1
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Goettig P, Chen X, Harris JM. Correlation of Experimental and Calculated Inhibition Constants of Protease Inhibitor Complexes. Int J Mol Sci 2024; 25:2429. [PMID: 38397107 PMCID: PMC10889394 DOI: 10.3390/ijms25042429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Predicting the potency of inhibitors is key to in silico screening of promising synthetic or natural compounds. Here we describe a predictive workflow that provides calculated inhibitory values, which concord well with empirical data. Calculations of the free interaction energy ΔG with the YASARA plugin FoldX were used to derive inhibition constants Ki from PDB coordinates of protease-inhibitor complexes. At the same time, corresponding KD values were obtained from the PRODIGY server. These results correlated well with the experimental values, particularly for serine proteases. In addition, analyses were performed for inhibitory complexes of cysteine and aspartic proteases, as well as of metalloproteases, whereby the PRODIGY data appeared to be more consistent. Based on our analyses, we calculated theoretical Ki values for trypsin with sunflower trypsin inhibitor (SFTI-1) variants, which yielded the more rigid Pro14 variant, with probably higher potency than the wild-type inhibitor. Moreover, a hirudin variant with an Arg1 and Trp3 is a promising basis for novel thrombin inhibitors with high potency. Further examples from antibody interaction and a cancer-related effector-receptor system demonstrate that our approach is applicable to protein interaction studies beyond the protease field.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Xingchen Chen
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia or (X.C.); (J.M.H.)
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2
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Muhammad T, Houssen WE, Thomas L, Alexandru-Crivac CN, Gunasekera S, Jaspars M, Göransson U. Exploring the Limits of Cyanobactin Macrocyclase PatGmac: Cyclization of PawS-Derived Peptide Sunflower Trypsin Inhibitor-1 and Cyclotide Kalata B1. JOURNAL OF NATURAL PRODUCTS 2023; 86:566-573. [PMID: 36917740 PMCID: PMC10043927 DOI: 10.1021/acs.jnatprod.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The subtilisin-like macrocyclase PatGmac is produced by the marine cyanobacterium Prochloron didemni. This enzyme is involved in the last step of the biosynthesis of patellamides, a cyanobactin type of ribosomally expressed and post-translationally modified cyclic peptides. PatGmac recognizes, cleaves, and cyclizes precursor peptides after a specific recognition motif comprised of a C-terminal tail with the sequence motif -AYDG. The result is the native macrocyclic patellamide, which has eight amino acid residues. Macrocyclase activity can be exploited by incorporating that motif in other short linear peptide precursors, which then are formed into head-to-tail cyclized peptides. Here, we explore the possibility of using PatGmac in the cyclization of peptides larger than the patellamides, namely, the PawS-derived peptide sunflower trypsin inhibitor-1 (SFTI-1) and the cyclotide kalata B1. These peptides fall under two distinct families of disulfide constrained macrocyclic plant peptides. They are both implicated as scaffolds for drug design due to their structures and unusual stability. We show that PatGmac can be used to efficiently cyclize the 14 amino acid residue long SFTI-1, but less so the 29 amino acid residue long kalata B1.
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Affiliation(s)
- Taj Muhammad
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
| | - Wael E Houssen
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Louise Thomas
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Cristina-Nicoleta Alexandru-Crivac
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
- Institute
of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K.
| | - Sunithi Gunasekera
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
| | - Marcel Jaspars
- Department
of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Aberdeen AB24 3UE, Scotland, U.K.
| | - Ulf Göransson
- Pharmacognosy,
Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Box 591, SE-75124 Uppsala, Sweden
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3
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Mazumder T, Hasan T, Ahmed KS, Hossain H, Debnath T, Jahan E, Rahman N, Rahman Shuvo MS, Daula AFMSU. Phenolic compounds and extracts from Crotalaria calycina Schrank potentially alleviate pain and inflammation through inhibition of cyclooxygenase-2: An in vivo and molecular dynamics studies. Heliyon 2022; 8:e12368. [PMID: 36590510 PMCID: PMC9800535 DOI: 10.1016/j.heliyon.2022.e12368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Crotalaria calycina Schrank is a local Bangladeshi plant well-accepted by the tribal population for its medicinal properties. The primary approach of our study was to uncover the analgesic and anti-inflammatory potential of methanol extract of C. calycina stem in mice model with in silico molecular docking and molecular dynamics simulation approach. Phenolic compounds were identified and quantified from the extract through high-performance liquid chromatography-diode array detector (HPLC-DAD) analysis. Writhing assay through injection of acetic acid, licking assay through formalin injection, and finally, hot plate assay was employed to observe the analgesic activity. The carrageenan-induced paw edema model was employed to determine the anti-inflammatory potential of the extract. In silico molecular docking and molecular dynamics were also run to validate the in vivo study results. Eight polyphenolic compounds from the extract were identified and quantified via HPLC-DAD analysis, and (-) epicatechin was most abundantly distributed (87.15 ± 0.24 mg/100 g dry extract). In vivo study revealed that 400 mg/kg dose significantly inhibited (P < 0.01) the writhing response in the writhing assay and demonstrated the highest percent of inhibition of licking (70.67%) in the late part of the licking test. The same extract dose produced the highest (74.71%) percent of maximal effect (% MPE) in the hot plate assay. It demonstrated the highest percent of edema inhibition (68.00%) in the fourth hour of the paw edema assay. Molecular docking and molecular dynamics simulation of (-) epicatechin, caffeic acid, and kaempferol with cyclooxygenase-2 revealed that they have similar interactions to the standard inhibitor celecoxib. These valuable bioactive compounds may induce significant analgesic and anti-inflammatory properties in MECCS. Therefore, based on the findings of this study, it can be concluded that C. calycina stem can be a prospect in the medicinal field due to its remarkable analgesic and anti-inflammatory effect.
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Affiliation(s)
- Tanoy Mazumder
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh
| | - Tarek Hasan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh
| | - Khondoker Shahin Ahmed
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Hemayet Hossain
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Tushar Debnath
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh
| | - Esrat Jahan
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh
| | - Naiemur Rahman
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh
| | - Md. Sadikur Rahman Shuvo
- Department of Microbiology, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh,Corresponding author.
| | - A F M Shahid Ud Daula
- Department of Pharmacy, Noakhali Science and Technology University, Sonapur, Noakhali, 3814, Bangladesh,Corresponding author.
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Jackson MA, Chan LY, Harding MD, Craik DJ, Gilding EK. Rational domestication of a plant-based recombinant expression system expands its biosynthetic range. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6103-6114. [PMID: 35724659 PMCID: PMC9578353 DOI: 10.1093/jxb/erac273] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/20/2022] [Indexed: 05/22/2023]
Abstract
Plant molecular farming aims to provide a green, flexible, and rapid alternative to conventional recombinant expression systems, capable of producing complex biologics such as enzymes, vaccines, and antibodies. Historically, the recombinant expression of therapeutic peptides in plants has proven difficult, largely due to their small size and instability. However, some plant species harbour the capacity for peptide backbone cyclization, a feature inherent in stable therapeutic peptides. One obstacle to realizing the potential of plant-based therapeutic peptide production is the proteolysis of the precursor before it is matured into its final stabilized form. Here we demonstrate the rational domestication of Nicotiana benthamiana within two generations to endow this plant molecular farming host with an expanded repertoire of peptide sequence space. The in planta production of molecules including an insecticidal peptide, a prostate cancer therapeutic lead, and an orally active analgesic is demonstrated.
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Affiliation(s)
- Mark A Jackson
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Maxim D Harding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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5
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de Almeida Barros R, Meriño-Cabrera Y, Castro JS, da Silva Junior NR, de Oliveira JVA, Schultz H, de Andrade RJ, de Oliveira Ramos HJ, de Almeida Oliveira MG. Bovine pancreatic trypsin inhibitor and soybean Kunitz trypsin inhibitor: Differential effects on proteases and larval development of the soybean pest Anticarsia gemmatalis (Lepidoptera: Noctuidae). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 187:105188. [PMID: 36127063 DOI: 10.1016/j.pestbp.2022.105188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Pest management is challenged with resistant herbivores and problems regarding human health and environmental issues. Indeed, the greatest challenge to modern agriculture is to protect crops from pests and still maintain environmental quality. This study aimed to analyze by in silico, in vitro, and in vivo approaches to the feasibility of using the inhibitory protein extracted from mammals - Bovine Pancreatic Trypsin Inhibitor (BPTI) as a potential inhibitor of digestive trypsins from the pest Anticarsia gemmatalis and comparing the results with the host-plant inhibitor - Soybean Kunitz Trypsin Inhibitor (SKTI). BPTI and SKTI interacts with A. gemmatalis trypsin-like enzyme competitively, through hydrogen and hydrophobic bonds. A. gemmatalis larvae exposed to BPTI did not show two common adaptative mechanisms i.e., proteolytic degradation and overproduction of proteases, presenting highly reduced trypsin-like activity. On the other hand, SKTI-fed larvae did not show reduced trypsin-like activity, presenting overproduction of proteases and SKTI digestion. In addition, the larval survival was reduced by BPTI similarly to SKTI, and additionally caused a decrease in pupal weight. The non-plant protease inhibitor BPTI presents intriguing element to compose biopesticide formulations to help decrease the use of conventional refractory pesticides into integrated pest management programs.
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Affiliation(s)
- Rafael de Almeida Barros
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Yaremis Meriño-Cabrera
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - José Severiche Castro
- Departamento de Física, Universidad de Sucre, Sincelejo, Colombia; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Neilier Rodrigues da Silva Junior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - João Vitor Aguilar de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Halina Schultz
- Departamento de Entomologia, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Rafael Júnior de Andrade
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Humberto Josué de Oliveira Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Maria Goreti de Almeida Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil.
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6
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Talukder S, Ahmed KS, Hossain H, Hasan T, Liya IJ, Amanat M, Nahar N, Shuvo MSR, Daula AFMSU. Fimbristylis aestivalis Vahl: a potential source of cyclooxygenase-2 (COX-2) inhibitors. Inflammopharmacology 2022; 30:2301-2315. [PMID: 36056995 DOI: 10.1007/s10787-022-01057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/14/2022] [Indexed: 11/27/2022]
Abstract
Cyclooxygenase-2 (COX-2) is an inducible enzyme that accelerates the biosynthesis of PGs during inflammation and has emerged as an important therapeutic target for anti-inflammatory drugs. Natural compounds may serve as a source of inspiration for pharmaceutical chemists and a foundation for developing innovative COX-2 inhibitors with fewer side effects. Therefore, the objective of this study was to identify the potent COX-2 inhibitor and anti-inflammatory activity of the Fimbristylis aestivalis whole plant extract (FAWE). The plant extract was found dominant with rosmarinic acid followed by catechin hydrate, syringic acid, rutin hydrate, (-) epicatechin, quercetin, myricetin, and catechol. FAWE exhibited considerable dose-dependent analgesic efficacy in all analgesic test models. FAWE also showed promising anti-inflammatory potential in carrageenan-induced inflammations in mice. This result was corroborated by molecular docking, revealing that the aforesaid natural polyphenols adopt the same orientation as celecoxib in the COX-2 active site. On the other hand, molecular dynamics (MD) simulations were performed between the most abundant components (rosmarinic acid, catechin hydrate, and syringic acid) and COX-2. Based on hydrogen bonding, RMSD, RMSF, radius of gyration, PCA, and Gibbs free energy landscape analysis, the results demonstrated that these compounds are very stable in the active site of COX-2, indicating substantial COX-2 inhibitory activity.
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Affiliation(s)
- Saduddin Talukder
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh
| | - Khondoker Shahin Ahmed
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Hemayet Hossain
- Chemical Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Tarek Hasan
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh
| | - Israt Jahan Liya
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh
| | - Muhammed Amanat
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh
| | - Nurun Nahar
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh
| | - Md Sadikur Rahman Shuvo
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh.
| | - A F M Shahid Ud Daula
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Sonapur, 3814, Bangladesh.
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Dürvanger Z, Boros E, Nagy ZA, Hegedüs R, Megyeri M, Dobó J, Gál P, Schlosser G, Ángyán AF, Gáspári Z, Perczel A, Harmat V, Mező G, Menyhárd DK, Pál G. Directed Evolution-Driven Increase of Structural Plasticity Is a Prerequisite for Binding the Complement Lectin Pathway Blocking MASP-Inhibitor Peptides. ACS Chem Biol 2022; 17:969-986. [PMID: 35378038 PMCID: PMC9016712 DOI: 10.1021/acschembio.2c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
MASP-1 and MASP-2
are key activator proteases of the complement
lectin pathway. The first specific mannose-binding lectin-associated
serine protease (MASP) inhibitors had been developed from the 14-amino-acid
sunflower trypsin inhibitor (SFTI) peptide by phage display, yielding
SFTI-based MASP inhibitors, SFMIs. Here, we present the crystal structure
of the MASP-1/SFMI1 complex that we analyzed in comparison to other
existing MASP-1/2 structures. Rigidified backbone structure has long
been accepted as a structural prerequisite for peptide inhibitors
of proteases. We found that a hydrophobic cluster organized around
the P2 Thr residue is essential for the structural stability of wild-type
SFTI. We also found that the same P2 Thr prevents binding of the rigid
SFTI-like peptides to the substrate-binding cleft of both MASPs as
the cleft is partially blocked by large gatekeeper enzyme loops. Directed
evolution removed this obstacle by replacing the P2 Thr with a Ser,
providing the SFMIs with high-degree structural plasticity, which
proved to be essential for MASP inhibition. To gain more insight into
the structural criteria for SFMI-based MASP-2 inhibition, we systematically
modified MASP-2-specific SFMI2 by capping its two termini and by replacing
its disulfide bridge with varying length thioether linkers. By doing
so, we also aimed to generate a versatile scaffold that is resistant
to reducing environment and has increased stability in exopeptidase-containing
biological environments. We found that the reduction-resistant disulfide-substituted l-2,3-diaminopropionic acid (Dap) variant possessed near-native
potency. As MASP-2 is involved in the life-threatening thrombosis
in COVID-19 patients, our synthetic, selective MASP-2 inhibitors could
be relevant coronavirus drug candidates.
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Affiliation(s)
- Zsolt Dürvanger
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Eszter Boros
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Zoltán Attila Nagy
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Rózsa Hegedüs
- MTA-ELTE Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Márton Megyeri
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - Péter Gál
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117 Budapest, Hungary
| | - Annamária F. Ángyán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, H-1083 Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, H-1083 Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- MTA-ELTE Protein Modelling Research Group, Eötvös
Loránd Research Network, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Veronika Harmat
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- MTA-ELTE Protein Modelling Research Group, Eötvös
Loránd Research Network, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
- Department of Organic Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest H-1117, Hungary
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
- MTA-ELTE Protein Modelling Research Group, Eötvös
Loránd Research Network, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gábor Pál
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
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8
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Babii O, Afonin S, Diel C, Huhn M, Dommermuth J, Schober T, Koniev S, Hrebonkin A, Nesterov‐Mueller A, Komarov IV, Ulrich AS. Diarylethene-Based Photoswitchable Inhibitors of Serine Proteases. Angew Chem Int Ed Engl 2021; 60:21789-21794. [PMID: 34268844 PMCID: PMC8519022 DOI: 10.1002/anie.202108847] [Citation(s) in RCA: 6] [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: 07/03/2021] [Indexed: 12/20/2022]
Abstract
A bicyclic peptide scaffold was chemically adapted to generate diarylethene-based photoswitchable inhibitors of serine protease Bos taurus trypsin 1 (T1). Starting from a prototype molecule-sunflower trypsin inhibitor-1 (SFTI-1)-we obtained light-controllable inhibitors of T1 with Ki in the low nanomolar range, whose activity could be modulated over 20-fold by irradiation. The inhibitory potency as well as resistance to proteolytic degradation were systematically studied on a series of 17 SFTI-1 analogues. The hydrogen bond network that stabilizes the structure of inhibitors and possibly the enzyme-inhibitor binding dynamics were affected by isomerization of the photoswitch. The feasibility of manipulating enzyme activity in time and space was demonstrated by controlled digestion of gelatin-based hydrogel and an antimicrobial peptide BP100-RW. Finally, our design principles of diarylethene photoswitches are shown to apply also for the development of other serine protease inhibitors.
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Affiliation(s)
- Oleg Babii
- Institute of Biological Interfaces (IBG-2)Karlsruhe Institute of Technology (KIT)POB 364076021KarlsruheGermany
- Institute of Microstructure Technology (IMT)KITHermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2)Karlsruhe Institute of Technology (KIT)POB 364076021KarlsruheGermany
| | - Christian Diel
- Institute of Organic Chemistry (IOC)KITFritz-Haber-Weg 676131KarlsruheGermany
| | - Marcel Huhn
- Institute of Organic Chemistry (IOC)KITFritz-Haber-Weg 676131KarlsruheGermany
| | - Jennifer Dommermuth
- Institute of Organic Chemistry (IOC)KITFritz-Haber-Weg 676131KarlsruheGermany
| | - Tim Schober
- Institute of Organic Chemistry (IOC)KITFritz-Haber-Weg 676131KarlsruheGermany
- Lumobiotics GmbHAuer Straße 276227KarlsruheGermany
| | - Serhii Koniev
- Taras Shevchenko National University of Kyivvul. Volodymyrska 601601KyivUkraine
| | - Andrii Hrebonkin
- Institute of Biological Interfaces (IBG-2)Karlsruhe Institute of Technology (KIT)POB 364076021KarlsruheGermany
| | - Alexander Nesterov‐Mueller
- Institute of Microstructure Technology (IMT)KITHermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyivvul. Volodymyrska 601601KyivUkraine
- Lumobiotics GmbHAuer Straße 276227KarlsruheGermany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2)Karlsruhe Institute of Technology (KIT)POB 364076021KarlsruheGermany
- Institute of Organic Chemistry (IOC)KITFritz-Haber-Weg 676131KarlsruheGermany
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9
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Babii O, Afonin S, Diel C, Huhn M, Dommermuth J, Schober T, Koniev S, Hrebonkin A, Nesterov‐Mueller A, Komarov IV, Ulrich AS. Diarylethen‐basierte lichtschaltbare Inhibitoren von Serinproteasen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Oleg Babii
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Deutschland
- Institute of Microstructure Technology (IMT) KIT Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Deutschland
| | - Christian Diel
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Marcel Huhn
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Jennifer Dommermuth
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Tim Schober
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
- Lumobiotics GmbH Auer Straße 2 76227 Karlsruhe Deutschland
| | - Serhii Koniev
- Taras Shevchenko National University of Kyiv vul. Volodymyrska 60 1601 Kyiv Ukraine
| | - Andrii Hrebonkin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Deutschland
| | - Alexander Nesterov‐Mueller
- Institute of Microstructure Technology (IMT) KIT Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Deutschland
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv vul. Volodymyrska 60 1601 Kyiv Ukraine
- Lumobiotics GmbH Auer Straße 2 76227 Karlsruhe Deutschland
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Deutschland
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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10
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de Veer SJ, White AM, Craik DJ. Sunflower Trypsin Inhibitor-1 (SFTI-1): Sowing Seeds in the Fields of Chemistry and Biology. Angew Chem Int Ed Engl 2020; 60:8050-8071. [PMID: 32621554 DOI: 10.1002/anie.202006919] [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: 05/13/2020] [Indexed: 12/24/2022]
Abstract
Nature-derived cyclic peptides have proven to be a vast source of inspiration for advancing modern pharmaceutical design and synthetic chemistry. The focus of this Review is sunflower trypsin inhibitor-1 (SFTI-1), one of the smallest disulfide-bridged cyclic peptides found in nature. SFTI-1 has an unusual biosynthetic pathway that begins with a dual-purpose albumin precursor and ends with the production of a high-affinity serine protease inhibitor that rivals other inhibitors much larger in size. Investigations on the molecular basis for SFTI-1's rigid structure and adaptable function have planted seeds for thought that have now blossomed in several different fields. Here we survey these applications to highlight the growing potential of SFTI-1 as a versatile template for engineering inhibitors, a prototypic peptide for studying inhibitory mechanisms, a stable scaffold for grafting bioactive peptides, and a model peptide for evaluating peptidomimetic motifs and platform technologies.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
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11
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Veer SJ, White AM, Craik DJ. Der Sonnenblumen‐Trypsin‐Inhibitor 1 (SFTI‐1) in der Chemie und Biologie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Simon J. Veer
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - Andrew M. White
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - David J. Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
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12
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Chen X, Leahy D, Van Haeften J, Hartfield P, Prentis PJ, van der Burg CA, Surm JM, Pavasovic A, Madio B, Hamilton BR, King GF, Undheim EAB, Brattsand M, Harris JM. A Versatile and Robust Serine Protease Inhibitor Scaffold from Actinia tenebrosa. Mar Drugs 2019; 17:E701. [PMID: 31842369 PMCID: PMC6950308 DOI: 10.3390/md17120701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022] Open
Abstract
Serine proteases play pivotal roles in normal physiology and a spectrum of patho-physiological processes. Accordingly, there is considerable interest in the discovery and design of potent serine protease inhibitors for therapeutic applications. This led to concerted efforts to discover versatile and robust molecular scaffolds for inhibitor design. This investigation is a bioprospecting study that aims to isolate and identify protease inhibitors from the cnidarian Actinia tenebrosa. The study isolated two Kunitz-type protease inhibitors with very similar sequences but quite divergent inhibitory potencies when assayed against bovine trypsin, chymostrypsin, and a selection of human sequence-related peptidases. Homology modeling and molecular dynamics simulations of these inhibitors in complex with their targets were carried out and, collectively, these methodologies enabled the definition of a versatile scaffold for inhibitor design. Thermal denaturation studies showed that the inhibitors were remarkably robust. To gain a fine-grained map of the residues responsible for this stability, we conducted in silico alanine scanning and quantified individual residue contributions to the inhibitor's stability. Sequences of these inhibitors were then used to search for Kunitz homologs in an A. tenebrosa transcriptome library, resulting in the discovery of a further 14 related sequences. Consensus analysis of these variants identified a rich molecular diversity of Kunitz domains and expanded the palette of potential residue substitutions for rational inhibitor design using this domain.
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Affiliation(s)
- Xingchen Chen
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Darren Leahy
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Jessica Van Haeften
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Perry Hartfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Peter J. Prentis
- School of Earth, Environmental and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Institute for Future Environments, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Chloé A. van der Burg
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Joachim M. Surm
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Ana Pavasovic
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Bruno Madio
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia; (B.M.); (G.F.K.)
| | - Brett R. Hamilton
- Centre for Advanced Imaging, University of Queensland, St Lucia, QLD 4072, Australia; (B.R.H.); (E.A.B.U.)
| | - Glenn F. King
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia; (B.M.); (G.F.K.)
| | - Eivind A. B. Undheim
- Centre for Advanced Imaging, University of Queensland, St Lucia, QLD 4072, Australia; (B.R.H.); (E.A.B.U.)
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Maria Brattsand
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden;
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia; (X.C.); (D.L.); (J.V.H.); (C.A.v.d.B.); (A.P.)
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4000, Australia;
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13
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Steinmetzer T, Pilgram O, Wenzel BM, Wiedemeyer SJA. Fibrinolysis Inhibitors: Potential Drugs for the Treatment and Prevention of Bleeding. J Med Chem 2019; 63:1445-1472. [PMID: 31658420 DOI: 10.1021/acs.jmedchem.9b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hyperfibrinolytic situations can lead to life-threatening bleeding, especially during cardiac surgery. The approved antifibrinolytic agents such as tranexamic acid, ε-aminocaproic acid, 4-aminomethylbenzoic acid, and aprotinin were developed in the 1960s without the structural insight of their respective targets. Crystal structures of the main antifibrinolytic targets, the lysine binding sites on plasminogen's kringle domains, and plasmin's serine protease domain greatly contributed to the structure-based drug design of novel inhibitor classes. Two series of ligands targeting the lysine binding sites have been recently described, which are more potent than the most-widely used antifibrinolytic agent, tranexamic acid. Furthermore, four types of promising active site inhibitors of plasmin have been developed: tranexamic acid conjugates targeting the S1 pocket and primed sites, substrate-analogue linear homopiperidylalanine-containing 4-amidinobenzylamide derivatives, macrocyclic inhibitors addressing nonprimed binding regions, and bicyclic 14-mer SFTI-1 analogues blocking both, primed and nonprimed binding sites of plasmin. Furthermore, several allosteric plasmin inhibitors based on heparin mimetics have been developed.
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Affiliation(s)
- Torsten Steinmetzer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Oliver Pilgram
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Benjamin M Wenzel
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Simon J A Wiedemeyer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
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14
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Franke B, Mylne JS, Rosengren KJ. Buried treasure: biosynthesis, structures and applications of cyclic peptides hidden in seed storage albumins. Nat Prod Rep 2019; 35:137-146. [PMID: 29379937 DOI: 10.1039/c7np00066a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Covering: 1999 up to the end of 2017The small cyclic peptide SunFlower Trypsin Inhibitor-1 (SFTI-1) from sunflower seeds is the prototypic member of a novel family of natural products. The biosynthesis of these peptides is intriguing as their gene-encoded peptide backbone emerges from a precursor protein that also contains a seed storage albumin. The peptide sequence is cleaved out from the precursor and cyclised by the albumin-maturing enzymatic machinery. Three-dimensional solution NMR structures of a number of these peptides, and of the intact precursor protein preproalbumin with SFTI-1, have now been elucidated. Furthermore, the evolution of the family has been described and a detailed understanding of the biosynthetic steps, which are necessary to produce cyclic SFTI-1, is emerging. Macrocyclisation provides peptide stability and thus represents a key strategy in peptide drug development. Consequently the constrained structure of SFTI-1 has been explored as a template for protein engineering, for tuning selectivity towards clinically relevant proteases and for grafting in sequences with completely novel functions. Here we review the discovery of the SFTI-1 peptide family, their evolution, biosynthetic origin, and structural features, as well as highlight the potential applications of this unique class of natural products.
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Affiliation(s)
- B Franke
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
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15
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Riley BT, Hoke DE, McGowan S, Buckle AM. Crystal structure of the inhibitor-free form of the serine protease kallikrein-4. Acta Crystallogr F Struct Biol Commun 2019; 75:543-546. [DOI: 10.1107/s2053230x19009610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/04/2019] [Indexed: 11/10/2022] Open
Abstract
Kallikrein 4 (KLK4) is a serine protease that is predominantly expressed in the prostate and is overexpressed in prostate cancer. As such, it has gained attention as an attractive target for prostate cancer therapeutics. Currently, only liganded structures of KLK4 exist in the Protein Data Bank. Until now, inferences about the subtle structural changes in KLK4 upon ligand binding have been made by comparison to other liganded forms, rather than to an apo form. In this study, an inhibitor-free form of KLK4 was crystallized. The crystals obtained belonged to space group P1, contained four molecules in the asymmetric unit and diffracted to 1.64 Å resolution. Interestingly, a nonstandard rotamer of the specificity-determining residue Asp189 was observed in all chains. This model will provide a useful unliganded structure for the future structure-guided design of KLK4 inhibitors.
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16
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Jackson MA, Yap K, Poth AG, Gilding EK, Swedberg JE, Poon S, Qu H, Durek T, Harris K, Anderson MA, Craik DJ. Rapid and Scalable Plant-Based Production of a Potent Plasmin Inhibitor Peptide. FRONTIERS IN PLANT SCIENCE 2019; 10:602. [PMID: 31156672 PMCID: PMC6530601 DOI: 10.3389/fpls.2019.00602] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/24/2019] [Indexed: 05/03/2023]
Abstract
The backbone cyclic and disulfide bridged sunflower trypsin inhibitor-1 (SFTI-1) peptide is a proven effective scaffold for a range of peptide therapeutics. For production at laboratory scale, solid phase peptide synthesis techniques are widely used, but these synthetic approaches are costly and environmentally taxing at large scale. Here, we developed a plant-based approach for the recombinant production of SFTI-1-based peptide drugs. We show that transient expression in Nicotiana benthamiana allows for rapid peptide production, provided that asparaginyl endopeptidase enzymes with peptide-ligase functionality are co-expressed with the substrate peptide gene. Without co-expression, no target cyclic peptides are detected, reflecting rapid in planta degradation of non-cyclized substrate. We test this recombinant production system by expressing a SFTI-1-based therapeutic candidate that displays potent and selective inhibition of human plasmin. By using an innovative multi-unit peptide expression cassette, we show that in planta yields reach ~60 μg/g dry weight at 6 days post leaf infiltration. Using nuclear magnetic resonance structural analysis and functional in vitro assays, we demonstrate the equivalence of plant and synthetically derived plasmin inhibitor peptide. The methods and insights gained in this study provide opportunities for the large scale, cost effective production of SFTI-1-based therapeutics.
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Affiliation(s)
- Mark A. Jackson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Aaron G. Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Edward K. Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Haiou Qu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Karen Harris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
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17
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Riley BT, Ilyichova O, de Veer SJ, Swedberg JE, Wilson E, Hoke DE, Harris JM, Buckle AM. KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors. Biochemistry 2019; 58:2524-2533. [PMID: 31058493 DOI: 10.1021/acs.biochem.9b00191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sunflower trypsin inhibitor (SFTI-1) is a 14 amino acid serine protease inhibitor. The dual antiparallel β-sheet arrangement of SFTI-1 is stabilized by an N-terminal-C-terminal backbone cyclization and a further disulfide bridge to form a final bicyclic structure. This constrained structure is further rigidified by an extensive network of internal hydrogen bonds. Thus, the structure of SFTI-1 in solution resembles the protease-bound structure, reducing the entropic penalty upon protease binding. When cleaved at the scissile bond, it is thought that the rigidifying features of SFTI-1 maintain its structure, allowing the scissile bond to be reformed. The lack of structural plasticity for SFTI-1 is proposed to favor initial protease binding and continued occupancy in the protease active site, resulting in an equilibrium between the cleaved and uncleaved inhibitor in the presence of a protease. We have determined, at 1.15 Å resolution, the X-ray crystal structures of complexes between human kallikrein-related peptidase 4 (KLK4) and SFTI-FCQR(Asn14) and between KLK4 and an acyclic form of the same inhibitor, SFTI-FCQR(Asn14)[1,14], with the latter displaying a cleaved scissile bond. Structural analysis and MD simulations together reveal the roles of the altered contact sequence, intramolecular hydrogen bonding network, and backbone cyclization in altering the state of SFTI's scissile bond ligation at the protease active site. Taken together, the data presented reveal insights into the role of dynamics in the standard-mechanism inhibition and suggest that modifications on the non-contact strand may be a useful, underexplored approach for generating further potent or selective SFTI-based inhibitors against members of the serine protease family.
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Affiliation(s)
- Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Monash University , Clayton , Victoria 3800 , Australia
| | - Olga Ilyichova
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Monash University , Clayton , Victoria 3800 , Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Emily Wilson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Monash University , Clayton , Victoria 3800 , Australia
| | - David E Hoke
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Monash University , Clayton , Victoria 3800 , Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation , Queensland University of Technology , Brisbane , Queensland 4059 , Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute , Monash University , Clayton , Victoria 3800 , Australia
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18
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Potent, multi-target serine protease inhibition achieved by a simplified β-sheet motif. PLoS One 2019; 14:e0210842. [PMID: 30668585 PMCID: PMC6342301 DOI: 10.1371/journal.pone.0210842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/02/2019] [Indexed: 11/19/2022] Open
Abstract
Engagement of an extended β-sheet is a common substrate/inhibitor interaction at the active site of serine proteases and is an important feature of Laskowski mechanism inhibitors that present a substrate-like loop to a target protease. This loop is cleaved but subsequently relegated forming a stable inhibitor/protease complex. Laskowski inhibitors are ubiquitous in nature and are used extensively in serine protease inhibitor design. However, most studies concentrate on introducing new sidechain interactions rather than the direct contributions of the substrate-like β-sheet to enzyme inhibition. Here we report the crystal structure of an simplified β-sheet inhibitory motif within the Sunflower Trypsin Inhibitor (SFTI) in complex with trypsin. We show that the intramolecular hydrogen bond network of this SFTI variant (SFTI-TCTR) engages the inhibitor sidechains that would normally interact with a target protease, giving mainchain interactions a more prominent role in complex formation. Despite having reduced sidechain interactions, this SFTI variant is remarkably potent and inhibits a diverse range of serine proteases. Crystal structural analysis and molecular modelling of SFTI-TCTR complexes again indicates an interface dominated by β–sheet interactions, highlighting the importance of this motif and the adaptability of SFTI as a scaffold for inhibitor design.
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19
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Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein-protein interactions. Biochem J 2019; 476:67-83. [PMID: 30635453 DOI: 10.1042/bcj20180792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The use of disulfide-rich backbone-cyclized polypeptides, as molecular scaffolds to design a new generation of bioimaging tools and drugs that are potent and specific, and thus might have fewer side effects than traditional small-molecule drugs, is gaining increasing interest among the scientific and in the pharmaceutical industries. Highly constrained macrocyclic polypeptides are exceptionally more stable to chemical, thermal and biological degradation and show better biological activity when compared with their linear counterparts. Many of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo These properties make them ideal tools for many biotechnological applications. The present study provides an overview of the new developments on the use of several disulfide-rich backbone-cyclized polypeptides, including cyclotides, θ-defensins and sunflower trypsin inhibitor peptides, in the development of novel bioimaging reagents and therapeutic leads.
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20
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Li M, Srp J, Gustchina A, Dauter Z, Mares M, Wlodawer A. Crystal structures of the complex of a kallikrein inhibitor from Bauhinia bauhinioides with trypsin and modeling of kallikrein complexes. Acta Crystallogr D Struct Biol 2019; 75:56-69. [PMID: 30644845 PMCID: PMC6333282 DOI: 10.1107/s2059798318016492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/19/2018] [Indexed: 11/11/2022] Open
Abstract
Structures of a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides (BbKI) complexed with bovine trypsin were determined in two crystal forms. The crystal structure with the L55R mutant of BbKI was determined in space group P64 at 1.94 Å resolution and that with native BbKI in the monoclinic space group P21 at 3.95 Å resolution. The asymmetric unit of the latter crystals contained 44 independent complexes, thus representing one of the largest numbers of independent objects deposited in the Protein Data Bank. Additionally, the structure of the complex with native BbKI was determined at 2.0 Å resolution from P64 crystals isomorphous to those of the mutant. Since BbKI has previously been found to be a potent inhibitor of the trypsin-like plasma kallikrein, it was also tested against several tissue kallikreins. It was found that BbKI is a potent inhibitor of human tissue kallikrein 4 (KLK4) and the chymotrypsin-like human tissue kallikrein 7 (KLK7). Structures of BbKI complexed with the catalytic domain of human plasma kallikrein were modeled, as well as those with KLK4 and KLK7, and the structures were analyzed in order to identify the interactions that are responsible for inhibitory potency.
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Affiliation(s)
- Mi Li
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jaroslav Srp
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, 128 40 Prague, Czech Republic
| | - Alla Gustchina
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, NCI, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Michael Mares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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21
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Swedberg JE, Ghani HA, Harris JM, de Veer SJ, Craik DJ. Potent, Selective, and Cell-Penetrating Inhibitors of Kallikrein-Related Peptidase 4 Based on the Cyclic Peptide MCoTI-II. ACS Med Chem Lett 2018; 9:1258-1262. [PMID: 30613336 DOI: 10.1021/acsmedchemlett.8b00422] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Kallikrein-related peptidase 4 (KLK4) is a serine protease that has putative intracellular and extracellular functions in prostate cancer progression. Here we show that MCoTI-II, a 34-amino acid cyclic peptide found in the seeds of red gac (Momordica cochinchinensis), is an inhibitor of KLK4. By grafting a preferred KLK4 cleavage sequence into MCoTI-II, we produced a highly potent KLK4 inhibitor (K i = 0.1 nM) that displayed 100,000-fold selectivity over related KLKs and the ability to penetrate cells. Additionally, by substituting positively charged noncontact residues in this compound, we produced a potent and selective KLK4 inhibitor that does not penetrate cells. The inhibitors were shown to be nontoxic to human cells and stable in human serum. These KLK4 inhibitors provide useful chemical tools to further define the role(s) of both intracellular and extracellular KLK4 in prostate cancer cell lines and disease models.
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Affiliation(s)
- Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Hafiza Abdul Ghani
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jonathan M. Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Simon J. de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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22
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Swedberg JE, Wu G, Mahatmanto T, Durek T, Caradoc-Davies TT, Whisstock JC, Law RHP, Craik DJ. Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma. J Med Chem 2018; 62:552-560. [DOI: 10.1021/acs.jmedchem.8b01139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - James C. Whisstock
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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23
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de Veer SJ, Li CY, Swedberg JE, Schroeder CI, Craik DJ. Engineering potent mesotrypsin inhibitors based on the plant-derived cyclic peptide, sunflower trypsin inhibitor-1. Eur J Med Chem 2018; 155:695-704. [PMID: 29936356 DOI: 10.1016/j.ejmech.2018.06.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/24/2018] [Accepted: 06/12/2018] [Indexed: 12/19/2022]
Abstract
Plants produce a diverse range of peptides and proteins that inhibit the activity of different serine proteases. The value of these inhibitors not only stems from their native role(s) in planta, but they are also regarded as promising templates for inhibitor engineering. Interest in this field has grown rapidly in recent years, particularly for therapeutic applications. The serine protease mesotrypsin has been implicated in several cancers, but is a challenging target for inhibitor engineering as a number of serine protease inhibitors that typically display broad-range activity show limited activity against mesotrypsin. In this study, we use a cyclic peptide isolated from sunflower seeds, sunflower trypsin inhibitor-1 (SFTI-1), as a scaffold for engineering potent mesotrypsin inhibitors. SFTI-1 comprises 14-amino acids and is a potent inhibitor of human cationic trypsin (Ki = 30 ± 0.8 pM) but shows 165,000-fold weaker activity against mesotrypsin (Ki = 4.96 ± 0.2 μM). Using an inhibitor library based on SFTI-1, we show that the inhibitor's P2' residue (Ile) is a key contributor to SFTI-1's limited activity against mesotrypsin. Substituting P2' Ile with chemically diverse amino acids, including non-canonical aromatic residues, produced new inhibitor variants that maintained a similar structure to SFTI-1 and showed marked improvements in activity (exceeding 100-fold). An assessment of the activity of the new inhibitors against closely-related trypsin paralogs revealed that the improved activity against mesotrypsin was accompanied by a loss in activity against off-target proteases, such that several engineered variants showed comparable activity against mesotrypsin and human cationic trypsin. Together, these findings identify potent mesotrypsin inhibitors that are suitable for further optimisation studies and demonstrate the potential gains in activity and selectivity that can be achieved by optimising the P2' residue, particularly for engineered SFTI-based inhibitors.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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24
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Masurier N, Arama DP, El Amri C, Lisowski V. Inhibitors of kallikrein-related peptidases: An overview. Med Res Rev 2017; 38:655-683. [DOI: 10.1002/med.21451] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/24/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Nicolas Masurier
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
| | - Dominique P. Arama
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
| | - Chahrazade El Amri
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8256; Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology; Paris France
| | - Vincent Lisowski
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS; Université de Montpellier, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques; Montpellier Cedex France
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25
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Swedberg JE, Li CY, de Veer SJ, Wang CK, Craik DJ. Design of Potent and Selective Cathepsin G Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold. J Med Chem 2017; 60:658-667. [PMID: 28045523 DOI: 10.1021/acs.jmedchem.6b01509] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neutrophils are directly responsible for destroying invading pathogens via reactive oxygen species, antimicrobial peptides, and neutrophil serine proteases (NSPs). Imbalance between NSP activity and endogenous protease inhibitors is associated with chronic inflammatory disorders, and engineered inhibitors of NSPs are a potential therapeutic pathway. In this study we characterized the extended substrate specificity (P4-P1) of the NSP cathepsin G using a peptide substrate library. Substituting preferred cathepsin G substrate sequences into sunflower trypsin inhibitor-1 (SFTI-1) produced a potent cathepsin G inhibitor (Ki = 0.89 nM). Cathepsin G's P2' preference was determined by screening against a P2' diverse SFTI-based library, and the most preferred residue at P2' was combined in SFTI-1 with a preferred substrate sequence (P4-P2) and a nonproteinogenic P1 residue (4-guanidyl-l-phenylalanine) to produce a potent (Ki = 1.6 nM) and the most selective (≥360-fold) engineered cathepsin G inhibitor reported to date. This compound is a promising lead for further development of cathepsin G inhibitors targeting chronic inflammatory disorders.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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26
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de Veer SJ, Swedberg JE, Brattsand M, Clements JA, Harris JM. Exploring the active site binding specificity of kallikrein-related peptidase 5 (KLK5) guides the design of new peptide substrates and inhibitors. Biol Chem 2016; 397:1237-1249. [DOI: 10.1515/hsz-2016-0112] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/16/2016] [Indexed: 12/24/2022]
Abstract
Abstract
Kallikrein-related peptidase 5 (KLK5) is a promising therapeutic target in several skin diseases, including Netherton syndrome, and is emerging as a potential target in various cancers. In this study, we used a sparse matrix library of 125 individually synthesized peptide substrates to characterize the binding specificity of KLK5. The sequences most favored by KLK5 were GRSR, YRSR and GRNR, and we identified sequence-specific interactions involving the peptide N-terminus by analyzing kinetic constants (kcat and KM) and performing molecular dynamics simulations. KLK5 inhibitors were subsequently engineered by substituting substrate sequences into the binding loop (P1, P2 and P4 residues) of sunflower trypsin inhibitor-1 (SFTI-1). These inhibitors were effective against KLK5 but showed limited selectivity, and performing a further substitution at P2′ led to the design of a new variant that displayed improved activity against KLK5 (Ki=4.2±0.2 nm), weak activity against KLK7 and 12-fold selectivity over KLK14. Collectively, these findings provide new insight into the design of highly favored binding sequences for KLK5 and reveal several opportunities for modulating inhibitor selectivity over closely related proteases that will be useful for future studies aiming to develop therapeutic molecules targeting KLK5.
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27
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Carstens BB, Swedberg J, Berecki G, Adams DJ, Craik DJ, Clark RJ. Effects of linker sequence modifications on the structure, stability, and biological activity of a cyclic α-conotoxin. Biopolymers 2016; 106:864-875. [DOI: 10.1002/bip.22848] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/28/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Bodil B. Carstens
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
- School of Biomedical Sciences; the University of Queensland; Brisbane Queensland 4072 Australia
| | - Joakim Swedberg
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
| | - Géza Berecki
- Health Innovations Research Institute, RMIT University; Melbourne Victoria 3083 Australia
| | - David J. Adams
- Health Innovations Research Institute, RMIT University; Melbourne Victoria 3083 Australia
| | - David J. Craik
- Institute for Molecular Bioscience, the University of Queensland; Brisbane Queensland 4072 Australia
| | - Richard J. Clark
- School of Biomedical Sciences; the University of Queensland; Brisbane Queensland 4072 Australia
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28
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Leenheer D, ten Dijke P, Hipolito CJ. A current perspective on applications of macrocyclic-peptide-based high-affinity ligands. Biopolymers 2016; 106:889-900. [PMID: 27352774 PMCID: PMC5132055 DOI: 10.1002/bip.22900] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.
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Affiliation(s)
- Daniël Leenheer
- Ph.D. Program in Human Biology, School of Integrative and Global MajorsUniversity of TsukubaTsukubaIbarakiJapan
| | - Peter ten Dijke
- Leiden University Medical Center, Department of Molecular Cell BiologyLeidenSouth HollandThe Netherlands
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| | - Christopher John Hipolito
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
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29
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Riley BT, Ilyichova O, Costa MGS, Porebski BT, de Veer SJ, Swedberg JE, Kass I, Harris JM, Hoke DE, Buckle AM. Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics. Sci Rep 2016; 6:35385. [PMID: 27767076 PMCID: PMC5073354 DOI: 10.1038/srep35385] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.
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Affiliation(s)
- Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Olga Ilyichova
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - David E Hoke
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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30
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Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
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Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Kromann-Hansen T, Oldenburg E, Yung KWY, Ghassabeh GH, Muyldermans S, Declerck PJ, Huang M, Andreasen PA, Ngo JCK. A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior. J Biol Chem 2016; 291:15156-68. [PMID: 27226628 DOI: 10.1074/jbc.m116.732503] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 01/15/2023] Open
Abstract
A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine the behavior a particular peptide segment will exhibit. Here, we describe the first x-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its complementary determining region-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30-40% of the nanobody remained intact and inhibitory after prolonged incubation with the protease. Biochemical analysis reveals that an intra-loop interaction network within the complementary determining region-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors.
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Affiliation(s)
- Tobias Kromann-Hansen
- From the Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark,
| | - Emil Oldenburg
- From the Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Kristen Wing Yu Yung
- the School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Gholamreza H Ghassabeh
- the Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussels, 1050 Brussels, Belgium, Nanobody Service Facility, Flanders Institute for Biotechnology, 1050 Brussels, Belgium
| | - Serge Muyldermans
- the Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussels, 1050 Brussels, Belgium
| | - Paul J Declerck
- the Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit, 3000 Leuven, Belgium, and
| | - Mingdong Huang
- the State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou, Fujian 350002, China
| | - Peter A Andreasen
- From the Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Jacky Chi Ki Ngo
- the School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
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de Veer SJ, Ukolova SS, Munro CA, Swedberg JE, Buckle AM, Harris JM. Mechanism-based selection of a potent kallikrein-related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI-1. Biopolymers 2016; 100:510-8. [PMID: 24078181 DOI: 10.1002/bip.22231] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/01/2013] [Accepted: 03/02/2013] [Indexed: 02/06/2023]
Abstract
Potent and specific enzyme inhibition is a key goal in the development of therapeutic inhibitors targeting proteolytic activity. The backbone-cyclized peptide, Sunflower Trypsin Inhibitor (SFTI-1) affords a scaffold that can be engineered to achieve both these aims. SFTI-1's mechanism of inhibition is unusual in that it shows fast-on/slow-off kinetics driven by cleavage and religation of a scissile bond. This phenomenon was used to select a nanomolar inhibitor of kallikrein-related peptidase 7 (KLK7) from a versatile library of SFTI variants with diversity tailored to exploit distinctive surfaces present in the active site of serine proteases. Inhibitor selection was achieved through the use of size exclusion chromatography to separate protease/inhibitor complexes from unbound inhibitors followed by inhibitor identification according to molecular mass ascertained by mass spectrometry. This approach identified a single dominant inhibitor species with molecular weight of 1562.4 Da, which is consistent with the SFTI variant SFTI-WCTF. Once synthesized individually this inhibitor showed an IC50 of 173.9 ± 7.6 nM against chromogenic substrates and could block protein proteolysis. Molecular modeling analysis suggested that selection of SFTI-WCTF was driven by specific aromatic interactions and stabilized by an enhanced internal hydrogen bonding network. This approach provides a robust and rapid route to inhibitor selection and design.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
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Avgeris M, Scorilas A. Kallikrein-related peptidases (KLKs) as emerging therapeutic targets: focus on prostate cancer and skin pathologies. Expert Opin Ther Targets 2016; 20:801-18. [PMID: 26941073 DOI: 10.1517/14728222.2016.1147560] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Tissue kallikrein and the kallikrein-related peptidases (KLKs) constitute a family of 15 homologous secreted serine proteases with trypsin- or chymotrypsin-like activities, which participate in a broad spectrum of physiological procedures. Deregulated expression and/or activation of the majority of the family members have been reported in several human diseases, thereby making KLKs ideal targets for therapeutic intervention. AREAS COVERED In the present review, we summarize the role of KLKs in normal human physiology and pathology, focusing on prostate cancer and skin diseases. Furthermore, we discuss the recent advances in the development of KLK-based therapies. A great number of diverse engineered KLKs inhibitors with improved potency, selectivity and immunogenicity have been synthesized by redesigning examples that are endogenous and naturally occurring. Moreover, encouraging results have been documented using KLKs-based vaccines and immunotherapies, as well as KLKs-mediated activation of pro-drugs. Finally, KLKs-targeting aptamers and KLKs-based imaging tools represent novel approaches towards the exploitation of KLKs' therapeutic value. EXPERT OPINION The central/critical roles of KLK family in several human pathologies highlight KLKs as attractive molecular targets for developing novel therapeutics.
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Affiliation(s)
- Margaritis Avgeris
- a Department of Biochemistry and Molecular Biology, Faculty of Biology , University of Athens , Athens , Greece
| | - Andreas Scorilas
- a Department of Biochemistry and Molecular Biology, Faculty of Biology , University of Athens , Athens , Greece
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34
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Jendrny C, Beck-Sickinger AG. Inhibition of Kallikrein-Related Peptidases 7 and 5 by Grafting Serpin Reactive-Center Loop Sequences onto Sunflower Trypsin Inhibitor-1 (SFTI-1). Chembiochem 2015; 17:719-26. [PMID: 26574674 DOI: 10.1002/cbic.201500539] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 01/30/2023]
Abstract
Serpin proteins irreversibly inhibit serine proteases, but only a small part of the serpin reactive-center loop (RCL) is responsible for the initial protein-protein interaction (PPI). To develop peptidic protease inhibitors, kallikrein-related peptidases 7 (KLK7) and 5 (KLK5) were chosen. Firstly, we demonstrated that short peptides derived from RCL sequences can be cleaved by KLK7 in a substrate-like manner. Next, these substrates were grafted onto the protease-binding loop of sunflower trypsin inhibitor-1 (SFTI-1). Peptides based on kallistatin, α1 -antichymotrypsin, and protein C inhibitor (PCI) inhibited KLK7 with Ki =0.4, 0.5, and 0.7 μm, respectively. In contrast, the trypsin-like KLK5 was only blocked by the peptide derived from PCI (Ki =0.6 μm). Thus, serpin function can be mimicked by introducing its PPI site into the rigid structure of the SFTI-1 scaffold. This approach might be applicable not only to KLKs but also to other serine protease members, thus opening up new therapeutic fields.
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Affiliation(s)
- Cathleen Jendrny
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Universität Leipzig, Brüderstrasse 34, 04103, Leipzig, Germany.
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35
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de Veer SJ, Wang CK, Harris JM, Craik DJ, Swedberg JE. Improving the Selectivity of Engineered Protease Inhibitors: Optimizing the P2 Prime Residue Using a Versatile Cyclic Peptide Library. J Med Chem 2015; 58:8257-68. [PMID: 26393374 DOI: 10.1021/acs.jmedchem.5b01148] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Standard mechanism inhibitors are attractive design templates for engineering reversible serine protease inhibitors. When optimizing interactions between the inhibitor and target protease, many studies focus on the nonprimed segment of the inhibitor's binding loop (encompassing the contact β-strand). However, there are currently few methods for screening residues on the primed segment. Here, we designed a synthetic inhibitor library (based on sunflower trypsin inhibitor-1) for characterizing the P2' specificity of various serine proteases. Screening the library against 13 different proteases revealed unique P2' preferences for trypsin, chymotrypsin, matriptase, plasmin, thrombin, four kallikrein-related peptidases, and several clotting factors. Using this information to modify existing engineered inhibitors yielded new variants that showed considerably improved selectivity, reaching up to 7000-fold selectivity over certain off-target proteases. Our study demonstrates the importance of the P2' residue in standard mechanism inhibition and unveils a new approach for screening P2' substitutions that will benefit future inhibitor engineering studies.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
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Cyclic alpha-conotoxin peptidomimetic chimeras as potent GLP-1R agonists. Eur J Med Chem 2015; 103:175-84. [DOI: 10.1016/j.ejmech.2015.08.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/18/2015] [Accepted: 08/24/2015] [Indexed: 12/25/2022]
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The kallikrein-related peptidase family: Dysregulation and functions during cancer progression. Biochimie 2015; 122:283-99. [PMID: 26343558 DOI: 10.1016/j.biochi.2015.09.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/01/2015] [Indexed: 01/07/2023]
Abstract
Cancer is the second leading cause of death with 14 million new cases and 8.2 million cancer-related deaths worldwide in 2012. Despite the progress made in cancer therapies, neoplastic diseases are still a major therapeutic challenge notably because of intra- and inter-malignant tumour heterogeneity and adaptation/escape of malignant cells to/from treatment. New targeted therapies need to be developed to improve our medical arsenal and counter-act cancer progression. Human kallikrein-related peptidases (KLKs) are secreted serine peptidases which are aberrantly expressed in many cancers and have great potential in developing targeted therapies. The potential of KLKs as cancer biomarkers is well established since the demonstration of the association between KLK3/PSA (prostate specific antigen) levels and prostate cancer progression. In addition, a constantly increasing number of in vitro and in vivo studies demonstrate the functional involvement of KLKs in cancer-related processes. These peptidases are now considered key players in the regulation of cancer cell growth, migration, invasion, chemo-resistance, and importantly, in mediating interactions between cancer cells and other cell populations found in the tumour microenvironment to facilitate cancer progression. These functional roles of KLKs in a cancer context further highlight their potential in designing new anti-cancer approaches. In this review, we comprehensively review the biochemical features of KLKs, their functional roles in carcinogenesis, followed by the latest developments and the successful utility of KLK-based therapeutics in counteracting cancer progression.
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Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition. Biochem J 2015; 469:243-53. [PMID: 25981970 DOI: 10.1042/bj20150412] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/18/2015] [Indexed: 11/17/2022]
Abstract
Laskowski inhibitors regulate serine proteases by an intriguing mode of action that involves deceiving the protease into synthesizing a peptide bond. Studies exploring naturally occurring Laskowski inhibitors have uncovered several structural features that convey the inhibitor's resistance to hydrolysis and exceptional binding affinity. However, in the context of Laskowski inhibitor engineering, the way that various modifications intended to fine-tune an inhibitor's potency and selectivity impact on its association and dissociation rates remains unclear. This information is important as Laskowski inhibitors are becoming increasingly used as design templates to develop new protease inhibitors for pharmaceutical applications. In this study, we used the cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), as a model system to explore how the inhibitor's sequence and structure relate to its binding kinetics and function. Using enzyme assays, MD simulations and NMR spectroscopy to study SFTI variants with diverse sequence and backbone modifications, we show that the geometry of the binding loop mainly influences the inhibitor's potency by modulating the association rate, such that variants lacking a favourable conformation show dramatic losses in activity. Additionally, we show that the inhibitor's sequence (including both the binding loop and its scaffolding) influences its potency and selectivity by modulating both the association and the dissociation rates. These findings provide new insights into protease inhibitor function and design that we apply by engineering novel inhibitors for classical serine proteases, trypsin and chymotrypsin and two kallikrein-related peptidases (KLK5 and KLK14) that are implicated in various cancers and skin diseases.
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Cereda V, Formica V, Menghi A, Pellicori S, Roselli M. Kallikrein-related peptidases targeted therapies in prostate cancer: perspectives and challenges. Expert Opin Investig Drugs 2015; 24:929-47. [PMID: 25858813 DOI: 10.1517/13543784.2015.1035708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Despite the emergence of several new effective treatments for metastatic castration-resistant prostate cancer patients, disease progression inevitably occurs, leading scientific community to carefully look for novel therapeutic targets of prostate cancer. Kallikrein (KLK)-related peptidases have been demonstrated to facilitate prostate tumorigenesis and disease progression through the development of an oncogenic microenvironment for prostate cells. AREAS COVERED This review first summarizes the large amount of preclinical data showing the involvement of KLKs in prostate cancer pathobiology. In the second part, the authors assess the current status and future directions for KLK-targeted therapy and briefly describe the advances and challenges implicated in the design of effective manufactured drugs. The authors then focus on the preclinical data and on Phase I/II studies of the most promising KLK-targeted agents in prostate cancer. The drugs discussed here are divided on the basis of their mechanism of action: KLK-engineered inhibitors; KLK-activated pro-drugs; KLK-targeted microRNAs and small interfering RNAs(-/)small hairpin RNAs; KLK vaccines and antibodies. EXPERT OPINION Targeting KLK expression and/or activity could be a promising direction in prostate cancer treatment. Future human clinical trials will help us to evaluate the real benefits, toxicities and the consequent optimal use of KLK-targeted drugs, as mono-therapy or in combination regimens.
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Affiliation(s)
- Vittore Cereda
- 1 University of Rome Tor Vergata, Tor Vergata University Clinical Center, Department of Systems Medicine, Medical Oncology , Viale Oxford 81, 00133 Rome , Italy +39 0620908190 ; +39 0620903504 ;
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Prassas I, Eissa A, Poda G, Diamandis EP. Unleashing the therapeutic potential of human kallikrein-related serine proteases. Nat Rev Drug Discov 2015; 14:183-202. [DOI: 10.1038/nrd4534] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Mahatmanto T, Mylne JS, Poth AG, Swedberg JE, Kaas Q, Schaefer H, Craik DJ. The evolution of Momordica cyclic peptides. Mol Biol Evol 2014; 32:392-405. [PMID: 25376175 DOI: 10.1093/molbev/msu307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclic proteins have evolved for millions of years across all kingdoms of life to confer structural stability over their acyclic counterparts while maintaining intrinsic functional properties. Here, we show that cyclic miniproteins (or peptides) from Momordica (Cucurbitaceae) seeds evolved in species that diverged from an African ancestor around 19 Ma. The ability to achieve head-to-tail cyclization of Momordica cyclic peptides appears to have been acquired through a series of mutations in their acyclic precursor coding sequences following recent and independent gene expansion event(s). Evolutionary analysis of Momordica cyclic peptides reveals sites that are under selection, highlighting residues that are presumably constrained for maintaining their function as potent trypsin inhibitors. Molecular dynamics of Momordica cyclic peptides in complex with trypsin reveals site-specific residues involved in target binding. In a broader context, this study provides a basis for selecting Momordica species to further investigate the biosynthesis of the cyclic peptides and for constructing libraries that may be screened against evolutionarily related serine proteases implicated in human diseases.
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Affiliation(s)
- Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth, WA, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Hanno Schaefer
- Plant Biodiversity Research, Technische Universität München, Freising, Germany
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
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Shariff L, Zhu Y, Cowper B, Di WL, Macmillan D. Sunflower trypsin inhibitor (SFTI-1) analogues of synthetic and biological origin via N→S acyl transfer: potential inhibitors of human Kallikrein-5 (KLK5). Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.059] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Hannu K, Johanna M, Ulf-Håkan S. KLK-targeted Therapies for Prostate Cancer. EJIFCC 2014; 25:207-18. [PMID: 27683469 PMCID: PMC4975297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alternative treatments are urgently needed for prostate cancer, especially to address the aggressive metastatic castration-resistant disease. Proteolytic enzymes are involved in cancer growth and progression. The prostate produces several proteases, the most abundant ones being two members of the kallikrein-related peptidase (KLK) family, prostate-specific antigen (PSA) and KLK2. Despite the wide use of PSA as a clinical marker, the function(s) of PSA and other KLKs in prostate cancer are poorly known. Hypothetic roles of KLKs in prostate cancer include activities that may both promote and inhibit cancer growth and metastasis, including the antiangiogenic activity of PSA. Thus it may be possible to control prostate cancer growth by modulating the proteolytic activities of KLKs. PSA and KLK2 are especially attractive targets for prostate cancer treatment because of their proposed roles in tumor development and inhibition of angiogenesis in combination with their prostate selective expression. So far the number of molecules affecting selectively the activity of KLKs is limited and none of these are used to treat prostate cancer. Prodrugs that, after cleavage of the peptide part by PSA or KLK2, release active drug molecules, and PSA-targeted therapeutic vaccines have already been tested clinically in humans and the first results have been encouraging. Although KLKs are attractive targets for prostate cancer treatment, much remains to be done before their potential can be fully elucidated. The objective of this review is to address the current state of the KLKs as novel therapeutic targets for prostate cancer treatment.
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Affiliation(s)
- Koistinen Hannu
- Department of Clinical Chemistry, Biomedicum Helsinki, P.O. Box 63, FIN-00014 University of Helsinki, Finland +358 9 471 71734 (HK) (JM) (UHS)
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Avanzo Caglič P, Renko M, Turk D, Kos J, Sabotič J. Fungal β-trefoil trypsin inhibitors cnispin and cospin demonstrate the plasticity of the β-trefoil fold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1749-56. [PMID: 25034500 DOI: 10.1016/j.bbapap.2014.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/04/2014] [Accepted: 07/08/2014] [Indexed: 10/25/2022]
Abstract
The recently identified fungal protease inhibitors cnispin, from Clitocybe nebularis, and cospin, from Coprinopsis cinerea, are both β-trefoil proteins highly specific for trypsin. The reactive site residue of cospin, Arg27, is located on the β2-β3 loop. We show here, that the reactive site residue in cnispin is Lys127, located on the β11-β12 loop. Cnispin is a substrate-like inhibitor and the β11-β12 loop is yet another β-trefoil fold loop recruited for serine protease inhibition. By site-directed mutagenesis of the P1 residues in the β2-β3 and β11-β12 loops in cospin and cnispin, protease inhibitors with different specificities for trypsin and chymotrypsin inhibition have been engineered. Double headed inhibitors of trypsin or trypsin and chymotrypsin were prepared by introducing a second specific site residue into the β2-β3 loop in cnispin and into the β11-β12 loop in cospin. These results show that β-trefoil protease inhibitors from mushrooms exhibit broad plasticity of loop utilization in protease inhibition.
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Affiliation(s)
- Petra Avanzo Caglič
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Miha Renko
- Department of Biochemistry, Molecular, and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular, and Structural Biology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Janko Kos
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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Fittler H, Avrutina O, Empting M, Kolmar H. Potent inhibitors of human matriptase-1 based on the scaffold of sunflower trypsin inhibitor. J Pept Sci 2014; 20:415-20. [DOI: 10.1002/psc.2629] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Heiko Fittler
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Olga Avrutina
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS); Department Drug Design and Optimization; Campus C2.3 66123 Saarbrücken Germany
| | - Harald Kolmar
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry; Technische Universität Darmstadt; Alarich-Weiss-Straße 4 64287 Darmstadt Germany
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Northfield SE, Wang CK, Schroeder CI, Durek T, Kan MW, Swedberg JE, Craik DJ. Disulfide-rich macrocyclic peptides as templates in drug design. Eur J Med Chem 2014; 77:248-57. [DOI: 10.1016/j.ejmech.2014.03.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/25/2014] [Accepted: 03/05/2014] [Indexed: 01/04/2023]
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Mavridis K, Avgeris M, Scorilas A. Targeting kallikrein-related peptidases in prostate cancer. Expert Opin Ther Targets 2014; 18:365-83. [DOI: 10.1517/14728222.2014.880693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Schroeder C, Swedberg J, Withka J, Rosengren K, Akcan M, Clayton D, Daly N, Cheneval O, Borzilleri K, Griffor M, Stock I, Colless B, Walsh P, Sunderland P, Reyes A, Dullea R, Ammirati M, Liu S, McClure K, Tu M, Bhattacharya S, Liras S, Price D, Craik D. Design and Synthesis of Truncated EGF-A Peptides that Restore LDL-R Recycling in the Presence of PCSK9 In Vitro. ACTA ACUST UNITED AC 2014; 21:284-94. [DOI: 10.1016/j.chembiol.2013.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 12/31/2022]
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Dong Y, Loessner D, Irving-Rodgers H, Obermair A, Nicklin JL, Clements JA. Metastasis of ovarian cancer is mediated by kallikrein related peptidases. Clin Exp Metastasis 2014; 31:135-47. [PMID: 24043563 PMCID: PMC3892111 DOI: 10.1007/s10585-013-9615-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/26/2013] [Indexed: 12/16/2022]
Abstract
Ovarian cancer, in particular epithelial ovarian cancer (EOC), is commonly diagnosed when the tumor has metastasized into the abdominal cavity with an accumulation of ascites fluid. Combining histopathology and genetic variations, EOC can be sub-grouped into Type-I and Type-II tumors, of which the latter are more aggressive and metastatic. Metastasis and chemoresistance are the key events associated with the tumor microenvironment that lead to a poor patient outcome. Kallikrein-related peptidases (KLKs) are aberrantly expressed in EOC, in particular, in the more metastatic Type-II tumors. KLKs are a family of 15 serine proteases that are expressed in diverse human tissues and involved in various patho-physiological processes. As extracellular enzymes, KLKs function in the hydrolysis of growth factors, proteases, cell membrane bound receptors, adhesion proteins, and cytokines initiating intracellular signaling pathways and their downstream events. High KLK levels are differentially associated with the prognosis of ovarian cancer patients, suggesting that they not only have application as biomarkers but also function in disease progression, and therefore are potential therapeutic targets. Recent studies have demonstrated the function of these proteases in promoting and/or suppressing the invasive behavior of ovarian cancer cells in metastasis in vitro and in vivo. Both conventional cell culture methods and three-dimensional platforms have been applied to mimic the ovarian cancer microenvironment of patients, such as the solid stromal matrix and ascites fluid. Here we summarize published studies to provide an overview of our understanding of the role of KLKs in EOC, and to lay the foundation for future research directions.
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Affiliation(s)
- Ying Dong
- Cancer Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia,
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Complementation of intramolecular interactions for structural-functional stability of plant serine proteinase inhibitors. Biochim Biophys Acta Gen Subj 2013; 1830:5087-94. [PMID: 23891708 DOI: 10.1016/j.bbagen.2013.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/15/2013] [Accepted: 07/18/2013] [Indexed: 11/20/2022]
Abstract
BACKGROUND Plant protease inhibitors (PIs) constitute a diverse group of proteins capable of inhibiting proteases. Among PIs, serine PIs (SPIs) display stability and conformational restrictions of the reactive site loop by virtue of their compact size, and by the presence of disulfide bonds, hydrogen bonds, and other weak interactions. SCOPE OF REVIEW The significance of various intramolecular interactions contributing to protein folding mechanism and their role in overall stability and activity of SPIs is discussed here. Furthermore, we have reviewed the effect of variation or manipulation of these interactions on the activity/stability of SPIs. MAJOR CONCLUSIONS The selective gain or loss of disulfide bond(s) in SPIs can be associated with their functional differentiation, which is likely to be compensated by non-covalent interactions (hydrogen bonding or electrostatic interactions). Thus, these intramolecular interactions are collectively responsible for the functional activity of SPIs, through the maintenance of scaffold framework, conformational rigidity and shape complementarities of reactive site loop. GENERAL SIGNIFICANCE Structural insight of these interactions will provide an in-depth understanding of kinetic and thermodynamic parameters involved in the folding and stability mechanisms of SPIs. These features can be explored for engineering canonical SPIs for optimizing their overall stability and functionality for various applications.
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