1 substrates remains unknown. Using peptide arrays, we recently discovered that each phosphorylated form of AKT1 (pAKT1S473, pAKT1T308, and ppAKT1S473,T308) has a distinct substrate specificity, and these data were used to predict potential new AKT1 substrates. To test the high-confidence predictions, we synthesized target peptides representing putative AKT1 substrates. Peptides substrates were synthesized by solid phase synthesis and their purity was confirmed by mass spectrometry. Most of the predicted peptides showed phosphate accepting activity similar to or greater than that observed with a peptide derived from a well-established AKT1 substrate, glycogen synthase kinase 3β (GSK-3β). Among the novel substrates, AKT1 was most active with peptides representing PIP3-binding protein Rab11 family-interacting protein 2 and cysteinyl leukotriene receptor 1, indicating their potential role in AKT1-dependent cellular signaling. The ppAKT1S473,T308 enzyme was highly selective for peptides containing a patch of basic residues at −5, −4, −3 and aromatic residues (Phe/Tyr) at +1 positions from the phosphorylation site. The pAKT1S473 variant preferred more acidic peptides, Ser or Pro at +4, and was agnostic to the residue at −5. The data further support our hypothesis that Ser473 phosphorylation plays a key role in modulating AKT1 substrate selectivity.
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Affiliation(s)
- McShane McKenna
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Shanshan Zhong
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Shawn Shun-Cheng Li
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada.,Department of Chemistry, The University of Western Ontario, London, ON, Canada
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7
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Balasuriya N, Davey NE, Johnson JL, Liu H, Biggar KK, Cantley LC, Li SSC, O'Donoghue P. Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1). J Biol Chem 2020; 295:8120-8134. [PMID: 32350110 DOI: 10.1074/jbc.ra119.012425] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/22/2020] [Indexed: 12/31/2022] Open
Abstract
Protein kinase B (AKT1) is a central node in a signaling pathway that regulates cell survival. The diverse pathways regulated by AKT1 are communicated in the cell via the phosphorylation of perhaps more than 100 cellular substrates. AKT1 is itself activated by phosphorylation at Thr-308 and Ser-473. Despite the fact that these phosphorylation sites are biomarkers for cancers and tumor biology, their individual roles in shaping AKT1 substrate selectivity are unknown. We recently developed a method to produce AKT1 with programmed phosphorylation at either or both of its key regulatory sites. Here, we used both defined and randomized peptide libraries to map the substrate selectivity of site-specific, singly and doubly phosphorylated AKT1 variants. To globally quantitate AKT1 substrate preferences, we synthesized three AKT1 substrate peptide libraries: one based on 84 "known" substrates and two independent and larger oriented peptide array libraries (OPALs) of ∼1011 peptides each. We found that each phospho-form of AKT1 has common and distinct substrate requirements. Compared with pAKT1T308, the addition of Ser-473 phosphorylation increased AKT1 activities on some, but not all of its substrates. This is the first report that Ser-473 phosphorylation can positively or negatively regulate kinase activity in a substrate-dependent fashion. Bioinformatics analysis indicated that the OPAL-activity data effectively discriminate known AKT1 substrates from closely related kinase substrates. Our results also enabled predictions of novel AKT1 substrates that suggest new and expanded roles for AKT1 signaling in regulating cellular processes.
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Affiliation(s)
- Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, New York, United States
| | - Huadong Liu
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.,Center for Mitochondrial Biology and Medicine, Xi'an Jiaotong University, Xi'an, Shanxi, China
| | - Kyle K Biggar
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada.,Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, New York, United States
| | - Shawn Shun-Cheng Li
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada .,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
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8
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Wei R, Liu X, Voss C, Qin W, Dagnino L, Li L, Vigny M, Li SSC. NUMB regulates the endocytosis and activity of the anaplastic lymphoma kinase in an isoform-specific manner. J Mol Cell Biol 2019; 11:994-1005. [PMID: 30726988 PMCID: PMC6927325 DOI: 10.1093/jmcb/mjz003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/07/2018] [Accepted: 02/04/2019] [Indexed: 12/11/2022] Open
Abstract
NUMB is an evolutionarily conserved protein that plays an important role in cell adhesion, migration, polarity, and cell fate determination. It has also been shown to play a role in the pathogenesis of certain cancers, although it remains controversial whether NUMB functions as an oncoprotein or tumor suppressor. Here, we show that NUMB binds to anaplastic lymphoma kinase (ALK), a receptor tyrosine kinase aberrantly activated in several forms of cancer, and this interaction regulates the endocytosis and activity of ALK. Intriguingly, the function of the NUMB-ALK interaction is isoform-dependent. While both p66-NUMB and p72-NUMB isoforms are capable of mediating the endocytosis of ALK, the former directs ALK to the lysosomal degradation pathway, thus decreasing the overall ALK level and the downstream MAP kinase signal. In contrast, the p72-NUMB isoform promotes ALK recycling back to the plasma membrane, thereby maintaining the kinase in its active state. Our work sheds light on the controversial role of different isoforms of NUMB in tumorigenesis and provides mechanistic insight into ALK regulation.
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Affiliation(s)
- Ran Wei
- Departments of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Dentistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Xuguang Liu
- Departments of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Courtney Voss
- Departments of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Wentao Qin
- Departments of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Lina Dagnino
- Physiology and Pharmacology and Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Lei Li
- School of Basic Medical Sciences, Qingdao University, Qingdao, Shandong, China
| | - Marc Vigny
- Université Pierre et Marie Curie, UPMC, INSERM UMRS-839, Paris, France
| | - Shawn Shun-Cheng Li
- Departments of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Oncology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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9
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PeSA: A software tool for peptide specificity analysis. Comput Biol Chem 2019; 83:107145. [DOI: 10.1016/j.compbiolchem.2019.107145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 10/08/2019] [Indexed: 12/11/2022]
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10
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Exon 3 of the NUMB Gene Emerged in the Chordate Lineage Coopting the NUMB Protein to the Regulation of MDM2. G3-GENES GENOMES GENETICS 2019; 9:3359-3367. [PMID: 31451549 PMCID: PMC6778778 DOI: 10.1534/g3.119.400494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
MDM2 regulates a variety of cellular processes through its dual protein:protein interaction and ubiquitin ligase activities. One major function of MDM2 is to bind and ubiquitinate P53, thereby regulating its proteasomal degradation. This function is in turn controlled by the cell fate determinant NUMB, which binds to and inhibits MDM2 via a short stretch of 11 amino acids, contained in its phosphotyrosine-binding (PTB) domain, encoded by exon 3 of the NUMB gene. The NUMB-MDM2-P53 circuitry is relevant to the specification of the stem cell fate and its subversion has been shown to be causal in breast cancer leading to the emergence of cancer stem cells. While extensive work on the evolutionary aspects of the MDM2/P53 circuitry has provided hints as to how these two proteins have evolved together to maintain conserved and linked functions, little is known about the evolution of the NUMB gene and, in particular, how it developed the ability to regulate MDM2 function. Here, we show that NUMB is a metazoan gene, which acquired exon 3 in the common ancestor of the Chordate lineage, first being present in the Cephalochordate and Tunicate subphyla, but absent in invertebrates. We provide experimental evidence showing that since its emergence, exon 3 conferred to the PTB domain of NUMB the ability to bind and to regulate MDM2 functions.
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