1
|
Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [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: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
Collapse
Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
2
|
Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [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: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
Collapse
Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| |
Collapse
|
3
|
Williams-Noonan BJ, Speer MN, Le TC, Sadek MM, Thompson PE, Norton RS, Yuriev E, Barlow N, Chalmers DK, Yarovsky I. Membrane Permeating Macrocycles: Design Guidelines from Machine Learning. J Chem Inf Model 2022; 62:4605-4619. [PMID: 36178379 DOI: 10.1021/acs.jcim.2c00809] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to predict cell-permeable candidate molecules has great potential to assist drug discovery projects. Large molecules that lie beyond the Rule of Five (bRo5) are increasingly important as drug candidates and tool molecules for chemical biology. However, such large molecules usually do not cross cell membranes and cannot access intracellular targets or be developed as orally bioavailable drugs. Here, we describe a random forest (RF) machine learning model for the prediction of passive membrane permeation rates developed using a set of over 1000 bRo5 macrocyclic compounds. The model is based on easily calculated chemical features/descriptors as independent variables. Our random forest (RF) model substantially outperforms a multiple linear regression model based on the same features and achieves better performance metrics than previously reported models using the same underlying data. These features include: (1) polar surface area in water, (2) the octanol-water partitioning coefficient, (3) the number of hydrogen-bond donors, (4) the sum of the topological distances between nitrogen atoms, (5) the sum of the topological distances between nitrogen and oxygen atoms, and (6) the multiple molecular path count of order 2. The last three features represent molecular flexibility, the ability of the molecule to adopt different conformations in the aqueous and membrane interior phases, and the molecular "chameleonicity." Guided by the model, we propose design guidelines for membrane-permeating macrocycles. It is anticipated that this model will be useful in guiding the design of large, bioactive molecules for medicinal chemistry and chemical biology applications.
Collapse
Affiliation(s)
- Billy J Williams-Noonan
- School of Engineering, RMIT University, Melbourne3001, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Melissa N Speer
- University of Melbourne, Faculty of Engineering and Information Technology, Carlton3053, Australia
| | - Tu C Le
- School of Engineering, RMIT University, Melbourne3001, Australia
| | - Maiada M Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia.,ARC Centre for Fragment-Based Design, Monash University, Parkville, 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville3052, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne3001, Australia
| |
Collapse
|
4
|
Rahman A, Matthews MA, Nowell CJ, Chalmers DK, Thompson PE, Nicholson SE, Barlow N, Norton RS. Enhanced nitric oxide production by macrophages treated with a cell-penetrating peptide conjugate. Bioorg Chem 2022; 123:105763. [DOI: 10.1016/j.bioorg.2022.105763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022]
|
5
|
Buchholz CR, Pomerantz WCK. 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery. RSC Chem Biol 2021; 2:1312-1330. [PMID: 34704040 PMCID: PMC8496043 DOI: 10.1039/d1cb00085c] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.
Collapse
Affiliation(s)
- Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
| | - William C K Pomerantz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
- Department of Chemistry, University of Minnesota 207 Pleasant St. SE Minneapolis Minnesota 55455 USA
| |
Collapse
|
6
|
Seo D, Roh J, Chae Y, Kim W. Gene expression profiling after LINC00472 overexpression in an NSCLC cell line. Cancer Biomark 2021; 32:175-188. [PMID: 34397405 DOI: 10.3233/cbm-210242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lung cancer accounts for a large proportion of cancer-related deaths worldwide. Personalized therapeutic medicine based on the genetic characteristics of non-small cell lung cancer (NSCLC) is a promising field, and discovering clinically applicable biomarkers of NSCLC is required. LINC00472 is a long non-coding RNA and has been recently suggested to be a biomarker of NSCLC, but little is known of its mechanism in NSCLC. Thus, the current study was performed to document changes in gene expression after LINC00472 overexpression in NSCLC cells. As a result of cell viability and migration assay, LINC00472 downregulated cell survival, proliferation, and motility. Transcriptome sequencing analysis showed 3,782 genes expression were changed in LINC00472 overexpressing cells. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed most genes were associated with intracellular metabolism. The PPP1R12B, RGS5, RBM5, RBL2, LDLR and PTPRM genes were upregulated by LINC00472 overexpression and these genes functioned as tumor suppressors in several cancers. In contrast, SPSB1, PCNA, CD24, CDK5, CDC25A, and EIF4EBP1 were downregulated by LINC00472, and they functioned as oncogenes in various cancers. Consequently, the function of LINC00472 in tumorigenesis might be related to changes in the expressions of other oncogenes and tumor suppressors.
Collapse
Affiliation(s)
- Danbi Seo
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Jungwook Roh
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Yeonsoo Chae
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Wanyeon Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Biology Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| |
Collapse
|
7
|
Li K, You T, Zhao P, Luo Y, Zhang D, Wei H, Wang Y, Yang J, Guan X, Kuang Z. Structural basis for the regulation of inducible nitric oxide synthase by the SPRY domain-containing SOCS box protein SPSB2, an E3 ubiquitin ligase. Nitric Oxide 2021; 113-114:1-6. [PMID: 33862200 DOI: 10.1016/j.niox.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/12/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022]
Abstract
Relatively high concentration of nitric oxide (NO) produced by inducible nitric oxide synthase (iNOS) in response to a variety of stimuli is a source of reactive nitrogen species, an important weapon of host innate immune defense. The SPRY domain-containing SOCS box protein 2 (SPSB2) is an E3 ubiquitin ligase that regulates the lifetime of iNOS. SPSB2 interacts with the N-terminal region of iNOS via a binding site on the SPRY domain of SPSB2, and recruits an E3 ubiquitin ligase complex to polyubiquitinate iNOS, leading to its proteasomal degradation. Although critical residues for the SPSB2-iNOS interaction have been identified, structural basis for the interaction remains to be explicitly determined. In this study, we have determined a crystal structure of the N-terminal region of iNOS in complex with the SPRY domain of SPSB2 at 1.24 Å resolution. We have resolved the roles of some flanking residues, whose contribution to the SPSB2-iNOS interaction was structurally unclear previously. Furthermore, we have evaluated the effects of SPSB2 inhibitors on NO production using transient transfection and cell-penetrating peptide approaches, and found that such inhibitors can elevate NO production in RAW264.7 macrophages. These results thus provide a useful basis for the development of potent SPSB2 inhibitors as well as recruiting ligands for proteolysis targeting chimera (PROTAC) design.
Collapse
Affiliation(s)
- Kefa Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Tingting You
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Panqi Zhao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Yanhong Luo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Danting Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Huan Wei
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Yuhui Wang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Jinjin Yang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Xueyan Guan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Zhihe Kuang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China.
| |
Collapse
|
8
|
Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
Collapse
Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| |
Collapse
|
9
|
Babu Reddiar S, Al-Wassiti H, Pouton CW, Nowell CJ, Matthews MA, Rahman A, Barlow N, Norton RS. Assessing the cellular toxicity of peptide inhibitors of intracellular protein-protein interactions by microinjection. Bioorg Med Chem 2021; 29:115906. [PMID: 33310547 DOI: 10.1016/j.bmc.2020.115906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Inhibitors of protein-protein interactions can be developed through a number of technologies to provide leads that include cell-impermeable molecules. Redesign of these impermeable leads to provide cell-permeable derivatives can be challenging and costly. We hypothesised that intracellular toxicity of leads could be assessed by microinjection prior to investing in the redesign process. We demonstrate this approach for our development of inhibitors of the protein-protein interaction between inducible nitric-oxide synthase (iNOS) and SPRY domain-containing SOCS box proteins (SPSBs). We microinjected a lead molecule into AD-293 cells and were able to perform an intracellular toxicity assessment. We also investigated the intracellular distribution and localisation of injected inhibitor using a fluorescently-labelled analogue. Our findings show that a lead peptide inhibitor, CP2, had no toxicity even at intracellular concentrations four orders of magnitude higher than its Kd for binding to SPSB2. This early toxicity assessment justifies further development of this cell-impermeable lead to confer cell permeability. Our investigation highlights the utility of microinjection as a tool for assessing toxicity during development of drugs targeting protein-protein interactions.
Collapse
Affiliation(s)
- Sanjeevini Babu Reddiar
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Hareth Al-Wassiti
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Colin W Pouton
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Macgregor A Matthews
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Arfatur Rahman
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia.
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia.
| |
Collapse
|
10
|
Barlow N, Chalmers DK, Williams-Noonan BJ, Thompson PE, Norton RS. Improving Membrane Permeation in the Beyond Rule-of-Five Space by Using Prodrugs to Mask Hydrogen Bond Donors. ACS Chem Biol 2020; 15:2070-2078. [PMID: 32628005 DOI: 10.1021/acschembio.0c00218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A wide range of drug targets can be effectively modulated by peptides and macrocycles. Unfortunately, the size and polarity of these compounds prevents them from crossing the cell membrane to reach target sites in the cell cytosol. As such, these compounds do not conform to standard measures of drug-likeness and exist in beyond the rule-of-five space. In this work, we investigate whether prodrug moieties that mask hydrogen bond donors can be applied in the beyond rule-of-five domain to improve the permeation of macrocyclic compounds. Using a cyclic peptide model, we show that masking hydrogen bond donors in the natural polar amino acid residues (His, Ser, Gln, Asn, Glu, Asp, Lys, and Arg) imparts membrane permeability to the otherwise impermeable parent molecules, even though the addition of the masking group increases the overall compound molecular weight and the number of hydrogen bond acceptors. We demonstrate this strategy in PAMPA and Caco2 membrane permeability assays and show that masking with groups that reduce the number of hydrogen-bond donors at the cost of additional mass and hydrogen bond acceptors, a donor-acceptor swap, is effective.
Collapse
Affiliation(s)
- Nicholas Barlow
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Billy J. Williams-Noonan
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Philip E. Thompson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Raymond S. Norton
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| |
Collapse
|
11
|
Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dellsén A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. J Am Chem Soc 2020; 142:4904-4915. [PMID: 32058716 PMCID: PMC7307906 DOI: 10.1021/jacs.0c00269] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
“Hot
loop” protein segments have variable structure
and conformation and contribute crucially to protein–protein
interactions. We describe a new hot loop mimicking modality, termed
PepNats, in which natural product (NP)-inspired structures are incorporated
as conformation-determining and -restricting structural elements into
macrocyclic hot loop-derived peptides. Macrocyclic PepNats representing
hot loops of inducible nitric oxide synthase (iNOS) and human agouti-related
protein (AGRP) were synthesized on solid support employing macrocyclization
by imine formation and subsequent stereoselective 1,3-dipolar cycloaddition
as key steps. PepNats derived from the iNOS DINNN hot loop and the
AGRP RFF hot spot sequence yielded novel and potent ligands of the
SPRY domain-containing SOCS box protein 2 (SPSB2) that binds to iNOS,
and selective ligands for AGRP-binding melanocortin (MC) receptors.
NP-inspired fragment absolute configuration determines the conformation
of the peptide part responsible for binding. These results demonstrate
that combination of NP-inspired scaffolds with peptidic epitopes enables
identification of novel hot loop mimics with conformationally constrained
and biologically relevant structure.
Collapse
Affiliation(s)
- Stéphanie M Guéret
- Department of Chemical Biology, AstraZeneca-Max Planck Institute Satellite Unit, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Sasikala Thavam
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Marco Potowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Göran Dahl
- Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| |
Collapse
|
12
|
Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov 2019; 18:949-963. [PMID: 31666732 DOI: 10.1038/s41573-019-0047-y] [Citation(s) in RCA: 475] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/19/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) and related molecules that induce targeted protein degradation by the ubiquitin-proteasome system represent a new therapeutic modality and are the focus of great interest, owing to potential advantages over traditional occupancy-based inhibitors with respect to dosing, side effects, drug resistance and modulating 'undruggable' targets. However, the technology is still maturing, and the design elements for successful PROTAC-based drugs are currently being elucidated. Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity. Here, we briefly discuss lessons learned about targeted protein degradation in chemical biology and drug discovery and systematically review the expression profile, domain architecture and chemical tractability of human E3 ligases that could expand the toolbox for PROTAC discovery.
Collapse
|
13
|
Zhong Y, Shobo A, Hancock MA, Multhaup G. Label-free distribution of anti-amyloid D-AIP in Drosophila melanogaster: prevention of Aβ42-induced toxicity without side effects in transgenic flies. J Neurochem 2019; 150:74-87. [PMID: 31077378 DOI: 10.1111/jnc.14720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/22/2019] [Accepted: 05/08/2019] [Indexed: 02/06/2023]
Abstract
Soluble oligomers of the 42-amino acid amyloid beta (Aβ42) peptide are highly toxic and suspected as the causative agent of synaptic dysfunction and neuronal loss in Alzheimer's disease (AD). Previously, we have shown that a small, D-amino acid Aβ42-oligomer interacting peptide (D-AIP) can neutralize human Aβ42-mediated toxicity using in vitro and cell-based assays. In the present longitudinal study using a transgenic Drosophila melanogaster model, advanced live confocal imaging and mass spectrometry imaging (MALDI-MSI) showed that the eight amino acid D-AIP can attenuate Aβ42-induced toxicity in vivo. By separating male and female flies into distinct groups, the resultant distribution of ingested D-AIP was different between the sexes. The Aβ42-induced 'rough eye' phenotype could be rescued in the female transgenics, likely because of the co-localization of D-AIP with human Aβ42 in the female fly heads. Interestingly, the phenotype could not be rescued in the male transgenics, likely because of the co-localization of D-AIP with a confounding male-specific sex peptide (Acp70A candidate in MSI spectra) in the gut of the male flies. As a novel, more cost-effective strategy to prevent toxic amyloid formation during the early stages of AD (i.e. neutralization of toxic low-order Aβ42 oligomers without creating larger aggregates in the process), our longitudinal study establishes that D-AIP is a stable and highly effective neutralizer of toxic Aβ42 peptides in vivo. Cover Image for this issue: doi: 10.1111/jnc.14512.
Collapse
Affiliation(s)
- Yifei Zhong
- Department of Pharmacology & Therapeutics, Life Sciences Complex, McGill University, Montreal, QC, Canada
| | - Adeola Shobo
- Department of Pharmacology & Therapeutics, Life Sciences Complex, McGill University, Montreal, QC, Canada
| | - Mark A Hancock
- Department of Pharmacology & Therapeutics, Life Sciences Complex, McGill University, Montreal, QC, Canada
| | - Gerhard Multhaup
- Department of Pharmacology & Therapeutics, Life Sciences Complex, McGill University, Montreal, QC, Canada
| |
Collapse
|
14
|
Luo Y, Li K, Yang J, Zhang D, Zhou Y, Kuang Z. Crystal structure of the SPRY domain of human SPSB2 in the apo state. Acta Crystallogr F Struct Biol Commun 2019; 75:412-418. [PMID: 31204687 PMCID: PMC6572098 DOI: 10.1107/s2053230x1900623x] [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: 03/10/2019] [Accepted: 05/02/2019] [Indexed: 11/10/2022] Open
Abstract
The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2-iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY domain in the apo state is reported at a resolution of 1.9 Å. Comparison of the apo and ligand-bound structures reveals that the iNOS-binding site is highly preformed and that major conformational changes do not occur upon ligand binding. Moreover, the C-terminal His6 tag of the recombinant protein binds to a shallow pocket adjacent to the iNOS-binding site on a crystallographically related SPSB2 molecule. These findings may help in structure-based and fragment-based SPSB2 inhibitor design in the future.
Collapse
Affiliation(s)
- Yanhong Luo
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Kefa Li
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Jinjin Yang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Danting Zhang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Yuying Zhou
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Zhihe Kuang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| |
Collapse
|