51
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Sun H, Wang J, Liu S, Zhou X, Dai L, Chen C, Xu Q, Wen X, Cheng K, Sun H, Yuan H. Discovery of Novel Small Molecule Inhibitors Disrupting the PCSK9-LDLR Interaction. J Chem Inf Model 2021; 61:5269-5279. [PMID: 34553597 DOI: 10.1021/acs.jcim.1c00521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proprotein convertase subtilisin kexin 9 (PCSK9) has been identified as a reliable therapeutic target for hypercholesterolemia and coronary artery heart diseases since the monoclonal antibodies of PCSK9 have launched. Disrupting the protein-protein interaction (PPI) between PCSK9 and the low-density lipoprotein receptor (LDLR) has been considered as a promising approach for developing PCSK9 inhibitors. However, PPIs have been traditionally considered difficult to target by small molecules since the PPI surface is usually large, flat, featureless, and without a "pocket" or "groove" for ligand binding. The PCSK9-LDLR PPI interface is such a typical case. In this study, a potential binding pocket was generated on the PCSK9-LDLR PPI surface of PCSK9 through induced-fit docking. On the basis of this induced binding pocket, virtual screening, molecular dynamics (MD) simulation, and biological evaluations have been applied for the identification of novel small molecule inhibitors of PCSK9-LDLR PPI. Among the selected compounds, compound 13 exhibited certain PCSK9-LDLR PPI inhibitory activity (IC50: 7.57 ± 1.40 μM). The direct binding affinity between 13 and PCSK9 was determined with a KD value of 2.50 ± 0.73 μM. The LDLR uptake function could be also restored to a certain extent by 13 in HepG2 cells. This well-characterized hit compound will facilitate the further development of novel small molecule inhibitors of PCSK9-LDLR PPI.
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Affiliation(s)
- Hengzhi Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jinzheng Wang
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Shengjie Liu
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xinyu Zhou
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Liang Dai
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Caiping Chen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Qinglong Xu
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Xiaoan Wen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Keguang Cheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, 15 Yucai Road, Guilin 541004, P. R. China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Haoliang Yuan
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, P. R. China
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52
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Truong J, George A, Holien JK. Analysis of physicochemical properties of protein-protein interaction modulators suggests stronger alignment with the "rule of five". RSC Med Chem 2021; 12:1731-1749. [PMID: 34778774 DOI: 10.1039/d1md00213a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the important roles played by protein-protein interactions (PPIs) in disease, they have been long considered as 'undruggable'. However, recent advances have suggested that PPIs are druggable but may not follow conventional rules of 'drug ability'. Here we explore which physicochemical parameters are essential for a PPI modulator to be a clinical drug by analysing the physicochemical properties of small-molecule PPI modulators in the market, in clinical trials, and published. Our analysis reveals that those compounds currently on the market have a larger range of values for most of the physicochemical parameters, whereas those in clinical trials fit much more stringently to standard drug-like parameters. This observation was particularly true for molecular weight, clog P and topological polar surface area, where aside from a few outliers, most of the compounds in clinical trials fit within standard drug-like parameters. This implies that the newer PPI modulators are more drug-like than those currently on the market, suggesting that designing new PPI-specific screening libraries should remain within standard drug-like parameters in order to obtain a clinical candidate. Taken together, our analysis has important implications for designing future drug discovery campaigns aimed at targeting PPIs.
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Affiliation(s)
- Jia Truong
- STEM College, RMIT University Vic Australia
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53
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Horianopoulos LC, Lee CWJ, Hu G, Caza M, Kronstad JW. Dnj1 Promotes Virulence in Cryptococcus neoformans by Maintaining Robust Endoplasmic Reticulum Homeostasis Under Temperature Stress. Front Microbiol 2021; 12:727039. [PMID: 34566931 PMCID: PMC8461255 DOI: 10.3389/fmicb.2021.727039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
The capacity of opportunistic fungal pathogens such as Cryptococcus neoformans to cause disease is dependent on their ability to overcome an onslaught of stresses including elevated temperature under mammalian host conditions. Protein chaperones and co-chaperones play key roles in thermotolerance. In this study, we characterized the role of the endoplasmic reticulum (ER) J-domain containing co-chaperone, Dnj1, in the virulence of C. neoformans. A strain expressing a Dnj1-GFP fusion protein was used to confirm localization to the ER, and a dnj1∆ deletion mutant was shown to be hypersensitive to the ER stress caused by tunicamycin (TM) or 4μ8C. Dnj1 and another ER chaperone, calnexin were found to coordinately maintain ER homeostasis and contribute to maintenance of cell wall architecture. Dnj1 also contributed to thermotolerance and increased in abundance at elevated temperatures representative of febrile patients (e.g., 39°C) thus highlighting its role as a temperature-responsive J domain protein. The elaboration of virulence factors such as the polysaccharide capsule and extracellular urease activity were also markedly impaired in the dnj1∆ mutant when induced at human body temperature (i.e., 37°C). These virulence factors are immunomodulatory and, indeed, infection with the dnj1∆ mutant revealed impaired induction of the cytokines IL-6, IL-10, and MCP-1 in the lungs of mice compared to infection with wild type or complemented strains. The dnj1∆ mutant also had attenuated virulence in an intranasal murine model of cryptococcosis. Altogether, our data indicate that Dnj1 is crucial for survival and virulence factor production at elevated temperatures. The characterization of this co-chaperone also highlights the importance of maintaining homeostasis in the ER for the pathogenesis of C. neoformans.
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Affiliation(s)
| | - Christopher W J Lee
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Guanggan Hu
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mélissa Caza
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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54
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Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion. Commun Biol 2021; 4:1041. [PMID: 34493804 PMCID: PMC8423723 DOI: 10.1038/s42003-021-02575-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Many cadherin family proteins are associated with diseases such as cancer. Since cell adhesion requires homodimerization of cadherin molecules, a small-molecule regulator of dimerization would have therapeutic potential. Herein, we describe identification of a P-cadherin-specific chemical fragment that inhibits P-cadherin-mediated cell adhesion. Although the identified molecule is a fragment compound, it binds to a cavity of P-cadherin that has not previously been targeted, indirectly prevents formation of hydrogen bonds necessary for formation of an intermediate called the X dimer and thus modulates the process of X dimerization. Our findings will impact on a strategy for regulation of protein-protein interactions and stepwise assembly of protein complexes using small molecules.
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55
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Kim J, Lim H, Moon S, Cho SY, Kim M, Park JH, Park HW, No KT. Hot Spot Analysis of YAP-TEAD Protein-Protein Interaction Using the Fragment Molecular Orbital Method and Its Application for Inhibitor Discovery. Cancers (Basel) 2021; 13:4246. [PMID: 34439400 PMCID: PMC8391968 DOI: 10.3390/cancers13164246] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/19/2021] [Indexed: 02/02/2023] Open
Abstract
The Hippo pathway is an important signaling pathway modulating growth control and cancer cell proliferation. Dysregulation of the Hippo pathway is a common feature of several types of cancer cells. The modulation of the interaction between yes-associated protein (YAP) and transcriptional enhancer associated domain (TEAD) in the Hippo pathway is considered an attractive target for cancer therapeutic development, although the inhibition of PPI is a challenging task. In order to investigate the hot spots of the YAP and TEAD1 interacting complex, an ab initio Fragment Molecular Orbital (FMO) method was introduced. With the hot spots, pharmacophores for the inhibitor design were constructed, then virtual screening was performed to an in-house library. Next, we performed molecular docking simulations and FMO calculations for screening results to study the binding modes and affinities between PPI inhibitors and TEAD1. As a result of the virtual screening, three compounds were selected as virtual hit compounds. In order to confirm their biological activities, cellular (luciferase activity, proximity ligation assay and wound healing assay in A375 cells, qRT-PCR in HEK 293T cells) and biophysical assays (surface plasmon resonance assays) were performed. Based on the findings of the study, we propose a novel PPI inhibitor BY03 and demonstrate a profitable strategy to analyze YAP-TEAD PPI and discover novel PPI inhibitors.
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Affiliation(s)
- Jongwan Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Korea;
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Korea
| | - Hocheol Lim
- The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicine, Yonsei University, Incheon 21983, Korea;
| | - Sungho Moon
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Seon Yeon Cho
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Minhye Kim
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
| | - Jae Hyung Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (J.H.P.); (H.W.P.)
| | - Hyun Woo Park
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (J.H.P.); (H.W.P.)
| | - Kyoung Tai No
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon 21983, Korea
- Baobab AiBIO Co., Ltd., Incheon 21983, Korea; (S.M.); (S.Y.C.); (M.K.)
- Institute of Convergence Science and Technology, Yonsei University, Incheon 21983, Korea
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56
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Tivon B, Gabizon R, Somsen BA, Cossar PJ, Ottmann C, London N. Covalent flexible peptide docking in Rosetta. Chem Sci 2021; 12:10836-10847. [PMID: 34476063 PMCID: PMC8372624 DOI: 10.1039/d1sc02322e] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/09/2021] [Indexed: 11/21/2022] Open
Abstract
Electrophilic peptides that form an irreversible covalent bond with their target have great potential for binding targets that have been previously considered undruggable. However, the discovery of such peptides remains a challenge. Here, we present Rosetta CovPepDock, a computational pipeline for peptide docking that incorporates covalent binding between the peptide and a receptor cysteine. We applied CovPepDock retrospectively to a dataset of 115 disulfide-bound peptides and a dataset of 54 electrophilic peptides. It produced a top-five scoring, near-native model, in 89% and 100% of the cases when docking from the native conformation, and 20% and 90% when docking from an extended peptide conformation, respectively. In addition, we developed a protocol for designing electrophilic peptide binders based on known non-covalent binders or protein-protein interfaces. We identified 7154 peptide candidates in the PDB for application of this protocol. As a proof-of-concept we validated the protocol on the non-covalent complex of 14-3-3σ and YAP1 phosphopeptide. The protocol identified seven highly potent and selective irreversible peptide binders. The predicted binding mode of one of the peptides was validated using X-ray crystallography. This case-study demonstrates the utility and impact of CovPepDock. It suggests that many new electrophilic peptide binders can be rapidly discovered, with significant potential as therapeutic molecules and chemical probes.
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Affiliation(s)
- Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel
| | - Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel
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57
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Sitthiyotha T, Chunsrivirot S. Computational design of SARS-CoV-2 peptide binders with better predicted binding affinities than human ACE2 receptor. Sci Rep 2021; 11:15650. [PMID: 34341401 PMCID: PMC8329052 DOI: 10.1038/s41598-021-94873-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/19/2021] [Indexed: 01/12/2023] Open
Abstract
SARS-CoV-2 is coronavirus causing COVID-19 pandemic. To enter human cells, receptor binding domain of S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) binds to peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptor. Employing peptides to inhibit binding between SARS-CoV-2-RBD and ACE2-PD is a therapeutic solution for COVID-19. Previous experimental study found that 23-mer peptide (SBP1) bound to SARS-CoV-2-RBD with lower affinity than ACE2. To increase SBP1 affinity, our previous study used residues 21–45 of α1 helix of ACE2-PD (SPB25) to design peptides with predicted affinity better than SBP1 and SPB25 by increasing interactions of residues that do not form favorable interactions with SARS-CoV-2-RBD. To design SPB25 with better affinity than ACE2, we employed computational protein design to increase interactions of residues reported to form favorable interactions with SARS-CoV-2-RBD and combine newly designed mutations with the best single mutations from our previous study. Molecular dynamics show that predicted binding affinities of three peptides (SPB25Q22R, SPB25F8R/K11W/L25R and SPB25F8R/K11F/Q22R/L25R) are better than ACE2. Moreover, their predicted stabilities may be slightly higher than SBP1 as suggested by their helicities. This study developed an approach to design SARS-CoV-2 peptide binders with predicted binding affinities better than ACE2. These designed peptides are promising candidates as SARS-CoV-2 inhibitors.
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Affiliation(s)
- Thassanai Sitthiyotha
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand. .,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
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58
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Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-1119. [PMID: 34280732 PMCID: PMC8253661 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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59
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Sadremomtaz A, Al-Dahmani ZM, Ruiz-Moreno AJ, Monti A, Wang C, Azad T, Bell JC, Doti N, Velasco-Velázquez MA, de Jong D, de Jonge J, Smit J, Dömling A, van Goor H, Groves MR. Synthetic Peptides That Antagonize the Angiotensin-Converting Enzyme-2 (ACE-2) Interaction with SARS-CoV-2 Receptor Binding Spike Protein. J Med Chem 2021; 65:2836-2847. [PMID: 34328726 PMCID: PMC8353989 DOI: 10.1021/acs.jmedchem.1c00477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
The SARS-CoV-2 viral
spike protein S receptor-binding domain (S-RBD)
binds ACE2 on host cells to initiate molecular events, resulting in
intracellular release of the viral genome. Therefore, antagonists
of this interaction could allow a modality for therapeutic intervention.
Peptides can inhibit the S-RBD:ACE2 interaction by interacting with
the protein–protein interface. In this study, protein contact
atlas data and molecular dynamics simulations were used to locate
interaction hotspots on the secondary structure elements α1,
α2, α3, β3, and β4 of ACE2. We designed a
library of discontinuous peptides based upon a combination of the
hotspot interactions, which were synthesized and screened in a bioluminescence-based
assay. The peptides demonstrated high efficacy in antagonizing the
SARS-CoV-2 S-RBD:ACE2 interaction and were validated by microscale
thermophoresis which demonstrated strong binding affinity (∼10
nM) of these peptides to S-RBD. We anticipate that such discontinuous
peptides may hold the potential for an efficient therapeutic treatment
for COVID-19.
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Affiliation(s)
- Afsaneh Sadremomtaz
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Zayana M Al-Dahmani
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands.,Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Angel J Ruiz-Moreno
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands.,Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico.,Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Chao Wang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Taha Azad
- Center for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, K1H 8L6 ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5 ON, Canada
| | - John C Bell
- Center for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, K1H 8L6 ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5 ON, Canada
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Marco A Velasco-Velázquez
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico.,Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
| | - Debora de Jong
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Jørgen de Jonge
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720BA Bilthoven, The Netherlands
| | - Jolanda Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Alexander Dömling
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Harry van Goor
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Matthew R Groves
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
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60
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Kozlovskii I, Popov P. Protein-Peptide Binding Site Detection Using 3D Convolutional Neural Networks. J Chem Inf Model 2021; 61:3814-3823. [PMID: 34292750 DOI: 10.1021/acs.jcim.1c00475] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides and peptide-based molecules represent a promising therapeutic modality targeting intracellular protein-protein interactions, potentially combining the beneficial properties of biologics and small-molecule drugs. Protein-peptide complexes occupy a unique niche of interaction interfaces with respect to protein-protein and protein-small molecule complexes. Protein-peptide binding site identification resembles image object detection, a field that had been revolutionalized with computer vision techniques. We present a new protein-peptide binding site detection method called BiteNetPp by harnessing the power of 3D convolutional neural network. Our method employs a tensor-based representation of spatial protein structures, which is fed to 3D convolutional neural network, resulting in probability scores and coordinates of the binding "hot spots" in the input structures. We used the domain adaptation technique to fine-tune model trained on protein-small molecule complexes using a manually curated set of protein-peptide structures. BiteNetPp consistently outperforms existing state-of-the-art methods in the independent test benchmark. It takes less than a second to analyze a single-protein structure, making BiteNetPp suitable for the large-scale analysis of protein-peptide binding sites.
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Affiliation(s)
- Igor Kozlovskii
- iMolecule, Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Petr Popov
- iMolecule, Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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61
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Shao H, Oltion K, Wu T, Gestwicki JE. Differential scanning fluorimetry (DSF) screen to identify inhibitors of Hsp60 protein-protein interactions. Org Biomol Chem 2021; 18:4157-4163. [PMID: 32458889 DOI: 10.1039/d0ob00928h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There are relatively few methods available for discovering inhibitors of the protein-protein interactions (PPIs) that hold together homo-oligomers. We envisioned that Differential Scanning Fluorimetry (DSF) might be a versatile way to discover this type of inhibitor because oligomers are often more thermally stable than monomers. Using the homo-heptameric chaperonin, Hsp60, as a model, we screened ∼5000 diverse compounds in 384-well plates by DSF, revealing molecules that partially inhibited oligomerization. Because DSF does not require protein labeling or structural information, we propose that it could be a versatile way to uncover PPI inhibitors.
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Affiliation(s)
- Hao Shao
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Keely Oltion
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Taia Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
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62
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Alexa A, Ember O, Szabó I, Mo'ath Y, Póti ÁL, Reményi A, Bánóczi Z. Peptide Based Inhibitors of Protein Binding to the Mitogen-Activated Protein Kinase Docking Groove. Front Mol Biosci 2021; 8:690429. [PMID: 34277705 PMCID: PMC8281026 DOI: 10.3389/fmolb.2021.690429] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important regulatory units in cells and they take part in the regulation of many cellular functions such as cell division, differentiation or apoptosis. All MAPKs have a shallow docking groove that interacts with linear binding motifs of their substrate proteins and their regulatory proteins such as kinases, phosphatases, scaffolds. Inhibition of these protein–protein interactions may reduce or abolish the activity of the targeted kinase. Based on the wide range of their biological activity, this kind of inhibition can be useful in the treatment of many disorders like tumors, inflammation or undesired cell apoptosis. In this study a linear binding motif from the RHDF1 protein—a 15 amino acids long peptide—was selected for optimization to increase its cellular uptake but retaining its low micromolar binding affinity. First, we synthesized an octaarginine conjugate that showed efficient cellular uptake. Next, we set out to reduce the size of this construct. We were able to decrease the length of the original peptide, and to increase its cellular uptake with specific chemical modifications. These new constructs bound better to ERK2 and p38 kinases than the original peptide and they showed markedly increased cellular uptake. The new octaarginine conjugate and one of the minimized bicyclic derivatives could inhibit the phosphorylation of intracellular ERK or p38. However, the modulation of MAPK phosphorylation levels by these cell-penetrating peptides were complex, despite that in biochemical assays they all inhibited MAPK-substrate binding as well as phosphorylation. The optimized peptides depending on the applied concentration caused an expected decrease, but also some unexpected increase in MAPK phosphorylation patterns in the cell. This possibly reflects the complexity of MAPK docking groove mediated protein–protein interactions including bone fide MAPK clients such activator kinases, deactivating phosphatases or regulatory scaffolds. Thus, our findings with optimized cell-penetrating “inhibitory” peptides highlight the opportunities but also the pitfalls of docking peptide based MAPK activity regulation and call for a better quantitative understanding of MAPK mediated protein–protein interactions in cells.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Orsolya Ember
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary.,Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös L. University, Budapest, Hungary
| | - Yousef Mo'ath
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Biomolecular Interactions Laboratory, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
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63
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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64
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Wanichawan P, Skogestad J, Lunde M, Støle TP, Stensland M, Nyman TA, Sjaastad I, Sejersted OM, Aronsen JM, Carlson CR. Design of a Proteolytically Stable Sodium-Calcium Exchanger 1 Activator Peptide for In Vivo Studies. Front Pharmacol 2021; 12:638646. [PMID: 34163352 PMCID: PMC8215385 DOI: 10.3389/fphar.2021.638646] [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: 12/15/2020] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
The cardiac sodium–calcium exchanger (NCX1) is important for normal Na+- and Ca2+-homeostasis and cardiomyocyte relaxation and contraction. It has been suggested that NCX1 activity is reduced by phosphorylated phospholemman (pSer68-PLM); however its direct interaction with PLM is debated. Disruption of the potentially inhibitory pSer68-PLM-NCX1 interaction might be a therapeutic strategy to increase NCX1 activity in cardiac disease. In the present study, we aimed to analyze the binding affinities and kinetics of the PLM-NCX1 and pSer68-PLM-NCX1 interactions by surface plasmon resonance (SPR) and to develop a proteolytically stable NCX1 activator peptide for future in vivo studies. The cytoplasmic parts of PLM (PLMcyt) and pSer68-PLM (pSer68-PLMcyt) were found to bind strongly to the intracellular loop of NCX1 (NCX1cyt) with similar KD values of 4.1 ± 1.0 nM and 4.3 ± 1.9 nM, but the PLMcyt-NCX1cyt interaction showed higher on/off rates. To develop a proteolytically stable NCX1 activator, we took advantage of a previously designed, high-affinity PLM binding peptide (OPT) that was derived from the PLM binding region in NCX1 and that reverses the inhibitory PLM (S68D)-NCX1 interaction in HEK293. We performed N- and C-terminal truncations of OPT and identified PYKEIEQLIELANYQV as the minimum sequence required for pSer68-PLM binding. To increase peptide stability in human serum, we replaced the proline with an N-methyl-proline (NOPT) after identification of N-terminus as substitution tolerant by two-dimensional peptide array analysis. Mass spectrometry analysis revealed that the half-life of NOPT was increased 17-fold from that of OPT. NOPT pulled down endogenous PLM from rat left ventricle lysate and exhibited direct pSer68-PLM binding in an ELISA-based assay and bound to pSer68-PLMcyt with a KD of 129 nM. Excess NOPT also reduced the PLMcyt-NCX1cyt interaction in an ELISA-based competition assay, but in line with that NCX1 and PLM form oligomers, NOPT was not able to outcompete the physical interaction between endogenous full length proteins. Importantly, cell-permeable NOPT-TAT increased NCX1 activity in cardiomyocytes isolated from both SHAM-operated and aorta banded heart failure (HF) mice, indicating that NOPT disrupted the inhibitory pSer68-PLM-NCX1 interaction. In conclusion, we have developed a proteolytically stable NCX1-derived PLM binding peptide that upregulates NCX1 activity in SHAM and HF cardiomyocytes.
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Affiliation(s)
- Pimthanya Wanichawan
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Jonas Skogestad
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marianne Lunde
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Thea Parsberg Støle
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Maria Stensland
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway
| | - Ivar Sjaastad
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Ole M Sejersted
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
| | - Jan Magnus Aronsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Pharmacology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Cathrine Rein Carlson
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,The KG Jebsen Cardiac Research Center and Center for Heart Failure Research, University of Oslo, Oslo, Norway
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65
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Du D, Xu D, Zhu L, Stazi G, Zwergel C, Liu Y, Luo Z, Li Y, Zhang Y, Zhu K, Ding Y, Liu J, Fan S, Zhao K, Zhang N, Kong X, Jiang H, Chen K, Zhao K, Valente S, Min J, Duan W, Luo C. Structure-Guided Development of Small-Molecule PRC2 Inhibitors Targeting EZH2-EED Interaction. J Med Chem 2021; 64:8194-8207. [PMID: 34077206 DOI: 10.1021/acs.jmedchem.0c02261] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Disruption of EZH2-embryonic ectoderm development (EED) protein-protein interaction (PPI) is a new promising cancer therapeutic strategy. We have previously reported the discovery of astemizole, a small-molecule inhibitor targeting the EZH2-EED PPI. Herein, we report the cocrystal structure of EED in complex with astemizole at 2.15 Å. The structure elucidates the detailed binding mode of astemizole to EED and provides a structure-guided design for the discovery of a novel EZH2-EED interaction inhibitor, DC-PRC2in-01, with an affinity Kd of 4.56 μM. DC-PRC2in-01 destabilizes the PRC2 complex, thereby leading to the degradation of PRC2 core proteins and the decrease of global H3K27me3 levels in cancer cells. The proliferation of PRC2-driven lymphomas cells is effectively inhibited, and the cell cycle is arrested in the G0/G1 phase. Together, these data demonstrate that DC-PRC2in-01 could be an effective chemical probe for investigating the PRC2-related physiology and pathology and providing a promising chemical scaffold for further development.
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Affiliation(s)
- Daohai Du
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023 Jiangsu, China.,Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Dandan Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Licheng Zhu
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto M5G1L7 Ontario, Canada.,Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.,School of Life Sciences, Jinggangshan University, Ji'an 343009 Jiangxi, China
| | - Giulia Stazi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome 00185, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome 00185, Italy
| | - Yanli Liu
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto M5G1L7 Ontario, Canada.,Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.,College of Pharmaceutical Sciences, Soochow University, Suzhou 215123 Jiangsu, China
| | - Zhongyuan Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023 Jiangsu, China.,Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Yuanqing Li
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Zhang
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Kongkai Zhu
- School of Biological Science and Technology, University of Jinan; Jinan 250022, China
| | - Yiluan Ding
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingqiu Liu
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Shijie Fan
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Kaiyan Zhao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naixia Zhang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiangqian Kong
- Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome 00185, Italy
| | - Jinrong Min
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto M5G1L7 Ontario, Canada.,Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Wenhu Duan
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023 Jiangsu, China.,Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 210203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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66
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Basu S, Chakravarty D, Bhattacharyya D, Saha P, Patra HK. Plausible blockers of Spike RBD in SARS-CoV2-molecular design and underlying interaction dynamics from high-level structural descriptors. J Mol Model 2021; 27:191. [PMID: 34057647 PMCID: PMC8165686 DOI: 10.1007/s00894-021-04779-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/26/2021] [Indexed: 12/24/2022]
Abstract
Abstract COVID-19 is characterized by an unprecedented abrupt increase in the viral transmission rate (SARS-CoV-2) relative to its pandemic evolutionary ancestor, SARS-CoV (2003). The complex molecular cascade of events related to the viral pathogenicity is triggered by the Spike protein upon interacting with the ACE2 receptor on human lung cells through its receptor binding domain (RBDSpike). One potential therapeutic strategy to combat COVID-19 could thus be limiting the infection by blocking this key interaction. In this current study, we adopt a protein design approach to predict and propose non-virulent structural mimics of the RBDSpike which can potentially serve as its competitive inhibitors in binding to ACE2. The RBDSpike is an independently foldable protein domain, resilient to conformational changes upon mutations and therefore an attractive target for strategic re-design. Interestingly, in spite of displaying an optimal shape fit between their interacting surfaces (attributed to a consequently high mutual affinity), the RBDSpike–ACE2 interaction appears to have a quasi-stable character due to a poor electrostatic match at their interface. Structural analyses of homologous protein complexes reveal that the ACE2 binding site of RBDSpike has an unusually high degree of solvent-exposed hydrophobic residues, attributed to key evolutionary changes, making it inherently “reaction-prone.” The designed mimics aimed to block the viral entry by occupying the available binding sites on ACE2, are tested to have signatures of stable high-affinity binding with ACE2 (cross-validated by appropriate free energy estimates), overriding the native quasi-stable feature. The results show the apt of directly adapting natural examples in rational protein design, wherein, homology-based threading coupled with strategic “hydrophobic ↔ polar” mutations serve as a potential breakthrough. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s00894-021-04779-0.
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Affiliation(s)
- Sankar Basu
- Department of Microbiology, Asutosh College (affiliated to University of Calcutta), Kolkata, 700026, West Bengal, India.
| | - Devlina Chakravarty
- Department of Chemistry, University of Rutgers-Camden, Camden, 08102, NJ, USA
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, 700064, West Bengal, India
| | - Pampa Saha
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Hirak K Patra
- Department of Surgical Biotechnology, Division of Surgery and Interventional Science, University College London, London, NW3 2PF, UK
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67
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Ghassabian H, Falchi F, Timmoneri M, Mercorelli B, Loregian A, Palù G, Alvisi G. Divide et impera: An In Silico Screening Targeting HCMV ppUL44 Processivity Factor Homodimerization Identifies Small Molecules Inhibiting Viral Replication. Viruses 2021; 13:v13050941. [PMID: 34065234 PMCID: PMC8160850 DOI: 10.3390/v13050941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a leading cause of severe diseases in immunocompromised individuals, including AIDS patients and transplant recipients, and in congenitally infected newborns. The utility of available drugs is limited by poor bioavailability, toxicity, and emergence of resistant strains. Therefore, it is crucial to identify new targets for therapeutic intervention. Among the latter, viral protein–protein interactions are becoming increasingly attractive. Since dimerization of HCMV DNA polymerase processivity factor ppUL44 plays an essential role in the viral life cycle, being required for oriLyt-dependent DNA replication, it can be considered a potential therapeutic target. We therefore performed an in silico screening and selected 18 small molecules (SMs) potentially interfering with ppUL44 homodimerization. Antiviral assays using recombinant HCMV TB4-UL83-YFP in the presence of the selected SMs led to the identification of four active compounds. The most active one, B3, also efficiently inhibited HCMV AD169 strain in plaque reduction assays and impaired replication of an AD169-GFP reporter virus and its ganciclovir-resistant counterpart to a similar extent. As assessed by Western blotting experiments, B3 specifically reduced viral gene expression starting from 48 h post infection, consistent with the inhibition of viral DNA synthesis measured by qPCR starting from 72 h post infection. Therefore, our data suggest that inhibition of ppUL44 dimerization could represent a new class of HCMV inhibitors, complementary to those targeting the DNA polymerase catalytic subunit or the viral terminase complex.
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Affiliation(s)
- Hanieh Ghassabian
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | | | - Martina Timmoneri
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Beatrice Mercorelli
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
- Correspondence:
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68
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Chitsike L, Duerksen-Hughes PJ. PPI Modulators of E6 as Potential Targeted Therapeutics for Cervical Cancer: Progress and Challenges in Targeting E6. Molecules 2021; 26:molecules26103004. [PMID: 34070144 PMCID: PMC8158384 DOI: 10.3390/molecules26103004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/05/2021] [Accepted: 05/15/2021] [Indexed: 12/13/2022] Open
Abstract
Advanced cervical cancer is primarily managed using cytotoxic therapies, despite evidence of limited efficacy and known toxicity. There is a current lack of alternative therapeutics to treat the disease more effectively. As such, there have been more research endeavors to develop targeted therapies directed at oncogenic host cellular targets over the past 4 decades, but thus far, only marginal gains in survival have been realized. The E6 oncoprotein, a protein of human papillomavirus origin that functionally inactivates various cellular antitumor proteins through protein–protein interactions (PPIs), represents an alternative target and intriguing opportunity to identify novel and potentially effective therapies to treat cervical cancer. Published research has reported a number of peptide and small-molecule modulators targeting the PPIs of E6 in various cell-based models. However, the reported compounds have rarely been well characterized in animal or human subjects. This indicates that while notable progress has been made in targeting E6, more extensive research is needed to accelerate the optimization of leads. In this review, we summarize the current knowledge and understanding of specific E6 PPI inhibition, the progress and challenges being faced, and potential approaches that can be utilized to identify novel and potent PPI inhibitors for cervical cancer treatment.
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69
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Abstract
The term "undruggable" is used to describe a protein that is not pharmacologically capable of being targeted; recently, however, substantial efforts have been made to turn these proteins into "druggable" targets. Thus, "difficult to drug" or "yet to be drugged" are perhaps more appropriate terms. In cancer, a number of elusive targets fall into this category, including transcription factors such as STAT3, TP53, and MYC. Pharmacologically targeting these intractable proteins is now a key challenge of modern drug development, requiring innovation and the development of new technologies. In this article, we discuss some of the recent technologic and pharmacologic advances that have underpinned the erosion of the concept of undruggability. We describe recent successes in drugging the undruggable RAS (KRAS G12C and HRAS), and discuss the advances that have led to the validation of further targets previously believed to be undruggable, such as HIF-2α, BCL-2, MDM2, and MLL. Finally, we look to the future and describe important advances that are likely to have a major impact on targeting undruggable targets, such as the advent of proteolysis-targeting chimeras and protein-protein modulators, which are leading to considerable excitement surrounding the development of cancer targets.
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Affiliation(s)
- Niamh Coleman
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- Division of Cancer Medicine, Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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70
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Adhikary P, Kandel S, Mamani UF, Mustafa B, Hao S, Qiu J, Fetse J, Liu Y, Ibrahim NM, Li Y, Lin CY, Omoscharka E, Cheng K. Discovery of Small Anti-ACE2 Peptides to Inhibit SARS-CoV-2 Infectivity. ADVANCED THERAPEUTICS 2021; 4:2100087. [PMID: 34179347 PMCID: PMC8212088 DOI: 10.1002/adtp.202100087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Indexed: 12/26/2022]
Abstract
COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infects host cells by binding its viral spike protein receptor-binding domain (RBD) to the angiotensin converting enzyme 2 (ACE2) on host cells. Blocking the SARS-CoV-2-RBD/ACE2 interaction is, therefore, a potential strategy to inhibit viral infections. Using a novel biopanning strategy, a small anti-ACE2 peptide is discovered, which shows high affinity and specificity to human ACE2. It blocks not only the SARS-CoV-2-RBD/ACE2 interaction but also the SARS-CoV-1-RBD/ACE2 interaction. Moreover, it inhibits SARS-CoV-2 infection in Vero-E6 cells. The peptide shows negligible cytotoxicity in Vero-E6 cells and Huh7 cells. In vivo short-term lung toxicity study also demonstrates a good safety of the peptide after intratracheal administration. The anti-ACE2 peptide can be potentially used as a prophylactic or therapeutic agent for SARS-CoV-2 or other ACE2-mediated viruses. The strategy used in this study also provides a fast-track platform to discover other antiviral peptides, which will prepare the world for future pandemics.
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Affiliation(s)
- Pratik Adhikary
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Sashi Kandel
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Umar-Farouk Mamani
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Bahaa Mustafa
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Siyuan Hao
- Department of Microbiology Molecular Genetics and Immunology University of Kansas Medical Center 3901 Rainbow Blvd Kansas City KS 66160 USA
| | - Jianming Qiu
- Department of Microbiology Molecular Genetics and Immunology University of Kansas Medical Center 3901 Rainbow Blvd Kansas City KS 66160 USA
| | - John Fetse
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Yanli Liu
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Nurudeen Mohammed Ibrahim
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Yongren Li
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Chien-Yu Lin
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
| | - Evanthia Omoscharka
- Department of Pathology Truman Medical Center School of Medicine University of Missouri-Kansas City 2301 Holmes Street Kansas City MO 64108 USA
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences School of Pharmacy University of Missouri-Kansas City 2464 Charlotte Street Kansas City MO 64108 USA
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71
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Slater O, Miller B, Kontoyianni M. Decoding Protein-protein Interactions: An Overview. Curr Top Med Chem 2021; 20:855-882. [PMID: 32101126 DOI: 10.2174/1568026620666200226105312] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
Abstract
Drug discovery has focused on the paradigm "one drug, one target" for a long time. However, small molecules can act at multiple macromolecular targets, which serves as the basis for drug repurposing. In an effort to expand the target space, and given advances in X-ray crystallography, protein-protein interactions have become an emerging focus area of drug discovery enterprises. Proteins interact with other biomolecules and it is this intricate network of interactions that determines the behavior of the system and its biological processes. In this review, we briefly discuss networks in disease, followed by computational methods for protein-protein complex prediction. Computational methodologies and techniques employed towards objectives such as protein-protein docking, protein-protein interactions, and interface predictions are described extensively. Docking aims at producing a complex between proteins, while interface predictions identify a subset of residues on one protein that could interact with a partner, and protein-protein interaction sites address whether two proteins interact. In addition, approaches to predict hot spots and binding sites are presented along with a representative example of our internal project on the chemokine CXC receptor 3 B-isoform and predictive modeling with IP10 and PF4.
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Affiliation(s)
- Olivia Slater
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
| | - Bethany Miller
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
| | - Maria Kontoyianni
- Department of Pharmaceutical Sciences, Southern Illinois University, Edwardsville, IL 62026, United States
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72
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Abdildinova A, Gong YD. Traceless solid-phase synthesis and β-turn propensity of 1,3-thiazole-based peptidomimetics. RSC Adv 2020; 11:1050-1056. [PMID: 35423674 PMCID: PMC8693395 DOI: 10.1039/d0ra10127c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
The design and solid-phase synthesis of 1,3-thiazole-based peptidomimetic molecules is described. The solid-phase synthesis was based on the utilization of a traceless linker strategy. The synthesis starts from the conversion of chloromethyl polystyrene resin to the resin with a sulfur linker unit. The key intermediate 4-amino-thiazole-5-carboxylic acid resin is prepared in three steps from Merrifield resin. The amide coupling proceeded at the C4 and C5 positions via an Fmoc solid-phase peptide synthesis strategy. After cleavage, the final compounds were obtained in moderate yields (average 9%, 11-step overall yields) with high purities (≥87%). Geometric measurements of Cα distances and dihedral angles along with an rmsd of 0.5434 for attachment with Cα of the β-turn template suggest type IV β-turn structural motifs. Additionally, the physicochemical properties of the molecules have been evaluated.
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Affiliation(s)
- Aizhan Abdildinova
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University 30, Pildong-ro 1-gil, Jung-gu Seoul 04620 Korea
| | - Young-Dae Gong
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University 30, Pildong-ro 1-gil, Jung-gu Seoul 04620 Korea
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73
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Sitthiyotha T, Chunsrivirot S. Computational Design of 25-mer Peptide Binders of SARS-CoV-2. J Phys Chem B 2020; 124:10930-10942. [PMID: 33200935 PMCID: PMC7687296 DOI: 10.1021/acs.jpcb.0c07890] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/25/2020] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2 is the novel coronavirus causing the COVID-19 pandemic. To enter human cells, the receptor-binding domain (RBD) of the S1 subunit of SARS-CoV-2 (SARS-CoV-2-RBD) initially binds to the peptidase domain of angiotensin-converting enzyme 2 receptor (ACE2-PD). Using peptides to inhibit SARS-CoV-2-RBD binding to ACE2 is a potential therapeutic solution for COVID-19. A previous study identified a 23-mer peptide (SBP1) that bound to SARS-CoV-2-RBD with comparable KD to ACE2. We employed computational protein design and molecular dynamics (MD) to design SARS-CoV-2-RBD 25-mer peptide binders (SPB25) with better predicted binding affinity than SBP1. Using residues 21-45 of the α1 helix of ACE2-PD as the template, our strategy is employing Rosetta to enhance SPB25 binding affinity to SARS-CoV-2-RBD and avoid disrupting existing favorable interactions by using residues that have not been reported to form favorable interactions with SARS-CoV-2-RBD as designed positions. Designed peptides with better predicted binding affinities, by Rosetta, than SPB25 were subjected to MD validation. The MD results show that five designed peptides (SPB25F8N, SPB25F8R, SPB25L25R, SPB25F8N/L25R, and SPB25F8R/L25R) have better predicted binding affinities, by the MM-GBSA method, than SPB25 and SBP1. This study developed an approach to design SARS-CoV-2-RBD peptide binders, and these peptides may be promising candidates as potential SARS-CoV-2 inhibitors.
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Affiliation(s)
- Thassanai Sitthiyotha
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
- Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Pathumwan, Bangkok 10330, Thailand
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74
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Armstrong I, Aldhumani AH, Schopis JL, Fang F, Parsons E, Zeng C, Hossain MI, Bergmeier SC, Hines JV. RNA drug discovery: Conformational restriction enhances specific modulation of the T-box riboswitch function. Bioorg Med Chem 2020; 28:115696. [PMID: 33069065 DOI: 10.1016/j.bmc.2020.115696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
Antibacterial drug resistance is a global health concern that requires multiple solution approaches including development of new antibacterial compounds acting at novel targets. Targeting regulatory RNA is an emerging area of drug discovery. The T-box riboswitch is a regulatory RNA mechanism that controls gene expression in Gram-positive bacteria and is an exceptional, novel target for antibacterial drug design. We report the design, synthesis and activity of a series of conformationally restricted oxazolidinone-triazole compounds targeting the highly conserved antiterminator RNA element of the T-box riboswitch. Computational binding energies correlated with experimentally-derived Kd values indicating the predictive capabilities for docking studies within this series of compounds. The conformationally restricted compounds specifically inhibited T-box riboswitch function and not overall transcription. Complex disruption, computational docking and RNA binding specificity data indicate that inhibition may result from ligand binding to an allosteric site. These results highlight the importance of both ligand affinity and RNA conformational outcome for targeted RNA drug design.
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Affiliation(s)
- Ian Armstrong
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Ali H Aldhumani
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Jia L Schopis
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Fang Fang
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Eric Parsons
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Chunxi Zeng
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH 45701, USA
| | - Md Ismail Hossain
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA
| | - Stephen C Bergmeier
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Edison Biotechnology Institute, Konneker Laboratories, Ohio University, Athens, OH 45701, USA
| | - Jennifer V Hines
- Department of Chemistry & Biochemistry, Clippinger Laboratory, Ohio University, Athens, OH 45701, USA; Molecular & Cellular Biology Program, Ohio University, Athens, OH 45701, USA.
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75
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Lu H, Zhou Q, He J, Jiang Z, Peng C, Tong R, Shi J. Recent advances in the development of protein-protein interactions modulators: mechanisms and clinical trials. Signal Transduct Target Ther 2020; 5:213. [PMID: 32968059 PMCID: PMC7511340 DOI: 10.1038/s41392-020-00315-3] [Citation(s) in RCA: 340] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 02/05/2023] Open
Abstract
Protein-protein interactions (PPIs) have pivotal roles in life processes. The studies showed that aberrant PPIs are associated with various diseases, including cancer, infectious diseases, and neurodegenerative diseases. Therefore, targeting PPIs is a direction in treating diseases and an essential strategy for the development of new drugs. In the past few decades, the modulation of PPIs has been recognized as one of the most challenging drug discovery tasks. In recent years, some PPIs modulators have entered clinical studies, some of which been approved for marketing, indicating that the modulators targeting PPIs have broad prospects. Here, we summarize the recent advances in PPIs modulators, including small molecules, peptides, and antibodies, hoping to provide some guidance to the design of novel drugs targeting PPIs in the future.
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Affiliation(s)
- Haiying Lu
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, 610072, Chengdu, China
| | - Qiaodan Zhou
- Department of Ultrasonic, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, 610072, Chengdu, China
| | - Jun He
- Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, 610041, Sichuan, China
| | - Zhongliang Jiang
- Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Cheng Peng
- The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicines of Ministry, State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Rongsheng Tong
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, 610072, Chengdu, China.
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, 610072, Chengdu, China.
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76
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Mindrebo JT, Misson LE, Johnson C, Noel JP, Burkart MD. Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis. Biochemistry 2020; 59:3626-3638. [PMID: 32857494 DOI: 10.1021/acs.biochem.0c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Laetitia E Misson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Caitlin Johnson
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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77
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Garlick JM, Mapp AK. Selective Modulation of Dynamic Protein Complexes. Cell Chem Biol 2020; 27:986-997. [PMID: 32783965 PMCID: PMC7469457 DOI: 10.1016/j.chembiol.2020.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic proteins are prime candidates for chemical probe and drug discovery but difficult targets because they do not conform to classical rules of design and screening. Selectivity is pivotal for candidate probe molecules due to the extensive interaction network of these dynamic hubs. Recognition that the traditional rules of probe discovery are not necessarily applicable to dynamic proteins and their complexes, as well as technological advances in screening, have produced remarkable results in the last 2-4 years. Particularly notable are the improvements in target selectivity for small-molecule modulators of dynamic proteins, especially with techniques that increase the discovery likelihood of allosteric regulatory mechanisms. We focus on approaches to small-molecule screening that appear to be more suitable for highly dynamic targets and have the potential to streamline identification of selective modulators.
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Affiliation(s)
- Julie M Garlick
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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78
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Niamsuphap S, Fercher C, Kumble S, Huda P, Mahler SM, Howard CB. Targeting the undruggable: emerging technologies in antibody delivery against intracellular targets. Expert Opin Drug Deliv 2020; 17:1189-1211. [DOI: 10.1080/17425247.2020.1781088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Suchada Niamsuphap
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Christian Fercher
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- ARC Centre of Excellence in Convergent BioNano Science and Technology, AIBN, University of Queensland, Brisbane, Australia
| | - Sumukh Kumble
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Pie Huda
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- Centre for Advanced Imaging (CAI), University of Queensland, Brisbane, Australia
| | - Stephen M Mahler
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
| | - Christopher B Howard
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, Australia
- Centre for Personalised Nanomedicine, AIBN, University of Queensland, Brisbane, Australia
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79
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Singh N, Chaput L, Villoutreix BO. Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein-Protein Interfaces. J Chem Inf Model 2020; 60:3910-3934. [PMID: 32786511 DOI: 10.1021/acs.jcim.0c00545] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.
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Affiliation(s)
- Natesh Singh
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
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80
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Das G, Ghosh S, Garg S, Ghosh S, Jana A, Samat R, Mukherjee N, Roy R, Ghosh S. An overview of key potential therapeutic strategies for combat in the COVID-19 battle. RSC Adv 2020; 10:28243-28266. [PMID: 35685027 PMCID: PMC9127683 DOI: 10.1039/d0ra05434h] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
The sudden ravaging outbreak of a novel coronavirus, or SARS-CoV-2, in terms of virulence, severity, and casualties has already overtaken previous versions of coronaviruses, like SARS CoV and MERS CoV. Originating from its epicenter in Wuhan, China, this mutated version of the influenza virus with its associated pandemic effects has engulfed the whole world with awful speed. In the midst of this bewildering situation, medical and scientific communities are on their toes to produce the potential vaccine-mediated eradication of this virus. Though the chances are really high, to date no such panacea has been reported. The time requirements for the onerous procedures of human trials for the successful clinical translation of any vaccine or potential therapeutics are also a major concern. In order to build some resistance against this massive pandemic, the repurposing of some earlier antiviral drugs has been done, along with the refurbishment of some immune-responsive alternative avenues, like monoclonal antibody mediated neutralization, interferon treatment, and plasma therapy. New drugs developed from the RBD domain of the virus spike protein and drugs targeting viral proteases are also undergoing further research and have shown potential from preliminary results. The sole purpose of this review article is to provide a brief collective overview of the recent status of therapeutics advances and approaches, and their current state of implementation for the management of COVID-19.
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Affiliation(s)
- Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 WB India +91-33-2473-5197 ext. 0284 +91-33-2499-5872
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surojit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Shubham Garg
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Satyajit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Aniket Jana
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Ramkamal Samat
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Nabanita Mukherjee
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
| | - Surajit Ghosh
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur NH 65, Surpura Bypass Road Karwar Rajasthan 342037 India +91-291-280-1212
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road, Jadavpur Kolkata 700 032 WB India +91-33-2473-5197 ext. 0284 +91-33-2499-5872
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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81
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Targeting epigenetic protein-protein interactions with small-molecule inhibitors. Future Med Chem 2020; 12:1305-1326. [PMID: 32551894 DOI: 10.4155/fmc-2020-0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic protein-protein interactions (PPIs) play essential roles in regulating gene expression, and their dysregulations have been implicated in many diseases. These PPIs are comprised of reader domains recognizing post-translational modifications on histone proteins, and of scaffolding proteins that maintain integrities of epigenetic complexes. Targeting PPIs have become focuses for development of small-molecule inhibitors and anticancer therapeutics. Here we summarize efforts to develop small-molecule inhibitors targeting common epigenetic PPI domains. Potent small molecules have been reported for many domains, yet small domains that recognize methylated lysine side chains on histones are challenging in inhibitor development. We posit that the development of potent inhibitors for difficult-to-prosecute epigenetic PPIs may be achieved by interdisciplinary approaches and extensive explorations of chemical space.
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82
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Yoo DY, Hauser AD, Joy ST, Bar-Sagi D, Arora PS. Covalent Targeting of Ras G12C by Rationally Designed Peptidomimetics. ACS Chem Biol 2020; 15:1604-1612. [PMID: 32378881 PMCID: PMC7739374 DOI: 10.1021/acschembio.0c00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions (PPIs) play a critical role in fundamental biological processes. Competitive inhibition of these interfaces requires compounds that can access discontinuous binding epitopes along a large, shallow binding surface area. Conformationally defined protein surface mimics present a viable route to target these interactions. However, the development of minimal protein mimics that engage intracellular targets with high affinity remains a major challenge because mimicry of a portion of the binding interface is often associated with the loss of critical binding interactions. Covalent targeting provides an attractive approach to overcome the loss of noncovalent contacts but have the inherent risk of dominating noncovalent contacts and increasing the likelihood of nonselective binding. Here, we report the iterative design of a proteolytically stable α3β chimeric helix mimic that covalently targets oncogenic Ras G12C as a model system. We explored several electrophiles to optimize preferential alkylation with the desired C12 on Ras. The designed lead peptide modulates nucleotide exchange, inhibits activation of the Ras-mediated signaling cascade, and is selectively toxic toward mutant Ras G12C cancer cells. The relatively high frequency of acquired cysteines as missense mutations in cancer and other diseases suggests that covalent peptides may offer an untapped therapeutic approach for targeting aberrant protein interactions.
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Affiliation(s)
- Daniel Y. Yoo
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Andrew D. Hauser
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Stephen T. Joy
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, 10003, U.S.A
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83
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Lanzarotti E, Defelipe LA, Marti MA, Turjanski AG. Aromatic clusters in protein-protein and protein-drug complexes. J Cheminform 2020; 12:30. [PMID: 33431014 PMCID: PMC7206889 DOI: 10.1186/s13321-020-00437-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/30/2020] [Indexed: 11/10/2022] Open
Abstract
Aromatic rings are important residues for biological interactions and appear to a large extent as part of protein-drug and protein-protein interactions. They are relevant for both protein stability and molecular recognition processes due to their natural occurrence in aromatic aminoacids (Trp, Phe, Tyr and His) as well as in designed drugs since they are believed to contribute to optimizing both affinity and specificity of drug-like molecules. Despite the mentioned relevance, the impact of aromatic clusters on protein-protein and protein-drug complexes is still poorly characterized, especially in those that go beyond a dimer. In this work, we studied protein-drug and protein-protein complexes and systematically analyzed the presence and structure of their aromatic clusters. Our results show that aromatic clusters are highly prevalent in both protein-protein and protein-drug complexes, and suggest that protein-protein aromatic clusters have idealized interactions, probably because they were optimized by evolution, as compared to protein-drug clusters that were manually designed. Interestingly, the configuration, solvent accessibility and secondary structure of aromatic residues in protein-drug complexes shed light on the relation between these properties and compound affinity, allowing researchers to better design new molecules.
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Affiliation(s)
- Esteban Lanzarotti
- Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,European Molecular Biology Laboratory Hamburg, Notkestraße 85, 22607, Hamburg, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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84
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Kim CK, Wang D, Bokesch HR, Fuller RW, Smith E, Henrich CJ, Durrant DE, Morrison DK, Bewley CA, Gustafson KR. Swinhopeptolides A and B: Cyclic Depsipeptides from the Sponge Theonella swinhoei That Inhibit Ras/Raf Interaction. JOURNAL OF NATURAL PRODUCTS 2020; 83:1288-1294. [PMID: 32191460 PMCID: PMC7183427 DOI: 10.1021/acs.jnatprod.0c00136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two new cyclic depsipeptides named swinhopeptolides A (1) and B (2) have been isolated from the marine sponge Theonella swinhoei cf. verrucosa, collected from Papua New Guinea. They each contain 11 diverse amino acid residues and 13-carbon polyketide moieties attached at the N-terminus. Compounds 1 and 2 each exist as two conformers in DMSO-d6 due to cis/trans isomerism of the proline residue, and their structures were successfully assigned by extensive NMR analyses complemented by chemical degradation and derivatization studies. Swinhopeptolide B (2) contains a previously undescribed 2,6,8-trimethyldeca-(2E,4E,6E)-trienoic acid moiety N-linked to a terminal serine residue. Swinhopeptolides A (1) and B (2) showed significant inhibition of the Ras/Raf signaling pathway with IC50 values of 5.8 and 8.5 μM, respectively.
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Affiliation(s)
- Chang-Kwon Kim
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Dongdong Wang
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Heidi R. Bokesch
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Richard W. Fuller
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Emily Smith
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - Curtis J. Henrich
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702-1201, United States
| | - David E. Durrant
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Deborah K. Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Carole A. Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20814, United States
| | - Kirk R. Gustafson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
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85
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Moustaqil M, Gambin Y, Sierecki E. Biophysical Techniques for Target Validation and Drug Discovery in Transcription-Targeted Therapy. Int J Mol Sci 2020; 21:E2301. [PMID: 32225120 PMCID: PMC7178067 DOI: 10.3390/ijms21072301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/13/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
In the post-genome era, pathologies become associated with specific gene expression profiles and defined molecular lesions can be identified. The traditional therapeutic strategy is to block the identified aberrant biochemical activity. However, an attractive alternative could aim at antagonizing key transcriptional events underlying the pathogenesis, thereby blocking the consequences of a disorder, irrespective of the original biochemical nature. This approach, called transcription therapy, is now rendered possible by major advances in biophysical technologies. In the last two decades, techniques have evolved to become key components of drug discovery platforms, within pharmaceutical companies as well as academic laboratories. This review outlines the current biophysical strategies for transcription manipulation and provides examples of successful applications. It also provides insights into the future development of biophysical methods in drug discovery and personalized medicine.
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Affiliation(s)
- Mehdi Moustaqil
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
| | | | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science and School of Medical Sciences, UNSW Sydney, NSW 2052, Australia;
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86
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Catz SD, McLeish KR. Therapeutic targeting of neutrophil exocytosis. J Leukoc Biol 2020; 107:393-408. [PMID: 31990103 PMCID: PMC7044074 DOI: 10.1002/jlb.3ri0120-645r] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/11/2022] Open
Abstract
Dysregulation of neutrophil activation causes disease in humans. Neither global inhibition of neutrophil functions nor neutrophil depletion provides safe and/or effective therapeutic approaches. The role of neutrophil granule exocytosis in multiple steps leading to recruitment and cell injury led each of our laboratories to develop molecular inhibitors that interfere with specific molecular regulators of secretion. This review summarizes neutrophil granule formation and contents, the role granule cargo plays in neutrophil functional responses and neutrophil-mediated diseases, and the mechanisms of granule release that provide the rationale for development of our exocytosis inhibitors. We present evidence for the inhibition of granule exocytosis in vitro and in vivo by those inhibitors and summarize animal data indicating that inhibition of neutrophil exocytosis is a viable therapeutic strategy.
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Affiliation(s)
- Sergio D. Catz
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA
| | - Kenneth R. McLeish
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY
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87
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Messick TE, Smith GR, Soldan SS, McDonnell ME, Deakyne JS, Malecka KA, Tolvinski L, van den Heuvel APJ, Gu BW, Cassel JA, Tran DH, Wassermann BR, Zhang Y, Velvadapu V, Zartler ER, Busson P, Reitz AB, Lieberman PM. Structure-based design of small-molecule inhibitors of EBNA1 DNA binding blocks Epstein-Barr virus latent infection and tumor growth. Sci Transl Med 2020; 11:11/482/eaau5612. [PMID: 30842315 DOI: 10.1126/scitranslmed.aau5612] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/07/2019] [Indexed: 12/14/2022]
Abstract
Epstein-Barr virus (EBV) is a DNA tumor virus responsible for 1 to 2% of human cancers including subtypes of Burkitt's lymphoma, Hodgkin's lymphoma, gastric carcinoma, and nasopharyngeal carcinoma (NPC). Persistent latent infection drives EBV-associated tumorigenesis. Epstein-Barr nuclear antigen 1 (EBNA1) is the only viral protein consistently expressed in all EBV-associated tumors and is therefore an attractive target for therapeutic intervention. It is a multifunctional DNA binding protein critical for viral replication, genome maintenance, viral gene expression, and host cell survival. Using a fragment-based approach and x-ray crystallography, we identify a 2,3-disubstituted benzoic acid series that selectively inhibits the DNA binding activity of EBNA1. We characterize these inhibitors biochemically and in cell-based assays, including chromatin immunoprecipitation and DNA replication assays. In addition, we demonstrate the potency of EBNA1 inhibitors to suppress tumor growth in several EBV-dependent xenograft models, including patient-derived xenografts for NPC. These inhibitors selectively block EBV gene transcription and alter the cellular transforming growth factor-β (TGF-β) signaling pathway in NPC tumor xenografts. These EBNA1-specific inhibitors show favorable pharmacological properties and have the potential to be further developed for the treatment of EBV-associated malignancies.
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Affiliation(s)
- Troy E Messick
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
| | - Garry R Smith
- Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Samantha S Soldan
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Mark E McDonnell
- Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA.,Vironika LLC, 3624 Market Street, Ste 5E, Philadelphia, PA 19104, USA
| | | | | | - Lois Tolvinski
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | - Bai-Wei Gu
- Vironika LLC, 3624 Market Street, Ste 5E, Philadelphia, PA 19104, USA
| | - Joel A Cassel
- Vironika LLC, 3624 Market Street, Ste 5E, Philadelphia, PA 19104, USA
| | - Donna H Tran
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | | | - Yan Zhang
- Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Venkata Velvadapu
- Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Edward R Zartler
- Quantum Tessera Consulting LLC, 508 Tawnyberry Lane, Collegeville, PA 19426, USA
| | - Pierre Busson
- Institut Gustave Roussy, 114 Rue Edouard Vaillant, 84800 Villejuif, France
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA
| | - Paul M Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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88
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Yang W, Gadgil P, Krishnamurthy VR, Landis M, Mallick P, Patel D, Patel PJ, Reid DL, Sanchez-Felix M. The Evolving Druggability and Developability Space: Chemically Modified New Modalities and Emerging Small Molecules. AAPS JOURNAL 2020; 22:21. [DOI: 10.1208/s12248-019-0402-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/26/2019] [Indexed: 12/17/2022]
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89
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Yuen TY, Brown CJ, Tan YS, Johannes CW. Synthesis of Chiral Alkenyl Cyclopropane Amino Acids for Incorporation into Stapled Peptides. J Org Chem 2019; 85:1556-1566. [DOI: 10.1021/acs.joc.9b02659] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 8 Biomedical Grove, #07-01, Neuros, Singapore 138665
| | - Christopher J. Brown
- P53 Laboratory, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Charles W. Johannes
- P53 Laboratory, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
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90
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Ngo TD, Plé S, Thomas A, Barette C, Fortuné A, Bouzidi Y, Fauvarque MO, Pereira de Freitas R, Francisco Hilário F, Attrée I, Wong YS, Faudry E. Chimeric Protein-Protein Interface Inhibitors Allow Efficient Inhibition of Type III Secretion Machinery and Pseudomonas aeruginosa Virulence. ACS Infect Dis 2019; 5:1843-1854. [PMID: 31525902 DOI: 10.1021/acsinfecdis.9b00154] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen naturally resistant to many common antibiotics and acquires new resistance traits at an alarming pace. Targeting the bacterial virulence factors by an antivirulence strategy, therefore, represents a promising alternative approach besides antibiotic therapy. The Type III secretion system (T3SS) of P. aeruginosa is one of its main virulence factors. It consists of more than 20 proteins building a complex syringe-like machinery enabling the injection of toxin into host cells. Previous works showed that disrupting interactions between components of this machinery efficiently lowers the bacterial virulence. Using automated target-based screening of commercial and in-house libraries of small molecules, we identified compounds inhibiting the protein-protein interaction between PscE and PscG, the two cognate chaperones of the needle subunit PscF of P. aeruginosa T3SS. Two hits were selected and assembled using Split/Mix/Click chemistry to build larger hybrid analogues. Their efficacy and toxicity were evaluated using phenotypic analysis including automated microscopy and image analysis. Two nontoxic hybrid leads specifically inhibited the T3SS and reduced the ex vivo cytotoxicity of bacteria and their virulence in Galleria mellonella.
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Affiliation(s)
- Tuan-Dung Ngo
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Sophie Plé
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Aline Thomas
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Caroline Barette
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, Genetics & Chemogenomics, 17 avenue des Martyrs, Grenoble 38054, France
| | - Antoine Fortuné
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Younes Bouzidi
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Marie-Odile Fauvarque
- Univ. Grenoble Alpes, CEA, Inserm, IRIG, BGE, Genetics & Chemogenomics, 17 avenue des Martyrs, Grenoble 38054, France
| | - Rossimiriam Pereira de Freitas
- Universidade Federal de Minas Gerais, Departamento de Química, UFMG, Av Pres Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Flaviane Francisco Hilário
- Universidade Federal de Ouro Preto, Departamento de Química, ICEB, Campus Universitário Morro do Cruzeiro, Ouro Preto, Minas Gerais 35400-000, Brazil
| | - Ina Attrée
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
| | - Yung-Sing Wong
- Univ. Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire,
UMR 5063, ICMG FR 2607, 470 rue de la chimie, Grenoble 38000, France
| | - Eric Faudry
- Univ. Grenoble Alpes, CEA, INSERM, CNRS, Bacterial Pathogenesis and Cellular Responses, UMR 1036/ERL 5261, 17 avenue des Martyrs, Grenoble 38054, France
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91
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Liu H, Zhao Z, Zhang L, Li Y, Jain A, Barve A, Jin W, Liu Y, Fetse J, Cheng K. Discovery of low-molecular weight anti-PD-L1 peptides for cancer immunotherapy. J Immunother Cancer 2019; 7:270. [PMID: 31640814 PMCID: PMC6805442 DOI: 10.1186/s40425-019-0705-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022] Open
Abstract
Background Immunotherapy using checkpoint inhibitors, especially PD-1/PD-L1 inhibitors, has now evolved into the most promising therapy for cancer patients. However, most of these inhibitors are monoclonal antibodies, and their large size may limit their tumor penetration, leading to suboptimal efficacy. As a result, there has been a growing interest in developing low-molecular-weight checkpoint inhibitors. Methods We developed a novel biopanning strategy to discover small peptide-based anti-PD-L1 inhibitors. The affinity and specificity of the peptides to PD-L1 were examined using various assays. Three-dimensional (3D) spheroid penetration study was performed to determine the tumor penetration capability of the peptides. Anti-tumor activity of the peptides was evaluated in mice bearing CT26 tumor cells. Results We discover several anti-PD-L1 peptide inhibitors to block PD-1/PD-L1 interaction. The peptides exhibit high affinity and specificity to human PD-L1 protein as well as PD-L1-overexpressing human cancer cells MDA-MB-231 and DU-145. Molecular docking studies indicate that the peptide CLP002 specifically binds to PD-L1 at the residues where PD-L1 interacts with PD-1. The peptide also blocks the CD80/PD-L1 interaction, which may further enhance the immune response of tumor-infiltrating T cells. Compared to antibody, the peptide CLP002 exhibits better tumor penetration in a 3D tumor spheroid model. The peptide CLP002 restores proliferation and prevents apoptosis of T cells that are co-cultured with cancer cells. The peptide CLP002 also inhibits tumor growth and increases survival of CT26 tumor-bearing mice. Conclusions This study demonstrated the feasibility of using phage display to discover small peptide-based checkpoint inhibitors. Our results also suggested that the anti-PD-L1 peptide represents a promising low-molecular-weight checkpoint inhibitor for cancer immunotherapy. Electronic supplementary material The online version of this article (10.1186/s40425-019-0705-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Liu
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Zhen Zhao
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Li Zhang
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Yuanke Li
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Akshay Jain
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Ashutosh Barve
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Wei Jin
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Yanli Liu
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - John Fetse
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA.
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92
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Investigation of Hot Spot Region in XIAP Inhibitor Binding Site by Fragment Molecular Orbital Method. Comput Struct Biotechnol J 2019; 17:1217-1225. [PMID: 31673305 PMCID: PMC6816037 DOI: 10.1016/j.csbj.2019.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 11/23/2022] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) is an important regulator of cancer cell survival whose BIR3 domain (XIAP-BIR3) recognizes the Smac N-terminal tetrapeptide sequence (AVPI), making it an attractive protein-protein interaction (PPI) target for cancer therapies. We used the fragment molecular orbital (FMO) method to study the binding modes and affinities between XIAP-BIR3 and a series of its inhibitors (1–8) that mimic the AVPI binding motif; the inhibitors had common interactions with key residues in a hot spot region of XIAP-BIR3 (P1–P4 subpockets) with increased binding affinity mainly attributed to specific interactions with the P1 and P4 subpockets. Based on the structural information from FMO results, we proposed a novel XIAP natural product inhibitor, neoeriocitrin 10, which was derived from our preciously reported XIAP-BIR3 inhibitor 9, can be used as a highly potent candidate for XIAP-BIR3 inhibition. We also performed pair interaction energy decomposition analysis to investigate the binding energies between specific binding residues and individual ligands, showing that the novel natural product neoeriocitrin 10 had a higher binding affinity than epicatechin gallate 9. Molecular docking and dynamics simulations were performed to explore the mode of binding between 10 and XIAP-BIR3, demonstrating that 10 binds more strongly to the P1 and P4 pockets than 9. Overall, we present a novel natural product, neoeriocitrin 10, and demonstrate that the FMO method can be used to identify hot spots in PPIs and design new compounds for XIAP inhibition.
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93
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Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D, Kumar P. Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus. J Mol Biol 2019; 431:3107-3123. [DOI: 10.1016/j.jmb.2019.06.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/28/2022]
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94
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Neira JL, Correa J, Rizzuti B, Santofimia-Castaño P, Abian O, Velázquez-Campoy A, Fernandez-Megia E, Iovanna JL. Dendrimers as Competitors of Protein–Protein Interactions of the Intrinsically Disordered Nuclear Chromatin Protein NUPR1. Biomacromolecules 2019; 20:2567-2576. [DOI: 10.1021/acs.biomac.9b00378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- José L. Neira
- Instituto de Biología
Molecular y Celular, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Juan Correa
- Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, La Coruña, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS
Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and
Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Olga Abian
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación
y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI,
and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Eduardo Fernandez-Megia
- Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, La Coruña, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and
Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
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95
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Santofimia-Castaño P, Rizzuti B, Xia Y, Abian O, Peng L, Velázquez-Campoy A, Iovanna JL, Neira JL. Designing and repurposing drugs to target intrinsically disordered proteins for cancer treatment: using NUPR1 as a paradigm. Mol Cell Oncol 2019; 6:e1612678. [PMID: 31528692 PMCID: PMC6736491 DOI: 10.1080/23723556.2019.1612678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) do not have a well-defined structure, but they have key biological tasks in cancer development. By using the disordered cancer-related protein NUPR1 as a proof-of-concept, we have developed a new multidisciplinary approach to tackle drug-design against IDPs, using it to repurpose drugs for treating pancreatic adenocarcinoma (PDAC).
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Affiliation(s)
- Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Rende, Italy
| | - Yi Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, P. R. China
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, Zaragoza, Spain
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Alicante, Spain
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96
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Ria F, Pirolli D, Di Sante G, Righino B, Gremese E, Gervasoni J, Nicolò C, Giardina B, Ferraccioli G, De Rosa MC. Selective Inhibitors of T Cell Receptor Recognition of Antigen-MHC Complexes for Rheumatoid Arthritis. ACS Med Chem Lett 2019; 10:644-649. [PMID: 30996811 DOI: 10.1021/acsmedchemlett.8b00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Autoreactive T cells specific to human collagen type II have a crucial role in the development of rheumatoid arthritis (RA) in the context of MHC class II allele HLA-DRB1-*04. The protein-protein interactions between the T cell receptor (TCR) and the type II collagen bound to the allele MHC of class II may thus represent the target for the development of new drugs against RA. In this study, a structure-based pharmacophore model for potential small molecule inhibitors was developed from protein-protein interface structure. The 3D model obtained was used for a virtual screening workflow, which resulted in three hits for experimental follow up. Three compounds have been identified that interfere with the TCR/collagenII-MHCII (K i values below 10 μM) and open up new possibilities in the treatment of RA.
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Affiliation(s)
- Francesco Ria
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
- Institute of General Pathology, Fondazione Policlinico Universitario “A. Gemelli” − I.R.C.C.S., Rome, Italy
| | - Davide Pirolli
- Institute of Chemistry of Molecular Recognition (ICRM) - CNR, Rome, Italy
| | - Gabriele Di Sante
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
- Institute of General Pathology, Fondazione Policlinico Universitario “A. Gemelli” − I.R.C.C.S., Rome, Italy
| | - Benedetta Righino
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Elisa Gremese
- Institute of Rheumatology, Università Cattolica del Sacro Cuore, Rome, Italy
- Division of Rheumatology, Fondazione Policlinico Universitario “A. Gemelli” − I.R.C.C.S., Rome, Italy
| | - Jacopo Gervasoni
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy
- U.O.C. Biochimica Clinica, Fondazione Policlinico Universitario “A. Gemelli” − I.R.C.C.S., Rome, Italy
| | - Chiara Nicolò
- Institute of General Pathology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Bruno Giardina
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianfranco Ferraccioli
- Institute of Rheumatology, Università Cattolica del Sacro Cuore, Rome, Italy
- Division of Rheumatology, Fondazione Policlinico Universitario “A. Gemelli” − I.R.C.C.S., Rome, Italy
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97
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Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
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Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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98
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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99
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Rahimi MN, McAlpine SR. Protein-protein inhibitor designed de novo to target the MEEVD region on the C-terminus of Hsp90 and block co-chaperone activity. Chem Commun (Camb) 2019; 55:846-849. [PMID: 30575826 DOI: 10.1039/c8cc07576j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions control all cellular functions. Presented is the first de novo designed protein-protein inhibitor that targets the C-terminus of heat shock protein 90 (Hsp90) and blocks co-chaperones from binding. Compound LB76, which was created from an Hsp90 co-chaperone, selectively pulls down Hsp90 from cell lysates, binds to Hsp90's C-terminal domain, and blocks the interactions between Hsp90 and TPR-containing co-chaperones. Through these interactions, LB76 inhibits the protein-folding function of Hsp90. Blocking these protein-protein interactions between Hsp90 and C-terminal co-chaperones regulate the cell's entire protein-folding machinery.
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Affiliation(s)
- Marwa N Rahimi
- School of Chemistry, Gate 2 High street, Dalton 219, University of New South Wales, Sydney, Australia.
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100
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Si Y, Xu D, Bum-Erdene K, Ghozayel MK, Yang B, Clemons PA, Meroueh SO. Chemical Space Overlap with Critical Protein-Protein Interface Residues in Commercial and Specialized Small-Molecule Libraries. ChemMedChem 2019; 14:119-131. [PMID: 30548204 PMCID: PMC7175409 DOI: 10.1002/cmdc.201800537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/29/2018] [Indexed: 12/14/2022]
Abstract
There is growing interest in the use of structure-based virtual screening to identify small molecules that inhibit challenging protein-protein interactions (PPIs). In this study, we investigated how effectively chemical library members docked at the PPI interface mimic the position of critical side-chain residues known as "hot spots". Three compound collections were considered, a commercially available screening collection (ChemDiv), a collection of diversity-oriented synthesis (DOS) compounds that contains natural-product-like small molecules, and a library constructed using established reactions (the "screenable chemical universe based on intuitive data organization", SCUBIDOO). Three different tight PPIs for which hot-spot residues have been identified were selected for analysis: uPAR⋅uPA, TEAD4⋅Yap1, and CaV α⋅CaV β. Analysis of library physicochemical properties was followed by docking to the PPI receptors. A pharmacophore method was used to measure overlap between small-molecule substituents and hot-spot side chains. Fragment-like conformationally restricted small molecules showed better hot-spot overlap for interfaces with well-defined pockets such as uPAR⋅uPA, whereas better overlap was observed for more complex DOS compounds in interfaces lacking a well-defined binding site such as TEAD4⋅Yap1. Virtual screening of conformationally restricted compounds targeting uPAR⋅uPA and TEAD4⋅Yap1 followed by experimental validation reinforce these findings, as the best hits were fragment-like and had few rotatable bonds for the former, while no hits were identified for the latter. Overall, such studies provide a framework for understanding PPIs in the context of additional chemical matter and new PPI definitions.
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Affiliation(s)
- Yubing Si
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, 46202, USA
| | - Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mona K Ghozayel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Baocheng Yang
- Henan Provincial Key Laboratory of Nanocomposites and Applications, Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan, 450006, China
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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