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Wang WZ, Liu C, Luo JQ, Lei LJ, Chen MH, Zhang YY, Sheng R, Li YN, Wang L, Jiang XH, Xiao TM, Zhang YH, Li SW, Wu YX, Xu Y, Xu YN, Si SY. A novel small-molecule PCSK9 inhibitor E28362 ameliorates hyperlipidemia and atherosclerosis. Acta Pharmacol Sin 2024:10.1038/s41401-024-01305-9. [PMID: 38811775 DOI: 10.1038/s41401-024-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the epidermal growth factor precursor homologous domain A (EGF-A) of low-density lipoprotein receptor (LDLR) in the liver and triggers the degradation of LDLR via the lysosomal pathway, consequently leading to an elevation in plasma LDL-C levels. Inhibiting PCSK9 prolongs the lifespan of LDLR and maintains cholesterol homeostasis in the body. Thus, PCSK9 is an innovative pharmacological target for treating hypercholesterolemia and atherosclerosis. In this study, we discovered that E28362 was a novel small-molecule PCSK9 inhibitor by conducting a virtual screening of a library containing 40,000 compounds. E28362 (5, 10, 20 μM) dose-dependently increased the protein levels of LDLR in both total protein and the membrane fraction in both HepG2 and AML12 cells, and enhanced the uptake of DiI-LDL in AML12 cells. MTT assay showed that E28362 up to 80 μM had no obvious toxicity in HepG2, AML12, and HEK293a cells. The effects of E28362 on hyperlipidemia and atherosclerosis were evaluated in three different animal models. In high-fat diet-fed golden hamsters, administration of E28362 (6.7, 20, 60 mg·kg-1·d-1, i.g.) for 4 weeks significantly reduced plasma total cholesterol (TC), triglyceride (TG), low-density lipoprotein-cholesterol (LDL-C) and PCSK9 levels, and reduced liver TC and TG contents. In Western diet-fed ApoE-/- mice (20, 60 mg·kg-1·d-1, i.g.) and human PCSK9 D374Y overexpression mice (60 mg·kg-1·d-1, i.g.), administration of E28362 for 12 weeks significantly decreased plasma LDL-C levels and the area of atherosclerotic lesions in en face aortas and aortic roots. Moreover, E28362 significantly increased the protein expression level of LDLR in the liver. We revealed that E28362 selectively bound to PCSK9 in HepG2 and AML12 cells, blocked the interaction between LDLR and PCSK9, and induced the degradation of PCSK9 through the ubiquitin-proteasome pathway, which finally resulted in increased LDLR protein levels. In conclusion, E28362 can block the interaction between PCSK9 and LDLR, induce the degradation of PCSK9, increase LDLR protein levels, and alleviate hyperlipidemia and atherosclerosis in three distinct animal models, suggesting that E28362 is a promising lead compound for the treatment of hyperlipidemia and atherosclerosis.
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Affiliation(s)
- Wei-Zhi Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Chao Liu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China.
| | - Jin-Que Luo
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
- Hunan Provincial Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, 410219, China
| | - Li-Juan Lei
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Ming-Hua Chen
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
- Xinjiang Key Laboratory of Uighur Medicine, Xinjiang Institute of Materia Medica, Urumqi, 830002, China
| | - Yu-Yan Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Ren Sheng
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Yi-Ning Li
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Li Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Xin-Hai Jiang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Tong-Mei Xiao
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Yu-Hao Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Shun-Wang Li
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Ye-Xiang Wu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Yang Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China
| | - Yan-Ni Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China.
| | - Shu-Yi Si
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, NHC Key Laboratory of Biotechnology for Microbial Drugs, National Center for New Microbial Drug Screening, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, 100050, China.
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2
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Arancillo M, Lin CM, Burgess K. Piptide Chemotypes for Perturbation of the Interaction of Urokinase with Its Receptor. J Med Chem 2022; 65:12925-12932. [PMID: 36166370 DOI: 10.1021/acs.jmedchem.2c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Only a few small molecules that disrupt the uPA and uPA receptor (uPAR) interaction have been discovered despite decades of research in the area, and none have been approved in clinical trials. Research reported here features two new ways of considering the problem of discovering small molecules to disrupt uPA•uPAR, specifically in terms of chemotype design and method of evaluation. Chemotypes used in this work are piptides (Arancillo . Angew. Chem., Int. Ed., 2021, 60, 6653-6659) with side chains corresponding to the uPA loop that binds uPAR. Further, hybrids of 1 and another uPAR ligand developed in these labs (2), i.e., 3 and 4, were also designed and tested. All the piptide chemotypes bound uPAR at concentrations of 50 μM or less. Members of this series had Ki values <3 μM and showed favorable responses in cellular assays; these data are comparable with the best small molecule uPA•uPAR disruptors in the literature (from conventional screening).
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Affiliation(s)
- Maritess Arancillo
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Chen-Ming Lin
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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3
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Lyu RL, Joy S, Packianathan C, Laganowsky A, Burgess K. Small molecule peptidomimetic trypsin inhibitors: validation of an EKO binding mode, but with a twist. Org Biomol Chem 2022; 20:2075-2080. [PMID: 35225309 PMCID: PMC10365224 DOI: 10.1039/d1ob02127c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examination of a series of naturally-occurring trypsin inhibitor proteins, led to identification of a set of three residues (which we call the "interface triplet") to be determinant of trypsin binding affinity, hence excellent templates for small molecule mimicry. Consequently, we attempted to use the Exploring Key Orientation (EKO) strategy developed in our lab to evaluate small molecules that mimic the interface triplet regions of natural trypsin inhibitors, and hence potentially might bind and inhibit the catalytic activity of trypsin. A bis-triazole scaffold ("TT-mer") was the most promising of the molecules evaluated in silico. Twelve such compounds were synthesized and assayed against trypsin, among which the best showed a Kd of 2.1 μM. X-ray crystallography revealed a high degree of matching between an illustrative TT-mer's actual binding mode and that of the mimics that overlaid the interface triplet in the crystal structure. Deviation of the third side chain from the PPI structure seems to be due to alleviation of an unfavorable dipole-dipole interaction in the small molecule's actual bound conformation.
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Affiliation(s)
- Rui-Liang Lyu
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
| | - Shaon Joy
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
| | - Charles Packianathan
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
| | - Arthur Laganowsky
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
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4
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Ahamad S, Mathew S, Khan WA, Mohanan K. Development of small-molecule PCSK9 inhibitors for the treatment of hypercholesterolemia. Drug Discov Today 2022; 27:1332-1349. [PMID: 35121175 DOI: 10.1016/j.drudis.2022.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 12/23/2022]
Abstract
When secreted into the circulation, proprotein convertase subtilisin kexin type 9 (PCSK9) blocks the low-density lipoprotein receptors (LDL-R) and, as a consequence, low-density lipoprotein cholesterol (LDL-C) levels increase. Therefore, PCSK9 has emerged as a potential therapeutic target for lowering LDL-C levels and preventing atherosclerosis. The US Food and Drug Administration (FDA) has approved two monoclonal antibodies (mAbs) against PCSK9, but the expensive manufacturing process limits their use. Subsequently, there have been tremendous efforts to develop cost-effective small molecules specific to PCSK9 over the past few years. These small molecules are promising therapeutics that act by preventing the synthesis of PCSK9, its secretion from cells, or the PCSK9-LDRL interaction. In this review, we summarize recent developments in the discovery of small-molecule PCSK9 inhibitors, focusing on their design, therapeutic effects, specific targets, and mechanisms of action.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202002 UP, India.
| | - Shintu Mathew
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute Lucknow, 226031 UP, India
| | - Waqas A Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh, 202002 UP, India
| | - Kishor Mohanan
- Medicinal and Process Chemistry Division CSIR-Central Drug Research Institute Lucknow, 226031 UP, India.
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5
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maritess Arancillo
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
| | | | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases Institute of Biosciences and Technology Texas A&M Health Science Center Houston TX 77030 USA
| | - Kevin Burgess
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
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6
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021; 60:6653-6659. [PMID: 33319463 PMCID: PMC7940574 DOI: 10.1002/anie.202015203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Small molecule probe development is pivotal in biomolecular science. Research described here was undertaken to develop a non-peptidic chemotype, piptides, that is amenable to convenient, iterative solid-phase syntheses, and useful in biomolecular probe discovery. Piptides can be made from readily accessible pip acid building blocks and have good proteolytic and pH stabilities. An illustrative application of piptides against a protein-protein interaction (PPI) target was explored. The Exploring Key Orientations (EKO) strategy was used to evaluate piptide candidates for this. A library of only 14 piptides contained five members that disrupted epidermal growth factor (EGF) and its receptor, EGFR, at low micromolar concentrations. These piptides also caused apoptotic cell death, and antagonized EGF-induced phosphorylation of intracellular tyrosine residues in EGFR.
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Affiliation(s)
- Maritess Arancillo
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Jaru Taechalertpaisarn
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, 77030, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
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7
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Celis S, Hobor F, James T, Bartlett GJ, Ibarra AA, Shoemark DK, Hegedüs Z, Hetherington K, Woolfson DN, Sessions RB, Edwards TA, Andrews DM, Nelson A, Wilson AJ. Query-guided protein-protein interaction inhibitor discovery. Chem Sci 2021; 12:4753-4762. [PMID: 34163731 PMCID: PMC8179539 DOI: 10.1039/d1sc00023c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 02/19/2021] [Indexed: 12/04/2022] Open
Abstract
Protein-protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein-protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and 1H-15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure-activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.
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Affiliation(s)
- Sergio Celis
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Thomas James
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Gail J Bartlett
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Amaurys A Ibarra
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Zsófia Hegedüs
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Kristina Hetherington
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol Life Sciences Building, Tyndall Avenue Bristol BS8 1TQ UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - David M Andrews
- Early Oncology, AstraZeneca Hodgkin Building, Chesterford Research Campus, Saffron Walden Cambridge CB10 1XL UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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8
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Lin CM, Jiang Z, Gao Z, Arancillo M, Burgess K. Small molecules targeting the NEDD8·NAE protein-protein interaction. Chem Sci 2020; 12:1535-1543. [PMID: 34163916 PMCID: PMC8179036 DOI: 10.1039/d0sc00958j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ubiquitination is a major controller of protein homeostasis in cells. Some ubiquitination pathways are modulated by a NEDDylation cascade, that also features E1 - 3 enzymes. The E1 enzyme in the NEDDylation cascade involves a protein-protein interaction (PPI) between NEDD8 (similar to ubiquitin) and NAE (NEDD8 Activating Enzyme). A small molecule inhibitor of the ATP binding site in NAE is in clinical trials. We hypothesized a similar effect could be induced by disrupting the NEDD8·NAE PPI, though, to the best of our knowledge, no small molecules have been reported to disrupt this to date. In the research described here, Exploring Key Orientations (EKO) was used to evaluate several chemotype designs for their potential to disrupt NEDD8·NAE; specifically, for their biases towards orientation of side-chains in similar ways to protein segments at the interface. One chemotype design was selected, and a targeted library of 24 compounds was made around this theme via solid phase synthesis. An entry level hit for disrupting NEDD8·NAE was identified from this library on the basis of its ability to bind NAE (K i of 6.4 ± 0.3 μM from fluorescence polarization), inhibit NEDDylation, suppress formation of the corresponding E1 - 3 complexes as monitored by cell-based immunoblotting, and cytotoxicity to K562 leukemia cells via early stage apoptosis. The cell-based immunoblot assay also showed the compound caused NEDD8 to accumulate in cells, presumably due to inhibition of the downstream pathways involving the E1 enzyme. The affinity and cellular activities of the hit compound are modest, but is interesting as first in class for this mode of inhibition of NEDDylation, and as another illustration of the way EKO can be used to evaluate user-defined chemotypes as potential inhibitors of PPIs.
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Affiliation(s)
- Chen-Ming Lin
- Department of Chemistry, Texas A & M University Box 30012 College Station TX 77842 USA
| | - Zhengyang Jiang
- Department of Chemistry, Texas A & M University Box 30012 College Station TX 77842 USA
| | - Zhe Gao
- Department of Chemistry, Texas A & M University Box 30012 College Station TX 77842 USA
| | - Maritess Arancillo
- Department of Chemistry, Texas A & M University Box 30012 College Station TX 77842 USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University Box 30012 College Station TX 77842 USA
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9
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Kellici TF, Pilka ES, Bodkin MJ. Small-molecule modulators of serine protease inhibitor proteins (serpins). Drug Discov Today 2020; 26:442-454. [PMID: 33259801 DOI: 10.1016/j.drudis.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Serine protease inhibitors (serpins) are a large family of proteins that regulate and control crucial physiological processes, such as inflammation, coagulation, thrombosis and thrombolysis, and immune responses. The extraordinary impact that these proteins have on numerous crucial pathways makes them an attractive target for drug discovery. In this review, we discuss recent advances in research on small-molecule modulators of serpins, examine their mode of action, analyse the structural data from crystallised protein-ligand complexes, and highlight the potential obstacles and possible therapeutic perspectives. The application of in silico methods for rational drug discovery is also summarised. In addition, we stress the need for continued research in this field.
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10
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Lin C, Arancillo M, Whisenant J, Burgess K. Unconventional Secondary Structure Mimics: Ladder‐Rungs. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chen‐Ming Lin
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
| | - Maritess Arancillo
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
| | - Jonathan Whisenant
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
| | - Kevin Burgess
- Department of Chemistry Texas A&M University Box 30012 College Station TX 77842 USA
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11
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Lin CM, Arancillo M, Whisenant J, Burgess K. Unconventional Secondary Structure Mimics: Ladder-Rungs. Angew Chem Int Ed Engl 2020; 59:9398-9402. [PMID: 32176815 DOI: 10.1002/anie.202002639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/06/2020] [Indexed: 01/31/2023]
Abstract
Secondary structures tend to be recognizable because they have repeating structural motifs, but mimicry of these does not have to follow such well-defined patterns. Bioinformatics studies to match side-chain orientations of a novel hydantoin triazole chemotype (1) to protein-protein interfaces revealed it tends to align well across parallel and antiparallel sheets, like rungs on a ladder. One set of these overlays was observed for the protein-protein interaction uPA⋅uPAR. Consequently, chemotype 1 was made with appropriate side-chains to mimic uPA at this interface. Biophysical assays indicate these compounds did in fact bind uPAR, and elicit cellular responses that affected invasion, migration, and wound healing.
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Affiliation(s)
- Chen-Ming Lin
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
| | - Maritess Arancillo
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
| | - Jonathan Whisenant
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A&M University, Box 30012, College Station, TX, 77842, USA
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12
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Tikhov RM, Kuznetsov NY. Construction of piperidine-2,4-dione-type azaheterocycles and their application in modern drug development and natural product synthesis. Org Biomol Chem 2020; 18:2793-2812. [DOI: 10.1039/d0ob00287a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The review surveys the existing routes to piperidine-2,4-dione-type heterocycles including derivatives with the most vital types of biological activity. This heterocyclic platform is ideal for the construction of modern drugs and natural products.
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Affiliation(s)
- Rabdan M. Tikhov
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russian Federation
| | - Nikolai Yu. Kuznetsov
- A.N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- Moscow
- Russian Federation
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13
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Bagheri Y, Shafiei F, Chedid S, Zhao B, You M. Lipid-DNA conjugates for cell membrane modification, analysis, and regulation. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1632454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yousef Bagheri
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Fatemeh Shafiei
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Sara Chedid
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
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14
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Taechalertpaisarn J, Lyu RL, Arancillo M, Lin CM, Jiang Z, Perez LM, Ioerger TR, Burgess K. Design criteria for minimalist mimics of protein-protein interface segments. Org Biomol Chem 2019; 17:908-915. [PMID: 30629068 DOI: 10.1039/c8ob02901f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Small molecules that can interrupt or inhibit protein-protein interactions (PPIs) are valuable as probes in chemical biology and medicinal chemistry, but they are also notoriously difficult to develop. Design of non-peptidic small molecules that mimic amino acid side-chain interactions in PPIs ("minimalist mimics") is seen as a way to fast track discovery of PPI inhibitors. However, there has been little comment on general design criteria for minimalist mimics, even though such guidelines could steer construction of libraries to screen against multiple PPI targets. We hypothesized insight into general design criteria for minimalist mimics could be gained by comparing preferred conformations of typical minimalist mimic designs against side-chain orientations on a huge number of PPI interfaces. That thought led to this work which features nine minimalist mimic designs: one from the literature, and eight new "hypothetical" ones conceived by us. Simulated preferred conformers of these were systematically aligned with >240 000 PPI interfaces from the Protein Data Bank. Conclusions from those analyses did indeed reveal various design considerations that are discussed here. Surprisingly, this study also showed one of the minimalist mimic designs aligned on PPI interface segments more than 15 times more frequently than any other in the series (according to uniform standards described herein); reasons for this are also discussed.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry and Laboratory For Molecular Simulation, Texas A & M University, Box 30012, College Station, TX 77842-3012, USA.
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15
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Small molecules as inhibitors of PCSK9: Current status and future challenges. Eur J Med Chem 2018; 162:212-233. [PMID: 30448414 DOI: 10.1016/j.ejmech.2018.11.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/13/2018] [Accepted: 11/05/2018] [Indexed: 12/11/2022]
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays an important role in regulating lipoprotein metabolism by binding to low-density lipoprotein receptors (LDLRs), leading to their degradation. LDL cholesterol (LDL-C) lowering drugs that operate through the inhibition of PCSK9 are being pursued for the management of hypercholesterolemia and reducing its associated atherosclerotic cardiovascular disease (CVD) risk. Two PCSK9-blocking monoclonal antibodies (mAbs), alirocumab and evolocumab, were approved in 2015. However, the high costs of PCSK9 antibody drugs impede their prior authorization practices and reduce their long-term adherence. Given the potential of small-molecule drugs, the development of small-molecule PCSK9 inhibitors has attracted considerable attention. This article provides an overview of the recent development of small-molecule PCSK9 inhibitors disclosed in the literature and patent applications, and different approaches that have been pursued to modulate the functional activity of PCSK9 using small molecules are described. Challenges and potential strategies in developing small-molecule PCSK9 inhibitors are also discussed.
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16
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Taechalertpaisarn J, Zhao B, Liang X, Burgess K. Small Molecule Inhibitors of the PCSK9·LDLR Interaction. J Am Chem Soc 2018; 140:3242-3249. [PMID: 29378408 DOI: 10.1021/jacs.7b09360] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The protein-protein interaction between proprotein convertase subtilisin/kexin type 9 (PCSK9) and low-density lipoprotein receptor (LDLR) is a relatively new, and extremely important, validated therapeutic target for treatment and prevention of heart disease. Experts in the area agree that the first small molecules to disrupt PCSK9·LDLR would represent a milestone in this field, yet few credible leads have been reported. This paper describes how side-chain orientations in preferred conformations of carefully designed chemotypes were compared with LDLR side chains at the PCSK9·LDLR interface to find molecules that would mimic interface regions of LDLR. This approach is an example of the procedure called EKO (Exploring Key Orientations). The guiding hypothesis on which EKO is based is that good matches indicate the chemotypes bearing the same side chains as the protein at the sites of overlay have the potential to disrupt the parent protein-protein interaction. In the event, the EKO procedure and one round of combinatorial fragment-based virtual docking led to the discovery of seven compounds that bound PCSK9 (SPR and ELISA) and had a favorable outcome in a cellular assay (hepatocyte uptake of fluorescently labeled low-density lipoprotein particles) and increased the expression LDLR on hepatocytes in culture. Three promising hit compounds in this series had dissociation constants for PCSK9 binding in the 20-40 μM range, and one of these was modified with a photoaffinity label and shown to form a covalent conjugate with PCSK9 on photolysis.
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Affiliation(s)
- Jaru Taechalertpaisarn
- Department of Chemistry , Texas A & M University , Box 30012, College Station , Texas 77842 , United States
| | - Bosheng Zhao
- Department of Chemistry , Texas A & M University , Box 30012, College Station , Texas 77842 , United States
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology (IBT), Texas A&M Health Science Center , Houston , Texas 77030 , United States
| | - Kevin Burgess
- Department of Chemistry , Texas A & M University , Box 30012, College Station , Texas 77842 , United States
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17
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Xin D, Jeffries A, Burgess K. Interplay Of Stereochemistry, Conformational Rigidity, And Ease Of Synthesis For 13-Membered Cyclic Peptidomimetics Containing APC Residues. ACS COMBINATORIAL SCIENCE 2017; 19:414-421. [PMID: 28561582 DOI: 10.1021/acscombsci.7b00041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a program to design small molecules that bind proteins, we require cyclic peptides (or peptidomimetics) that are severely constrained such that they adopt one predominant conformation in solution. This paper describes syntheses of the 13-membered cyclic tetrapeptides 1 containing aminopyrrolidine carboxyl (APC) residues. A linear precursor was prepared and used to determine optimal conditions for cyclization of that substrate. A special linker was prepared to enable cyclization of similar linear peptidomimetics on a solid phase, and the solution-phase cyclization conditions were shown to be appropriate for this too. Stereochemical variations were then used to determine the ideal APC configuration for cyclization of the linear precursors (on a solid phase, using the conditions identified previously). Consequently, a series of compounds were prepared that are representative of compounds 1. Conformational studies of representative compounds in DMSO solution were performed primarily using (i) NOE studies, (ii) quenched molecular dynamics simulations using no constraints from experiment, and (iii) MacroModel calculations with NMR constraints. All three strategies converged to the same conclusion: the backbone of molecules based on 1 tends to adopt one preferential conformation in solution and that conformation can be predicted from the stereochemistries of the α-amino acids involved.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Andrew Jeffries
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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18
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Wilson AJ. Helix mimetics: Recent developments. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:33-40. [DOI: 10.1016/j.pbiomolbio.2015.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 494] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Xin D, Raghuraman A, Burgess K. Extended Piperidine–Piperidinone Protein Interface Mimics. J Org Chem 2015; 80:4450-8. [DOI: 10.1021/acs.joc.5b00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Arjun Raghuraman
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, United States
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