1
|
Chang J, Fan X, Tian B. DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation. J Chem Inf Model 2024; 64:3149-3160. [PMID: 38587937 DOI: 10.1021/acs.jcim.4c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Cytochrome P450 enzymes (CYPs) play a crucial role in Phase I drug metabolism in the human body, and CYP activity toward compounds can significantly affect druggability, making early prediction of CYP activity and substrate identification essential for therapeutic development. Here, we established a deep learning model for assessing potential CYP substrates, DeepP450, by fine-tuning protein and molecule pretrained models through feature integration with cross-attention and self-attention layers. This model exhibited high prediction accuracy (0.92) on the test set, with area under the receiver operating characteristic curve (AUROC) values ranging from 0.89 to 0.98 in substrate/nonsubstrate predictions across the nine major human CYPs, surpassing current benchmarks for CYP activity prediction. Notably, DeepP450 uses only one model to predict substrates/nonsubstrates for any of the nine CYPs and exhibits certain generalizability on novel compounds and different categories of human CYPs, which could greatly facilitate early stage drug design by avoiding CYP-reactive compounds.
Collapse
Affiliation(s)
- Jiamin Chang
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoyu Fan
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Boxue Tian
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
2
|
Cai B, Krusemark CJ. Multiplexed Small-Molecule-Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis. Angew Chem Int Ed Engl 2022; 61:e202113515. [PMID: 34758183 PMCID: PMC8748404 DOI: 10.1002/anie.202113515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/04/2021] [Indexed: 01/19/2023]
Abstract
Small-molecule binding assays to target proteins are a core component of drug discovery and development. While a number of assay formats are available, significant drawbacks still remain in cost, sensitivity, and throughput. To improve assays by capitalizing on the power of DNA sequence analysis, we have developed an assay method that combines DNA encoding with split-and-pool sample handling. The approach involves affinity labeling of DNA-linked ligands to a protein target. Critically, the labeling event assesses ligand binding and enables subsequent pooling of several samples. Application of a purifying selection on the pool for protein-labeled DNAs allows detection of ligand binding by quantification of DNA barcodes. We demonstrate the approach in both ligand displacement and direct binding formats and demonstrate its utility in determination of relative ligand affinity, profiling ligand specificity, and high-throughput small-molecule screening.
Collapse
Affiliation(s)
- Bo Cai
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Casey J Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
3
|
Khalil BD, Sanchez R, Rahman T, Rodriguez-Tirado C, Moritsch S, Martinez AR, Miles B, Farias E, Mezei M, Nobre AR, Singh D, Kale N, Sproll KC, Sosa MS, Aguirre-Ghiso JA. An NR2F1-specific agonist suppresses metastasis by inducing cancer cell dormancy. J Exp Med 2022; 219:e20210836. [PMID: 34812843 PMCID: PMC8614154 DOI: 10.1084/jem.20210836] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/20/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
We describe the discovery of an agonist of the nuclear receptor NR2F1 that specifically activates dormancy programs in malignant cells. The agonist led to a self-regulated increase in NR2F1 mRNA and protein and downstream transcription of a novel dormancy program. This program led to growth arrest of an HNSCC PDX line, human cell lines, and patient-derived organoids in 3D cultures and in vivo. This effect was lost when NR2F1 was knocked out by CRISPR-Cas9. RNA sequencing revealed that agonist treatment induces transcriptional changes associated with inhibition of cell cycle progression and mTOR signaling, metastasis suppression, and induction of a neural crest lineage program. In mice, agonist treatment resulted in inhibition of lung HNSCC metastasis, even after cessation of the treatment, where disseminated tumor cells displayed an NR2F1hi/p27hi/Ki-67lo/p-S6lo phenotype and remained in a dormant single-cell state. Our work provides proof of principle supporting the use of NR2F1 agonists to induce dormancy as a therapeutic strategy to prevent metastasis.
Collapse
Affiliation(s)
- Bassem D. Khalil
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Western Atlantic University School of Medicine, Plantation, FL
| | - Roberto Sanchez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tasrina Rahman
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Stefan Moritsch
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alba Rodriguez Martinez
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Brett Miles
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eduardo Farias
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ana Rita Nobre
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Deepak Singh
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nupura Kale
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Karl Christoph Sproll
- Department of Oral, Maxillofacial and Plastic Facial Surgery, Medical Faculty, University Hospital of the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Maria Soledad Sosa
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Julio A. Aguirre-Ghiso
- Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| |
Collapse
|
4
|
Chen Q, Zhu J. DEL Selections Against a Soluble Protein Target. Methods Mol Biol 2022; 2541:155-164. [PMID: 36083554 DOI: 10.1007/978-1-0716-2545-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Affinity-based DNA-encoded library (DEL) selection is considered a powerful tool for small molecule drug discovery. Such selections are a multi-round process that involves incubation of a target protein with the DEL, capture of the protein and associated DEL compounds on a solid support, separation of bound molecules from the bulk DEL that is unbound, and recovery of bound DEL molecules. Each step is of great importance in order to achieve successful selections. Here we describe the selection process against a soluble target protein in both the immobilized and in-solution modes.
Collapse
|
5
|
Swain M, Ageeli AA, Kasprzak W, Li M, Miller JT, Sztuba-Solinska J, Schneekloth J, Koirala D, Piccirili J, Fraboni AJ, Murelli RP, Wlodawer A, Shapiro B, Baird N, Le Grice SFJ. Dynamic bulge nucleotides in the KSHV PAN ENE triple helix provide a unique binding platform for small molecule ligands. Nucleic Acids Res 2021; 49:13179-13193. [PMID: 34871450 PMCID: PMC8682744 DOI: 10.1093/nar/gkab1170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 10/24/2021] [Accepted: 11/18/2021] [Indexed: 11/14/2022] Open
Abstract
Cellular and virus-coded long non-coding (lnc) RNAs support multiple roles related to biological and pathological processes. Several lncRNAs sequester their 3' termini to evade cellular degradation machinery, thereby supporting disease progression. An intramolecular triplex involving the lncRNA 3' terminus, the element for nuclear expression (ENE), stabilizes RNA transcripts and promotes persistent function. Therefore, such ENE triplexes, as presented here in Kaposi's sarcoma-associated herpesvirus (KSHV) polyadenylated nuclear (PAN) lncRNA, represent targets for therapeutic development. Towards identifying novel ligands targeting the PAN ENE triplex, we screened a library of immobilized small molecules and identified several triplex-binding chemotypes, the tightest of which exhibits micromolar binding affinity. Combined biophysical, biochemical, and computational strategies localized ligand binding to a platform created near a dinucleotide bulge at the base of the triplex. Crystal structures of apo (3.3 Å) and ligand-soaked (2.5 Å) ENE triplexes, which include a stabilizing basal duplex, indicate significant local structural rearrangements within this dinucleotide bulge. MD simulations and a modified nucleoside analog interference technique corroborate the role of the bulge and the base of the triplex in ligand binding. Together with recently discovered small molecules that reduce nuclear MALAT1 lncRNA levels by engaging its ENE triplex, our data supports the potential of targeting RNA triplexes with small molecules.
Collapse
MESH Headings
- Base Sequence
- Crystallography, X-Ray
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/metabolism
- Herpesvirus 8, Human/physiology
- Humans
- Ligands
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Molecular Structure
- Nucleic Acid Conformation
- Nucleotides/genetics
- Nucleotides/metabolism
- Poly A/chemistry
- Poly A/genetics
- Poly A/metabolism
- RNA Stability/genetics
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sarcoma, Kaposi/virology
- Small Molecule Libraries/chemistry
- Small Molecule Libraries/metabolism
Collapse
Affiliation(s)
- Monalisa Swain
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Abeer A Ageeli
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104, USA
- Chemistry Department, Faculty of Science (Female Section), Jazan University, Jazan 82621, Saudi Arabia
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mi Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Jennifer T Miller
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | | | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Joseph Piccirili
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Americo J Fraboni
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, 11210, USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, City University of New York, Brooklyn, NY, 11210, USA
- PhD Program in Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathan Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19104, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
6
|
Pemovska T, Bigenzahn JW, Srndic I, Lercher A, Bergthaler A, César-Razquin A, Kartnig F, Kornauth C, Valent P, Staber PB, Superti-Furga G. Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. Nat Commun 2021; 12:7190. [PMID: 34907165 PMCID: PMC8671470 DOI: 10.1038/s41467-021-27329-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Interrogation of cellular metabolism with high-throughput screening approaches can unravel contextual biology and identify cancer-specific metabolic vulnerabilities. To systematically study the consequences of distinct metabolic perturbations, we assemble a comprehensive metabolic drug library (CeMM Library of Metabolic Drugs; CLIMET) covering 243 compounds. We, next, characterize it phenotypically in a diverse panel of myeloid leukemia cell lines and primary patient cells. Analysis of the drug response profiles reveals that 77 drugs affect cell viability, with the top effective compounds targeting nucleic acid synthesis, oxidative stress, and the PI3K/mTOR pathway. Clustering of individual drug response profiles stratifies the cell lines into five functional groups, which link to specific molecular and metabolic features. Mechanistic characterization of selective responses to the PI3K inhibitor pictilisib, the fatty acid synthase inhibitor GSK2194069, and the SLC16A1 inhibitor AZD3965, bring forth biomarkers of drug response. Phenotypic screening using CLIMET represents a valuable tool to probe cellular metabolism and identify metabolic dependencies at large.
Collapse
Affiliation(s)
- Tea Pemovska
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ismet Srndic
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alexander Lercher
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Andreas Bergthaler
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Adrián César-Razquin
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Kornauth
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Peter Valent
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Hematology and Oncology, Medical University of Vienna, Vienna, Austria
| | - Philipp B Staber
- Department of Medicine I, Division of Hematology & Hemostaseology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center Vienna, Vienna General Hospital, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
7
|
Llanos MA, Alberca LN, Larrea SCV, Schoijet AC, Alonso GD, Bellera CL, Gavenet L, Talevi A. Homology Modeling and Molecular Dynamics Simulations of Trypanosoma cruzi Phosphodiesterase b1. Chem Biodivers 2021; 19:e202100712. [PMID: 34813143 DOI: 10.1002/cbdv.202100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/22/2021] [Indexed: 11/07/2022]
Abstract
Cyclic nucleotide phosphodiesterases have been implicated in the proliferation, differentiation and osmotic regulation of trypanosomatids; in some trypanosomatid species, they have been validated as molecular targets for the development of new therapeutic agents. Because the experimental structure of Trypanosoma cruzi PDEb1 (TcrPDEb1) has not been solved so far, an homology model of the target was created using the structure of Trypanosoma brucei PDEb1 (TbrPDEb1) as a template. The model was refined by extensive enhanced sampling molecular dynamics simulations, and representative snapshots were extracted from the trajectory by combined clustering analysis. This structural ensemble was used to develop a structure-based docking model of the target. The docking accuracy of the model was validated by redocking and cross-docking experiments using all available crystal structures of TbrPDEb1, whereas the scoring accuracy was validated through a retrospective screen, using a carefully curated dataset of compounds assayed against TbrPDEb1 and/or TcrPDEb1. Considering the results from in silico validations, the model may be applied in prospective virtual screening campaigns to identify novel hits, as well as to guide the rational design of potent and selective inhibitors targeting this enzyme.
Collapse
Affiliation(s)
- Manuel A Llanos
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of Exact Sciences, University of La Plata - 47 and 115, La Plata, Buenos Aires, Argentina
| | - Lucas N Alberca
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of Exact Sciences, University of La Plata - 47 and 115, La Plata, Buenos Aires, Argentina
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Salomé C Vilchez Larrea
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Alejandra C Schoijet
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Guillermo D Alonso
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI-CONICET), Buenos Aires, Argentina
| | - Carolina L Bellera
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of Exact Sciences, University of La Plata - 47 and 115, La Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET) - CCT, La Plata, Argentina
| | - Luciana Gavenet
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of Exact Sciences, University of La Plata - 47 and 115, La Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET) - CCT, La Plata, Argentina
| | - Alan Talevi
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of Exact Sciences, University of La Plata - 47 and 115, La Plata, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET) - CCT, La Plata, Argentina
| |
Collapse
|
8
|
Wang Y, Gao Y, Yuan D, Ling L, Liu J, Wu S, Chen R, Li H, Xiong Y, Liu H, Ma J. Discovery of quinazoline derivatives as novel small-molecule inhibitors targeting the programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) interaction. Eur J Med Chem 2021; 229:113998. [PMID: 34839997 DOI: 10.1016/j.ejmech.2021.113998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/29/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022]
Abstract
Development of small molecule PD-1/PD-L1 inhibitors as a novel immunotherapy strategy exhibits great promise. Herein, a novel series of quinazoline derivatives were designed, synthesized and their inhibitory activity against the PD-1/PD-L1 interaction was evaluated through a homogenous time-resolved fluorescence (HTRF) assay. Among them, the compound 39 exhibited the most potent inhibitory activity with an IC50 value of 1.57 nM. Furthermore, the cellular level assays revealed that 39 could inhibit the PD-1/PD-L1 interaction and restore T-cell function, and showed low toxicity on the PBMCs. In addition, the structure-activity relationships (SARs) of the novel quinazoline derivatives were explored and the binding mode of 39 with dimeric PD-L1 was analyzed by molecular docking. This work demonstrates that incorporation of pyrimidine group between the 2 and 3-positions of the biphenyl structure is an effective strategy for designing novel and more potent small molecule PD-1/PD-L1 inhibitors, and 39 can be regarded as a promising lead compound for further investigation.
Collapse
Affiliation(s)
- Yu Wang
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Yali Gao
- Pharmacy Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, China
| | - Dandan Yuan
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Lin Ling
- Quanzhou First Hospital, Fujian Medical University, Fuzhou, 350108, China
| | - Jieqing Liu
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Sihai Wu
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Roufen Chen
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - He Li
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Yizu Xiong
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Han Liu
- School of Medicine, Huaqiao University, Quanzhou, 362000, China
| | - Junjie Ma
- School of Medicine, Huaqiao University, Quanzhou, 362000, China.
| |
Collapse
|
9
|
Moon JD, Wu J, Dey SK, Litke JL, Li X, Kim H, Jaffrey SR. Naturally occurring three-way junctions can be repurposed as genetically encoded RNA-based sensors. Cell Chem Biol 2021; 28:1569-1580.e4. [PMID: 34010626 PMCID: PMC8573057 DOI: 10.1016/j.chembiol.2021.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Small molecules can be imaged in living cells using biosensors composed of RNA. However, RNA-based devices are difficult to design. Here, we describe a versatile platform for designing RNA-based fluorescent small-molecule sensors using naturally occurring highly stable three-way junction RNAs. We show that ligand-binding aptamers and fluorogenic aptamers can be inserted into three-way junctions and connected in a way that enables the three-way junction to function as a small-molecule-regulated fluorescent sensor in vitro and in cells. The sensors are designed so that the interhelical stabilizing interactions in the three-way junction are only induced upon ligand binding. We use these RNA-based devices to measure the dynamics of S-adenosylmethionine levels in mammalian cells in real time. We show that this strategy is compatible with diverse metabolite-binding RNA aptamers, fluorogenic aptamers, and three-way junctions. Overall, these data demonstrate a versatile method for readily generating RNA devices that function in living cells.
Collapse
Affiliation(s)
- Jared D Moon
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Sourav K Dey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Jacob L Litke
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Xing Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
| |
Collapse
|
10
|
Ren YS, Li HL, Piao XH, Yang ZY, Wang SM, Ge YW. Drug affinity responsive target stability (DARTS) accelerated small molecules target discovery: Principles and application. Biochem Pharmacol 2021; 194:114798. [PMID: 34678227 DOI: 10.1016/j.bcp.2021.114798] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022]
Abstract
Drug affinity responsive target stability (DARTS) is a novel target discovery approach and is particularly adept at screening small molecule (SM) targets without requiring any structural modifications. The DARTS method is capable of revealing drug-target interactions from cells or tissues by tracking changes in the stability of proteins acting as receptors of bioactive SMs. Due to its simple operation and high efficiency, the DARTS method has been applied to uncover the drug-action mechanism. This review summarized analytical principles, protocols, validation approaches, applications, and challenges involved in the DARTS method. Due to the innate advantages of the DARTS method, it is expected to be a powerful tool to accelerate SM target discovery, especially for bioactive natural products with unknown mechanisms.
Collapse
Affiliation(s)
- Ying-Shan Ren
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui-Lin Li
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xiu-Hong Piao
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Zhi-You Yang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shu-Mei Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Yue-Wei Ge
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| |
Collapse
|
11
|
Xiong Y, Donovan KA, Eleuteri NA, Kirmani N, Yue H, Razov A, Krupnick NM, Nowak RP, Fischer ES. Chemo-proteomics exploration of HDAC degradability by small molecule degraders. Cell Chem Biol 2021; 28:1514-1527.e4. [PMID: 34314730 PMCID: PMC9339248 DOI: 10.1016/j.chembiol.2021.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/01/2021] [Accepted: 06/29/2021] [Indexed: 12/25/2022]
Abstract
Targeted protein degradation refers to the use of small molecules that recruit a ubiquitin ligase to a target protein for ubiquitination and subsequent proteasome-dependent degradation. While degraders have been developed for many targets, key questions regarding degrader development and the consequences of acute pharmacological degradation remain, specifically for targets that exist in obligate multi-protein complexes. Here, we synthesize a pan-histone deacetylase (HDAC) degrader library for the chemo-proteomic exploration of acute degradation of a key class of chromatin-modifying enzymes. Using chemo-proteomics, we not only map the degradability of the zinc-dependent HDAC family identifying leads for targeting HDACs 1-8 and 10 but also explore important aspects of degrading epigenetic enzymes. We discover cell line-driven target specificity and that HDAC degradation often results in collateral loss of HDAC-containing repressive complexes. These findings potentially offer a new mechanism toward controlling chromatin structure, and our resource will facilitate accelerated degrader design and development for HDACs.
Collapse
Affiliation(s)
- Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas A Eleuteri
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nadia Kirmani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Razov
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Noah M Krupnick
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
12
|
Eissa IH, Khalifa MM, Elkaeed EB, Hafez EE, Alsfouk AA, Metwaly AM. In Silico Exploration of Potential Natural Inhibitors against SARS-Cov-2 nsp10. Molecules 2021; 26:6151. [PMID: 34684735 PMCID: PMC8539059 DOI: 10.3390/molecules26206151] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
In continuation of our previous effort, different in silico selection methods were applied to 310 naturally isolated metabolites that exhibited antiviral potentialities before. The applied selection methods aimed to pick the most relevant inhibitor of SARS-CoV-2 nsp10. At first, a structural similarity study against the co-crystallized ligand, S-Adenosyl Methionine (SAM), of SARS-CoV-2 nonstructural protein (nsp10) (PDB ID: 6W4H) was carried out. The similarity analysis culled 30 candidates. Secondly, a fingerprint study against SAM preferred compounds 44, 48, 85, 102, 105, 182, 220, 221, 282, 284, 285, 301, and 302. The docking studies picked 48, 182, 220, 221, and 284. While the ADMET analysis expected the likeness of the five candidates to be drugs, the toxicity study preferred compounds 48 and 182. Finally, a density-functional theory (DFT) study suggested vidarabine (182) to be the most relevant SARS-Cov-2 nsp10 inhibitor.
Collapse
Affiliation(s)
- Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Mohamed M. Khalifa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, Almaarefa University, Riyadh 13713, Saudi Arabia;
| | - Elsayed E. Hafez
- Department of Plant Protection and Biomolecular Diagnosis, ALCRI, City of Scientific Research and Technological Applications, New Borg El-Arab City 21934, Egypt;
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| |
Collapse
|
13
|
Naqvi T, Amin A, Ali S, Lone MY, Bashir N, Khan SU, Htar TT, Rizvi MA. In vitro and In silico Evaluation of Structurally Diverse Benzyl-pyrrolidine-3-ol Analogues as Apoptotic Agents via Caspase Activation. Acta Chim Slov 2021; 68:667-682. [PMID: 34897536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] Open
Abstract
The activation of caspases is central to apoptotic process in living systems. Defects in apoptosis have been implicated with carcinogenesis. Need to develop smart agents capable of inducing apoptosis in tumor cells is obvious. With this motive, diversity oriented synthesis of 1-benzylpyrrolidin-3-ol analogues was envisaged. The multi component Ugi reaction synthesized library of electronically diverse analogues was explored for cytotoxic propensity towards a panel of human cancer cell lines at 10 µM. The lead compounds exhibit a selective cytotoxicity towards HL-60 cells as compared to cell lines derived from solid tumors. Besides, their milder cytotoxic effect on non-cancerous cell lines reaffirm their selective action towards cancer cells only. The lead molecules were tested for their ability to target caspase-3, as a vital protease triggering apoptosis. The lead compounds were observed to induce apoptosis in HL-60 cells around 10 µM concentration. The lead compounds exhibited various non-covalent supra type interactions with caspase-3 key residues around the active site. The binding ability of lead compounds with caspase-3 was studied via molecular docking and molecular dynamic (MD) simulations. MD simulations indicated the stability of compound-caspase-3 complex throughout the 50 ns simulation run. The stability and bio-availability of the lead compounds under physiological conditions was assessed by their interaction with Bovine Serum Albumin (BSA) as model protein. BSA interactions of lead compounds were studied by various bio-physical methods and further substantiated with in silico MD simulations.
Collapse
|
14
|
Xu C, Zou H, Yu X, Xie Y, Cai J, Shang Q, Ouyang N, Wang Y, Xu P, He Z, Wu H. Repurposing FDA-Approved Compounds for the Discovery of Glutaminyl Cyclase Inhibitors as Drugs Against Alzheimer's Disease. ChemistryOpen 2021; 10:877-881. [PMID: 33377311 PMCID: PMC8409088 DOI: 10.1002/open.202000235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/07/2020] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative causes of dementia, the pathology of which is still not much clear. It's challenging to discover the disease modifying agents for the prevention and treatment of AD over the years. Emerging evidence has been accumulated to reveal the crucial role of up-regulated glutaminyl cyclase (QC) in the initiation of AD. In the current study, the QC inhibitory potency of a library consisting of 1621 FDA-approved compounds was assessed. A total of 54 hits, 3.33 % of the pool, exhibited QC inhibitory activities. The Ki of the top 5 compounds with the highest QC inhibitory activities were measured. Among these selected hits, compounds affecting neuronal signaling pathways and other mechanisms were recognized. Moreover, several polyphenol derivatives with QC inhibitory activities were also identified. Frameworks and subsets contained in these hits were analyzed. Taken together, our results may contribute to the discovery and development of novel QC inhibitors as potential anti-AD agents.
Collapse
Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Haoman Zou
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Xi Yu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Yazhou Xie
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Jiaxin Cai
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Qi Shang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Na Ouyang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Yinan Wang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Pan Xu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Zhendan He
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| |
Collapse
|
15
|
Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021; 60:19191-19200. [PMID: 34161644 PMCID: PMC8426693 DOI: 10.1002/anie.202103693] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.
Collapse
|
16
|
Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021; 60:18231-18239. [PMID: 34097796 PMCID: PMC8456925 DOI: 10.1002/anie.202105584] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/31/2021] [Indexed: 12/24/2022]
Abstract
Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However, recent progress in PX could allow for a more integrated role into early drug discovery. Here, we demonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe a practical multicomponent reaction approach to acrylamides and -esters from diverse building blocks suitable for mmol scale synthesis on 96-well format and on a high-throughput nanoscale format in a highly automated fashion. High-throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID-19 causing agent, SARS-CoV-2. Our results demonstrate, that the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.
Collapse
Affiliation(s)
- Fandi Sutanto
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Shabnam Shaabani
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Rick Oerlemans
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Deniz Eris
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | - Pravin Patil
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Mojgan Hadian
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Meitian Wang
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | | | - Matthew R. Groves
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Alexander Dömling
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| |
Collapse
|
17
|
Bai B, Zou R, Chan HCS, Li H, Yuan S. MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions. Molecules 2021; 26:molecules26154625. [PMID: 34361778 PMCID: PMC8347168 DOI: 10.3390/molecules26154625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022] Open
Abstract
Protein-ligand interaction analysis is important for drug discovery and rational protein design. The existing online tools adopt only a single conformation of the complex structure for calculating and displaying the interactions, whereas both protein residues and ligand molecules are flexible to some extent. The interactions evolved with time in the trajectories are of greater interest. MolADI is a user-friendly online tool which analyzes the protein-ligand interactions in detail for either a single structure or a trajectory. Interactions can be viewed easily with both 2D graphs and 3D representations. MolADI is available as a web application.
Collapse
Affiliation(s)
- Bing Bai
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China; (B.B.); (R.Z.); (H.C.S.C.)
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China
| | - Rongfeng Zou
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China; (B.B.); (R.Z.); (H.C.S.C.)
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China
- AlphaMol Science Ltd., 1068 Xueyuan Avenue, Shenzhen 518055, China
| | - H. C. Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China; (B.B.); (R.Z.); (H.C.S.C.)
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China
| | - Hongchun Li
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China; (B.B.); (R.Z.); (H.C.S.C.)
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China
- Correspondence: (H.L.); (S.Y.)
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China; (B.B.); (R.Z.); (H.C.S.C.)
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen 518055, China
- AlphaMol Science Ltd., 1068 Xueyuan Avenue, Shenzhen 518055, China
- Correspondence: (H.L.); (S.Y.)
| |
Collapse
|
18
|
Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
Collapse
Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| |
Collapse
|
19
|
Wang S, Alpsoy A, Sood S, Ordonez-Rubiano SC, Dhiman A, Sun Y, Jiao G, Krusemark CJ, Dykhuizen EC. A Potent, Selective CBX2 Chromodomain Ligand and Its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation. Chembiochem 2021; 22:2335-2344. [PMID: 33950564 PMCID: PMC8358665 DOI: 10.1002/cbic.202100118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/04/2021] [Indexed: 12/16/2022]
Abstract
Polycomb group (PcG) proteins are epigenetic regulators that facilitate both embryonic development and cancer progression. PcG proteins form Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). PRC2 trimethylates histone H3 lysine 27 (H3K27me3), a histone mark recognized by the N-terminal chromodomain (ChD) of the CBX subunit of canonical PRC1. There are five PcG CBX paralogs in humans. CBX2 in particular is upregulated in a variety of cancers, particularly in advanced prostate cancers. Using CBX2 inhibitors to understand and target CBX2 in prostate cancer is highly desirable; however, high structural similarity among the CBX ChDs has been challenging for developing selective CBX ChD inhibitors. Here, we utilize selections of focused DNA encoded libraries (DELs) for the discovery of a selective CBX2 chromodomain probe, SW2_152F. SW2_152F binds to CBX2 ChD with a Kd of 80 nM and displays 24-1000-fold selectivity for CBX2 ChD over other CBX paralogs in vitro. SW2_152F is cell permeable, selectively inhibits CBX2 chromatin binding in cells, and blocks neuroendocrine differentiation of prostate cancer cell lines in response to androgen deprivation.
Collapse
Affiliation(s)
- Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Aktan Alpsoy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Life Science Interdisciplinary Graduate Program, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Sandra Carolina Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Yixing Sun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Casey J. Krusemark
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
| | - Emily C. Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 201 S. University St. West Lafayette, IN, 47907 USA
- Purdue Center for Cancer Research, 201 S. University St. West Lafayette, IN, 47907 USA
| |
Collapse
|
20
|
Di Gaetano S, Capasso D, Delre P, Pirone L, Saviano M, Pedone E, Mangiatordi GF. More Is Always Better Than One: The N-Terminal Domain of the Spike Protein as Another Emerging Target for Hampering the SARS-CoV-2 Attachment to Host Cells. Int J Mol Sci 2021; 22:6462. [PMID: 34208755 PMCID: PMC8235207 DOI: 10.3390/ijms22126462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/31/2022] Open
Abstract
Although the approved vaccines are proving to be of utmost importance in containing the Coronavirus disease 2019 (COVID-19) threat, they will hardly be resolutive as new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, a single-stranded RNA virus) variants might be insensitive to the immune response they induce. In this scenario, developing an effective therapy is still a dire need. Different targets for therapeutic antibodies and diagnostics have been identified, among which the SARS-CoV-2 spike (S) glycoprotein, particularly its receptor-binding domain, has been defined as crucial. In this context, we aim to focus attention also on the role played by the S N-terminal domain (S1-NTD) in the virus attachment, already recognized as a valuable target for neutralizing antibodies, in particular, building on a cavity mapping indicating the presence of two druggable pockets and on the recent literature hypothesizing the presence of a ganglioside-binding domain. In this perspective, we aim at proposing S1-NTD as a putative target for designing small molecules hopefully able to hamper the SARS-CoV-2 attachment to host cells.
Collapse
Affiliation(s)
- Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
| | - Domenica Capasso
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
- CESTEV, University of Naples “Federico II”, 80145 Naples, Italy
| | - Pietro Delre
- Institute of Crystallography, CNR, 70126 Bari, Italy; (P.D.); (G.F.M.)
- Chemistry Department, University of Bari, 70121 Bari, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
| | - Michele Saviano
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
- Institute of Crystallography, CNR, 70126 Bari, Italy; (P.D.); (G.F.M.)
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
| | | |
Collapse
|
21
|
Shatalin K, Nuthanakanti A, Kaushik A, Shishov D, Peselis A, Shamovsky I, Pani B, Lechpammer M, Vasilyev N, Shatalina E, Rebatchouk D, Mironov A, Fedichev P, Serganov A, Nudler E. Inhibitors of bacterial H 2S biogenesis targeting antibiotic resistance and tolerance. Science 2021; 372:1169-1175. [PMID: 34112687 PMCID: PMC10723041 DOI: 10.1126/science.abd8377] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics. Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide (H2S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H2S in two major human pathogens, Staphylococcus aureus and Pseudomonas aeruginosa, and discovered small molecules that inhibit bacterial CSE. These inhibitors potentiate bactericidal antibiotics against both pathogens in vitro and in mouse models of infection. CSE inhibitors also suppress bacterial tolerance, disrupting biofilm formation and substantially reducing the number of persister bacteria that survive antibiotic treatment. Our results establish bacterial H2S as a multifunctional defense factor and CSE as a drug target for versatile antibiotic enhancers.
Collapse
Affiliation(s)
- Konstantin Shatalin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Abhishek Kaushik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mirna Lechpammer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Elena Shatalina
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | | | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| |
Collapse
|
22
|
Lanyon‐Hogg T, Ritzefeld M, Zhang L, Andrei SA, Pogranyi B, Mondal M, Sefer L, Johnston CD, Coupland CE, Greenfield JL, Newington J, Fuchter MJ, Magee AI, Siebold C, Tate EW. Photochemical Probe Identification of a Small-Molecule Inhibitor Binding Site in Hedgehog Acyltransferase (HHAT)*. Angew Chem Int Ed Engl 2021; 60:13542-13547. [PMID: 33768725 PMCID: PMC8252026 DOI: 10.1002/anie.202014457] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/26/2021] [Indexed: 11/30/2022]
Abstract
The mammalian membrane-bound O-acyltransferase (MBOAT) superfamily is involved in biological processes including growth, development and appetite sensing. MBOATs are attractive drug targets in cancer and obesity; however, information on the binding site and molecular mechanisms underlying small-molecule inhibition is elusive. This study reports rational development of a photochemical probe to interrogate a novel small-molecule inhibitor binding site in the human MBOAT Hedgehog acyltransferase (HHAT). Structure-activity relationship investigation identified single enantiomer IMP-1575, the most potent HHAT inhibitor reported to-date, and guided design of photocrosslinking probes that maintained HHAT-inhibitory potency. Photocrosslinking and proteomic sequencing of HHAT delivered identification of the first small-molecule binding site in a mammalian MBOAT. Topology and homology data suggested a potential mechanism for HHAT inhibition which was confirmed by kinetic analysis. Our results provide an optimal HHAT tool inhibitor IMP-1575 (Ki =38 nM) and a strategy for mapping small molecule interaction sites in MBOATs.
Collapse
Affiliation(s)
| | | | - Leran Zhang
- Department of ChemistryImperial College LondonLondonW12 0BZUK
| | | | - Balazs Pogranyi
- Department of ChemistryImperial College LondonLondonW12 0BZUK
| | - Milon Mondal
- Department of ChemistryImperial College LondonLondonW12 0BZUK
| | - Lea Sefer
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | - Claire E. Coupland
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | | | | | | | - Anthony I. Magee
- National Heart & Lung InstituteImperial College LondonLondonSW7 2AZUK
| | - Christian Siebold
- Division of Structural BiologyWellcome Centre for Human GeneticsUniversity of OxfordOxfordOX3 7BNUK
| | - Edward W. Tate
- Department of ChemistryImperial College LondonLondonW12 0BZUK
| |
Collapse
|
23
|
Garcia M, Hoffer L, Leblanc R, Benmansour F, Feracci M, Derviaux C, Egea-Jimenez AL, Roche P, Zimmermann P, Morelli X, Barral K. Fragment-based drug design targeting syntenin PDZ2 domain involved in exosomal release and tumour spread. Eur J Med Chem 2021; 223:113601. [PMID: 34153575 DOI: 10.1016/j.ejmech.2021.113601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 11/17/2022]
Abstract
Syntenin stimulates exosome production and its expression is upregulated in many cancers and implicated in the spread of metastatic tumor. These effects are supported by syntenin PDZ domains interacting with syndecans. We therefore aimed to develop, through a fragment-based drug design approach, novel inhibitors targeting syntenin-syndecan interactions. We describe here the optimization of a fragment, 'hit' C58, identified by in vitro screening of a PDZ-focused fragment library, which binds specifically to the syntenin-PDZ2 domain at the same binding site as the syndecan-2 peptide. X-ray crystallographic structures and computational docking were used to guide our optimization process and lead to compounds 45 and 57 (IC50 = 33 μM and 47 μM; respectively), two representatives of syntenin-syndecan interactions inhibitors, that selectively affect the syntenin-exosome release. These findings demonstrate that it is possible to identify small molecules inhibiting syntenin-syndecan interaction and exosome release that may be useful for cancer therapy.
Collapse
Affiliation(s)
- Manon Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Laurent Hoffer
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Raphaël Leblanc
- Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Université, Inserm1068, CNRS7258, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Fatiha Benmansour
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Mikael Feracci
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Carine Derviaux
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Antonio Luis Egea-Jimenez
- Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Université, Inserm1068, CNRS7258, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Pascale Zimmermann
- Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Université, Inserm1068, CNRS7258, Institut Paoli-Calmettes, 13009 Marseille, France; Department of Human Genetics, K. U. Leuven, B-3000, Leuven, Belgium
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France
| | - Karine Barral
- Centre de Recherche en Cancérologie de Marseille (CRCM), Integrative Structural & Chemical Biology, Aix-Marseille Université, Inserm 1068, CNRS 7258, Institut Paoli Calmettes, 13009, Marseille, France.
| |
Collapse
|
24
|
Baisden JT, Childs-Disney JL, Ryan LS, Disney MD. Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity. Curr Opin Chem Biol 2021; 62:119-129. [PMID: 34118759 PMCID: PMC9264282 DOI: 10.1016/j.cbpa.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure-activity relationships across genomic RNA. Binding compounds can be identified and optimized into structure-specific ligands by using sequence-based design with various modes of action, for example, inhibiting translation or directing pre-mRNA splicing outcomes. In addition, strategies to direct protein activity against an RNA of interest via chemically induced proximity is a burgeoning area that has been validated both in cells and in preclinical animal models, and we describe that it may allow rapid access to new avenues to affect RNA biology. These approaches and the unique modes of action suggest that more RNAs are potentially amenable to targeting than proteins.
Collapse
Affiliation(s)
- Jared T Baisden
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Lucas S Ryan
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA.
| |
Collapse
|
25
|
Abstract
Nuclear export factor chromosome region maintenance 1 (CRM1) is an attractive anticancer and antiviral drug target that spurred several research efforts to develop its inhibitor. Noncovalent CRM1 inhibitors are desirable, but none is reported to date. Here, we present the crystal structure of yeast CRM1 in complex with S109, a substructure of CBS9106 (under clinical test). Superimposition with the LFS-829 (another covalent CRM1 inhibitor) complex inspired the design of a noncovalent CRM1 inhibitor. Among nine synthesized compounds, noncovalent CRM1 inhibitor 1 (NCI-1) showed a high affinity to human and yeast CRM1 in the absence or presence of GST-bound Ras-related nuclear protein (RanGTP). Unlike covalent inhibitors, the crystal structure showed that NCI-1 is bound in the "open" nuclear export signal (NES) groove of CRM1, simultaneously occupying two hydrophobic pockets. NCI-1 additionally inhibited the nuclear export and proliferation of cells harboring the human CRM1-C528S mutant. Our work opens up the avenue of noncovalent CRM1 inhibitor development toward a more potent, less toxic, and broad-spectrum anticancer/antiviral therapy.
Collapse
Affiliation(s)
- Yuqin Lei
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| | - Qi An
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| | - Xiao-Fei Shen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Division of Neurology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Min Sui
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| | - Chungen Li
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Division of Neurology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| | - Qingxiang Sun
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University and Collaborative Innovation Centre of Biotherapy, Chengdu 610041, China
| |
Collapse
|
26
|
Onguka O, Babin BM, Lakemeyer M, Foe IT, Amara N, Terrell SM, Lum KM, Cieplak P, Niphakis MJ, Long JZ, Bogyo M. Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host. Cell Chem Biol 2021; 28:1501-1513.e5. [PMID: 34043961 DOI: 10.1016/j.chembiol.2021.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/09/2021] [Accepted: 05/04/2021] [Indexed: 12/24/2022]
Abstract
The intracellular protozoan parasite Toxoplasma gondii must scavenge cholesterol and other lipids from the host to facilitate intracellular growth and replication. Enzymes responsible for neutral lipid synthesis have been identified but there is no evidence for enzymes that catalyze lipolysis of cholesterol esters and esterified lipids. Here, we characterize several T. gondii serine hydrolases with esterase and thioesterase activities that were previously thought to be depalmitoylating enzymes. We find they do not cleave palmitoyl thiol esters but rather hydrolyze short-chain lipid esters. Deletion of one of the hydrolases results in alterations in levels of multiple lipids species. We also identify small-molecule inhibitors of these hydrolases and show that treatment of parasites results in phenotypic defects reminiscent of parasites exposed to excess cholesterol or oleic acid. Together, these data characterize enzymes necessary for processing lipids critical for infection and highlight the potential for targeting parasite hydrolases for therapeutic applications.
Collapse
Affiliation(s)
- Ouma Onguka
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brett M Babin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Markus Lakemeyer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian T Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neri Amara
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kenneth M Lum
- Lundbeck La Jolla Research Center, San Diego, CA 92121, USA
| | - Piotr Cieplak
- Infectious & Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
27
|
Bayle E, Svensson F, Atkinson BN, Steadman D, Willis NJ, Woodward HL, Whiting P, Vincent JP, Fish PV. Carboxylesterase Notum Is a Druggable Target to Modulate Wnt Signaling. J Med Chem 2021; 64:4289-4311. [PMID: 33783220 PMCID: PMC8172013 DOI: 10.1021/acs.jmedchem.0c01974] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Indexed: 12/12/2022]
Abstract
Regulation of the Wnt signaling pathway is critically important for a number of cellular processes in both development and adult mammalian biology. This Perspective will provide a summary of current and emerging therapeutic opportunities in modulating Wnt signaling, especially through inhibition of Notum carboxylesterase activity. Notum was recently shown to act as a negative regulator of Wnt signaling through the removal of an essential palmitoleate group. Inhibition of Notum activity may represent a new approach to treat disease where aberrant Notum activity has been identified as the underlying cause. Reliable screening technologies are available to identify inhibitors of Notum, and structural studies are accelerating the discovery of new inhibitors. A selection of these hits have been optimized to give fit-for-purpose small molecule inhibitors of Notum. Three noteworthy examples are LP-922056 (26), ABC99 (27), and ARUK3001185 (28), which are complementary chemical tools for exploring the role of Notum in Wnt signaling.
Collapse
Affiliation(s)
- Elliott
D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - David Steadman
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Nicky J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| |
Collapse
|
28
|
Liang Q, He J, Zhao X, Xue Y, Zuo H, Xu R, Jin Y, Wang J, Li Q, Zhao X. Selective Discovery of GPCR Ligands within DNA-Encoded Chemical Libraries Derived from Natural Products: A Case Study on Antagonists of Angiotensin II Type I Receptor. J Med Chem 2021; 64:4196-4205. [PMID: 33784102 DOI: 10.1021/acs.jmedchem.1c00123] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Natural products have failed to meet the urgent need for drug discovery in recent decades due to limited resources, necessitating new strategies for re-establishing the key role of natural products in hit screening. This work introduced DNA-encoding techniques into the synthesis of phenolic acid-focused libraries containing 32 000 diverse compounds. Online selection of the library using immobilized angiotensin II type I receptor (AT1R) resulted in seven phenolic acid derivatives. The half-maximal concentration (IC50) of hit 1 for the right shift of the [125I]-Sar1-AngII competition curve was 19.6 nM. Pharmacological examination of renovascular hypertensive rats demonstrated that hit 1 significantly lowered the blood pressure of the animals without changing their heart rates. These results were used to create a general strategy for rapid and unbiased discovery of hits derived from natural products with high throughput and efficiency.
Collapse
Affiliation(s)
- Qi Liang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jianyu He
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xue Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Xue
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haiyue Zuo
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ru Xu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yan Jin
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qian Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| |
Collapse
|
29
|
Williams-Noonan BJ, Todorova N, Kulkarni K, Aguilar MI, Yarovsky I. An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2. J Phys Chem B 2021; 125:2533-2550. [PMID: 33657325 PMCID: PMC7945587 DOI: 10.1021/acs.jpcb.0c11321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/28/2021] [Indexed: 12/12/2022]
Abstract
The novel RNA virus, severe acute respiratory syndrome coronavirus II (SARS-CoV-2), is currently the leading cause of mortality in 2020, having led to over 1.6 million deaths and infecting over 75 million people worldwide by December 2020. While vaccination has started and several clinical trials for a number of vaccines are currently underway, there is a pressing need for a cure for those already infected with the virus. Of particular interest in the design of anti-SARS-CoV-2 therapeutics is the human protein angiotensin converting enzyme II (ACE2) to which this virus adheres before entry into the host cell. The SARS-CoV-2 virion binds to cell-surface bound ACE2 via interactions of the spike protein (s-protein) on the viral surface with ACE2. In this paper, we use all-atom molecular dynamics simulations and binding enthalpy calculations to determine the effect that a bound ACE2 active site inhibitor (MLN-4760) would have on the binding affinity of SARS-CoV-2 s-protein with ACE2. Our analysis indicates that the binding enthalpy could be reduced for s-protein adherence to the active site inhibitor-bound ACE2 protein by as much as 1.48-fold as an upper limit. This weakening of binding strength was observed to be due to the destabilization of the interactions between ACE2 residues Glu-35, Glu-37, Tyr-83, Lys-353, and Arg-393 and the SARS-CoV-2 s-protein receptor binding domain (RBD). The conformational changes were shown to lead to weakening of ACE2 interactions with SARS-CoV-2 s-protein, therefore reducing s-protein binding strength. Further, we observed increased conformational lability of the N-terminal helix and a conformational shift of a significant portion of the ACE2 motifs involved in s-protein binding, which may affect the kinetics of the s-protein binding when the small molecule inhibitor is bound to the ACE2 active site. These observations suggest potential new ways for interfering with the SARS-CoV-2 adhesion by modulating ACE2 conformation through distal active site inhibitor binding.
Collapse
Affiliation(s)
| | - Nevena Todorova
- School of Engineering, RMIT
University, Melbourne, Victoria 3001, Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology,
Monash University, Clayton, Victoria 3800,
Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology,
Monash University, Clayton, Victoria 3800,
Australia
| | - Irene Yarovsky
- School of Engineering, RMIT
University, Melbourne, Victoria 3001, Australia
| |
Collapse
|
30
|
Sahani RL, Diana-Rivero R, Vernekar SKV, Wang L, Du H, Zhang H, Castaner AE, Casey MC, Kirby KA, Tedbury PR, Xie J, Sarafianos SG, Wang Z. Design, Synthesis and Characterization of HIV-1 CA-Targeting Small Molecules: Conformational Restriction of PF74. Viruses 2021; 13:v13030479. [PMID: 33804121 PMCID: PMC8000227 DOI: 10.3390/v13030479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
Small molecules targeting the PF74 binding site of the HIV-1 capsid protein (CA) confer potent and mechanistically unique antiviral activities. Structural modifications of PF74 could further the understanding of ligand binding modes, diversify ligand chemical classes, and allow identification of new variants with balanced antiviral activity and metabolic stability. In the current work, we designed and synthesized three series of PF74-like analogs featuring conformational constraints at the aniline terminus or the phenylalanine carboxamide moiety, and characterized them using a biophysical thermal shift assay (TSA), cell-based antiviral and cytotoxicity assays, and in vitro metabolic stability assays in human and mouse liver microsomes. These studies showed that the two series with the phenylalanine carboxamide moiety replaced by a pyridine or imidazole ring can provide viable hits. Subsequent SAR identified an improved analog 15 which effectively inhibited HIV-1 (EC50 = 0.31 μM), strongly stabilized CA hexamer (ΔTm = 8.7 °C), and exhibited substantially enhanced metabolic stability (t1/2 = 27 min for 15 vs. 0.7 min for PF74). Metabolic profiles from the microsomal stability assay also indicate that blocking the C5 position of the indole ring could lead to increased resistance to oxidative metabolism.
Collapse
Affiliation(s)
- Rajkumar Lalji Sahani
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Raquel Diana-Rivero
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Sanjeev Kumar V. Vernekar
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Lei Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Haijuan Du
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Huanchun Zhang
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Andres Emanuelli Castaner
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mary C. Casey
- Department of Molecular Microbiology and Immunology, School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Karen A. Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
- Correspondence: ; Tel.: +1-612-626-7025
| |
Collapse
|
31
|
Peñalver L, Schmid P, Szamosvári D, Schildknecht S, Globisch C, Sawade K, Peter C, Böttcher T. A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2. Angew Chem Int Ed Engl 2021; 60:6799-6806. [PMID: 33350010 PMCID: PMC7986205 DOI: 10.1002/anie.202016113] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Indexed: 01/05/2023]
Abstract
Activity-based probes are valuable tools for chemical biology. However, finding probes that specifically target the active site of an enzyme remains a challenging task. Herein, we present a ligand selection strategy that allows to rapidly tailor electrophilic probes to a target of choice and showcase its application for the two cysteine proteases of SARS-CoV-2 as proof of concept. The resulting probes were specific for the active site labeling of 3CLpro and PLpro with sufficient selectivity in a live cell model as well as in the background of a native human proteome. Exploiting the probes as tools for competitive profiling of a natural product library identified salvianolic acid derivatives as promising 3CLpro inhibitors. We anticipate that our ligand selection strategy will be useful to rapidly develop customized probes and discover inhibitors for a wide range of target proteins also beyond corona virus proteases.
Collapse
Affiliation(s)
- Lilian Peñalver
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Philipp Schmid
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
| | - Dávid Szamosvári
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
| | - Stefan Schildknecht
- In Vitro Toxicology and BiomedicineDepartment of BiologyUniversity of KonstanzKonstanzGermany
- Albstadt-Sigmaringen UniversitySigmaringenGermany
| | | | - Kevin Sawade
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Christine Peter
- Department of ChemistryUniversity of KonstanzKonstanzGermany
| | - Thomas Böttcher
- Department of ChemistryKonstanz Research School Chemical BiologyZukunftskollegUniversity of KonstanzKonstanzGermany
- Faculty of ChemistryDepartment of Biological Chemistry & Centre for Microbiology and Environmental Systems ScienceDivision of Microbial EcologyUniversity of ViennaViennaAustria
| |
Collapse
|
32
|
Xu M, Zhao C, Zhu B, Wang L, Zhou H, Yan D, Gu Q, Xu J. Discovering High Potent Hsp90 Inhibitors as Antinasopharyngeal Carcinoma Agents through Fragment Assembling Approach. J Med Chem 2021; 64:2010-2023. [PMID: 33543615 DOI: 10.1021/acs.jmedchem.0c01521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hsp90 is a new promising target for cancer treatment. Many inhibitors have been discovered as therapeutic agents, and some have passed Phase I and II. However, no one is approved by FDA yet. Novel and druggable Hsp90 inhibitors are still demanding. Here, we report a new way to discover high potent Hsp90 inhibitors as antinasopharyngeal carcinoma agents through assembling fragments. With chemotyping analysis, we extract seven chemotypes from 3482 known Hsp90 inhibitors, screen 500 fragments that are compatible with the chemotypes, and confirm 15 anti-Hsp90 fragments. Click chemistry is employed to construct 172 molecules and synthesize 21 compounds among them. The best inhibitor 3d was further optimized and resulted in more potent 4f (IC50 = 0.16 μM). In vitro and in vivo experiments confirmed that 4f is a promising agent against nasopharyngeal carcinoma. This study may provide a strategy in discovering new ligands against targets without well-understood structures.
Collapse
Affiliation(s)
- Mengyang Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Chao Zhao
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- Shenzhen Cell Inspire Therapeutics Co., Ltd., Shenzhen 518101, China
| | - Biying Zhu
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liangyue Wang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Huihao Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Daoguang Yan
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- School of Biotechnology and Health Sciences, Wuyi University, 99 Yingbin Road, Jiangmen 529020, China
| |
Collapse
|
33
|
Horning KJ, Tang X, Thomas MG, Aschner M, Bowman AB. Identification of Three Small Molecules That Can Selectively Influence Cellular Manganese Levels in a Mouse Striatal Cell Model. Molecules 2021; 26:molecules26041175. [PMID: 33671818 PMCID: PMC7931103 DOI: 10.3390/molecules26041175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/03/2022] Open
Abstract
Manganese (Mn) is a biologically essential metal, critical as a cofactor for numerous enzymes such a glutamine synthetase and kinases such as ataxia-telangiectasia mutated (ATM). Similar to other essential metals such as iron and zinc, proper levels of Mn need to be achieved while simultaneously being careful to avoid excess levels of Mn that can be neurotoxic. A lifetime of occupational exposure to Mn can often lead to a Parkinsonian condition, also known as “manganism”, characterized by impaired gait, muscle spasms, and tremors. Despite the importance of its regulation, the mechanisms underlying the transport and homeostasis of Mn are poorly understood. Rather than taking a protein or gene-targeted approach, our lab recently took a high-throughput-screening approach to identify 41 small molecules that could significantly increase or decrease intracellular Mn in a neuronal cell model. Here, we report characterization of these small molecules, which we refer to as the “Mn toolbox”. We adapted a Fura-2-based assay for measuring Mn concentration and for measuring relative concentrations of other divalent metals: nickel, copper, cobalt, and zinc. Of these 41 small molecules, we report here the identification of three that selectively influence cellular Mn but do not influence the other divalent metals tested. The patterns of activity across divalent metals and the discovery of Mn-selective small molecules has potential pharmacological and scientific utility.
Collapse
Affiliation(s)
- Kyle J. Horning
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA;
| | - Xueqi Tang
- School of Health Sciences, Purdue University, West Lafayette, IN 47906, USA; (X.T.); (M.G.T.)
| | - Morgan G. Thomas
- School of Health Sciences, Purdue University, West Lafayette, IN 47906, USA; (X.T.); (M.G.T.)
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine Bronx, New York, NY 10461, USA
- Correspondence: (M.A.); (A.B.B.)
| | - Aaron B. Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN 47906, USA; (X.T.); (M.G.T.)
- Correspondence: (M.A.); (A.B.B.)
| |
Collapse
|
34
|
Savva L, Georgiades SN. Recent Developments in Small-Molecule Ligands of Medicinal Relevance for Harnessing the Anticancer Potential of G-Quadruplexes. Molecules 2021; 26:molecules26040841. [PMID: 33562720 PMCID: PMC7914483 DOI: 10.3390/molecules26040841] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
G-quadruplexes, a family of tetraplex helical nucleic acid topologies, have emerged in recent years as novel targets, with untapped potential for anticancer research. Their potential stems from the fact that G-quadruplexes occur in functionally-important regions of the human genome, such as the telomere tandem sequences, several proto-oncogene promoters, other regulatory regions and sequences of DNA (e.g., rDNA), as well as in mRNAs encoding for proteins with roles in tumorigenesis. Modulation of G-quadruplexes, via interaction with high-affinity ligands, leads to their stabilization, with numerous observed anticancer effects. Despite the fact that only a few lead compounds for G-quadruplex modulation have progressed to clinical trials so far, recent advancements in the field now create conditions that foster further development of drug candidates. This review highlights biological processes through which G-quadruplexes can exert their anticancer effects and describes, via selected case studies, progress of the last few years on the development of efficient and drug-like G-quadruplex-targeted ligands, intended to harness the anticancer potential offered by G-quadruplexes. The review finally provides a critical discussion of perceived challenges and limitations that have previously hampered the progression of G-quadruplex-targeted lead compounds to clinical trials, concluding with an optimistic future outlook.
Collapse
|
35
|
Lightwood DJ, Munro RJ, Porter J, McMillan D, Carrington B, Turner A, Scott-Tucker A, Hickford ES, Schmidt A, Fox D, Maloney A, Ceska T, Bourne T, O'Connell J, Lawson ADG. A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF. Nat Commun 2021; 12:583. [PMID: 33495445 PMCID: PMC7835358 DOI: 10.1038/s41467-020-20825-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer-small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF-TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein-protein interactions.
Collapse
Affiliation(s)
| | | | - John Porter
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | | | | | | | | | | | | | - David Fox
- UCB Pharma, 7869 NE Day Road W, Bainbridge Island, WA, 98110, USA
| | | | - Tom Ceska
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | - Tim Bourne
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | | | | |
Collapse
|
36
|
Qi L, Zhang Y, Song F, Han Y, Ding Y. A newly identified small molecular compound acts as a protein kinase inhibitor to suppress metastasis of colorectal cancer. Bioorg Chem 2021; 107:104625. [PMID: 33454506 DOI: 10.1016/j.bioorg.2021.104625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Targeted therapy has demonstrated high efficacy in the treatment of advanced cancer, and protein kinase inhibitors are a major focus of that therapy; therefore, our study aimed to identify a new protein kinase inhibitor that could be used in the treatment of advanced cancers. METHODS We analyzed the expression profile of colorectal cancer (CRC), combined the driver gene and drug target databases, and identified protein kinase kalirin RhoGEF kinase (kalirin/KALRN) which is related to CRC metastasis. Based on the structure of kalirin, we screened for the small molecular compound ZINC65387069. We first compared the kinase inhibitory activities and molecular properties of ZINC65387069 and tyrosine kinase inhibitors (TKIs). We then determined the effects of ZINC65387069 on the phosphorylation of protein kinase B-Raf. Finally, we determined the effects of ZINC65387069 on migration and apoptosis of HCT116 cells as well as RKO cells. The cell cytoskeleton was also determined. RESULTS Compared with traditional TKIs, ZINC65387069 had stronger kinase inhibitory activity, a simpler structure, higher water solubility, a smaller polar surface area, and lower molecular weight and volume. In CRC cells, ZINC65387069 could significantly inhibit the phosphorylation of B-Raf as well as inhibit cell migration, destroy the cell cytoskeleton, and promote cell apoptosis. CONCLUSION ZINC65387069 is a newly identified protein kinase inhibitor that deserves additional research as a lead compound for drug development to help create targeted therapy against CRC.
Collapse
Affiliation(s)
- Lu Qi
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China.
| | - Ying Zhang
- Department of Radiation Medicine, School of Public Health, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Tropical Disease Research, Guangzhou 510515, China
| | - Fuyao Song
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China
| | - Yue Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, China.
| |
Collapse
|
37
|
Kelly ML, Chu CC, Shi H, Ganser LR, Bogerd HP, Huynh K, Hou Y, Cullen BR, Al-Hashimi HM. Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays. RNA 2021; 27:12-26. [PMID: 33028652 PMCID: PMC7749633 DOI: 10.1261/rna.076257.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 09/26/2020] [Indexed: 05/30/2023]
Abstract
Identifying small molecules that selectively bind an RNA target while discriminating against all other cellular RNAs is an important challenge in RNA-targeted drug discovery. Much effort has been directed toward identifying drug-like small molecules that minimize electrostatic and stacking interactions that lead to nonspecific binding of aminoglycosides and intercalators to many stem-loop RNAs. Many such compounds have been reported to bind RNAs and inhibit their cellular activities. However, target engagement and cellular selectivity assays are not routinely performed, and it is often unclear whether functional activity directly results from specific binding to the target RNA. Here, we examined the propensities of three drug-like compounds, previously shown to bind and inhibit the cellular activities of distinct stem-loop RNAs, to bind and inhibit the cellular activities of two unrelated HIV-1 stem-loop RNAs: the transactivation response element (TAR) and the rev response element stem IIB (RREIIB). All compounds bound TAR and RREIIB in vitro, and two inhibited TAR-dependent transactivation and RRE-dependent viral export in cell-based assays while also exhibiting off-target interactions consistent with nonspecific activity. A survey of X-ray and NMR structures of RNA-small molecule complexes revealed that aminoglycosides and drug-like molecules form hydrogen bonds with functional groups commonly accessible in canonical stem-loop RNA motifs, in contrast to ligands that specifically bind riboswitches. Our results demonstrate that drug-like molecules can nonspecifically bind stem-loop RNAs most likely through hydrogen bonding and electrostatic interactions and reinforce the importance of assaying for off-target interactions and RNA selectivity in vitro and in cells when assessing novel RNA-binders.
Collapse
Affiliation(s)
- Megan L Kelly
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Honglue Shi
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Laura R Ganser
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kelly Huynh
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yuze Hou
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Chemistry, Center for Virology, Duke University Medical Center, Durham, North Carolina 27710, USA
| |
Collapse
|
38
|
Abstract
In silico simulations of biological systems are of the significant importance to obtain insights on specific processes that experimental protocols have difficulty to elucidate. More particularly, and to ensure that a given molecule is able to reach its cellular target, the development of computational methods able to quickly estimate the cellular permeabilities for small molecules can become an important tool in the early stages of drug development. Herein, a computational protocol for predicting permeability coefficients, concerning both membranes and proteins, is presented and discussed.
Collapse
|
39
|
Munoz-Tello P, Lin H, Khan P, de Vera IMS, Kamenecka TM, Kojetin DJ. Assessment of NR4A Ligands That Directly Bind and Modulate the Orphan Nuclear Receptor Nurr1. J Med Chem 2020; 63:15639-15654. [PMID: 33289551 PMCID: PMC8006468 DOI: 10.1021/acs.jmedchem.0c00894] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nurr1/NR4A2 is an orphan nuclear receptor transcription factor implicated as a drug target for neurological disorders including Alzheimer's and Parkinson's diseases. Previous studies identified small-molecule NR4A nuclear receptor modulators, but it remains unclear if these ligands affect transcription via direct binding to Nurr1. We assessed 12 ligands reported to affect NR4A activity for Nurr1-dependent and Nurr1-independent transcriptional effects and the ability to bind the Nurr1 ligand-binding domain (LBD). Protein NMR structural footprinting data show that amodiaquine, chloroquine, and cytosporone B bind the Nurr1 LBD; ligands that do not bind include C-DIM12, celastrol, camptothecin, IP7e, isoalantolactone, ethyl 2-[2,3,4-trimethoxy-6-(1-octanoyl)phenyl]acetate (TMPA), and three high-throughput screening hit derivatives. Importantly, ligands that modulate Nurr1 transcription also show Nurr1-independent effects on transcription in a cell type-specific manner, indicating that care should be taken when interpreting the functional response of these ligands in transcriptional assays. These findings should help focus medicinal chemistry efforts that desire to optimize Nurr1-binding ligands.
Collapse
Affiliation(s)
- Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Hua Lin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Pasha Khan
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Ian Mitchelle S. de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Theodore M. Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Douglas J. Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, 33458, USA
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida 33458, USA
| |
Collapse
|
40
|
Koster AK, Reese AL, Kuryshev Y, Wen X, McKiernan KA, Gray EE, Wu C, Huguenard JR, Maduke M, Du Bois J. Development and validation of a potent and specific inhibitor for the CLC-2 chloride channel. Proc Natl Acad Sci U S A 2020; 117:32711-32721. [PMID: 33277431 PMCID: PMC7768775 DOI: 10.1073/pnas.2009977117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CLC-2 is a voltage-gated chloride channel that is widely expressed in mammalian tissues. In the central nervous system, CLC-2 appears in neurons and glia. Studies to define how this channel contributes to normal and pathophysiological function in the central nervous system raise questions that remain unresolved, in part due to the absence of precise pharmacological tools for modulating CLC-2 activity. Herein, we describe the development and optimization of AK-42, a specific small-molecule inhibitor of CLC-2 with nanomolar potency (IC50 = 17 ± 1 nM). AK-42 displays unprecedented selectivity (>1,000-fold) over CLC-1, the closest CLC-2 homolog, and exhibits no off-target engagement against a panel of 61 common channels, receptors, and transporters expressed in brain tissue. Computational docking, validated by mutagenesis and kinetic studies, indicates that AK-42 binds to an extracellular vestibule above the channel pore. In electrophysiological recordings of mouse CA1 hippocampal pyramidal neurons, AK-42 acutely and reversibly inhibits CLC-2 currents; no effect on current is observed on brain slices taken from CLC-2 knockout mice. These results establish AK-42 as a powerful tool for investigating CLC-2 neurophysiology.
Collapse
Affiliation(s)
- Anna K Koster
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Austin L Reese
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305
| | - Yuri Kuryshev
- Charles River Laboratories Cleveland, Inc., Cleveland, OH 44128
| | - Xianlan Wen
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Keri A McKiernan
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Erin E Gray
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Caiyun Wu
- Charles River Laboratories Cleveland, Inc., Cleveland, OH 44128
| | - John R Huguenard
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305;
| | - Merritt Maduke
- Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305;
| | - J Du Bois
- Department of Chemistry, Stanford University, Stanford, CA 94305;
| |
Collapse
|
41
|
Pobbati AV, Rubin BP. Protein-Protein Interaction Disruptors of the YAP/TAZ-TEAD Transcriptional Complex. Molecules 2020; 25:molecules25246001. [PMID: 33352993 PMCID: PMC7766469 DOI: 10.3390/molecules25246001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
The identification of protein-protein interaction disruptors (PPIDs) that disrupt the YAP/TAZ-TEAD interaction has gained considerable momentum. Several studies have shown that YAP/TAZ are no longer oncogenic when their interaction with the TEAD family of transcription factors is disrupted. The transcriptional co-regulator YAP (its homolog TAZ) interact with the surface pockets of TEADs. Peptidomimetic modalities like cystine-dense peptides and YAP cyclic and linear peptides exploit surface pockets (interface 2 and interface 3) on TEADs and function as PPIDs. The TEAD surface might pose a challenge for generating an effective small molecule PPID. Interestingly, TEADs also have a central pocket that is distinct from the surface pockets, and which small molecules leverage exclusively to disrupt the YAP/TAZ-TEAD interaction (allosteric PPIDs). Although small molecules that occupy the central pocket belong to diverse classes, they display certain common features. They are flexible, which allows them to adopt a palmitate-like conformation, and they have a predominant hydrophobic portion that contacts several hydrophobic residues and a small hydrophilic portion that faces the central pocket opening. Despite such progress, more selective PPIDs that also display favorable pharmacokinetic properties and show tolerable toxicity profiles are required to evaluate the feasibility of using these PPIDs for cancer therapy.
Collapse
Affiliation(s)
- Ajaybabu V. Pobbati
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Correspondence: (A.V.P.); (B.P.R.); Tel.: +1-216-445-4472 (A.V.P.)
| | - Brian P. Rubin
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Correspondence: (A.V.P.); (B.P.R.); Tel.: +1-216-445-4472 (A.V.P.)
| |
Collapse
|
42
|
Cotrina EY, Vilà M, Nieto J, Arsequell G, Planas A. Preparative Scale Production of Recombinant Human Transthyretin for Biophysical Studies of Protein-Ligand and Protein-Protein Interactions. Int J Mol Sci 2020; 21:ijms21249640. [PMID: 33348885 PMCID: PMC7766448 DOI: 10.3390/ijms21249640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022] Open
Abstract
Human transthyretin (hTTR), a serum protein with a main role in transporting thyroid hormones and retinol through binding to the retinol-binding protein, is an amyloidogenic protein involved in familial amyloidotic polyneuropathy (FAP), familial amyloidotic cardiomyopathy, and central nervous system selective amyloidosis. hTTR also has a neuroprotective role in Alzheimer disease, being the major Aβ binding protein in human cerebrospinal fluid (CSF) that prevents amyloid-β (Aβ) aggregation with consequent abrogation of toxicity. Here we report an optimized preparative expression and purification protocol of hTTR (wt and amyloidogenic mutants) for in vitro screening assays of TTR ligands acting as amyloidogenesis inhibitors or acting as molecular chaperones to enhance the TTR:Aβ interaction. Preparative yields were up to 660 mg of homogenous protein per L of culture in fed-batch bioreactor. The recombinant wt protein is mainly unmodified at Cys10, the single cysteine in the protein sequence, whereas the highly amyloidogenic Y78F variant renders mainly the S-glutathionated form, which has essentially the same amyloidogenic behavior than the reduced protein with free Cys10. The TTR production protocol has shown inter-batch reproducibility of expression and protein quality for in vitro screening assays.
Collapse
Affiliation(s)
- Ellen Y. Cotrina
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain; (E.Y.C.); (M.V.); (J.N.)
- Institut de Química Avançada de Catalunya, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), 08034 Barcelona, Spain;
| | - Marta Vilà
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain; (E.Y.C.); (M.V.); (J.N.)
| | - Joan Nieto
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain; (E.Y.C.); (M.V.); (J.N.)
| | - Gemma Arsequell
- Institut de Química Avançada de Catalunya, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), 08034 Barcelona, Spain;
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, 08017 Barcelona, Spain; (E.Y.C.); (M.V.); (J.N.)
- Correspondence:
| |
Collapse
|
43
|
Khan Tareque R, Hassell-Hart S, Krojer T, Bradley A, Velupillai S, Talon R, Fairhead M, Day IJ, Bala K, Felix R, Kemmitt PD, Brennan P, von Delft F, Díaz Sáez L, Huber K, Spencer J. Deliberately Losing Control of C-H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism. ChemMedChem 2020; 15:2513-2520. [PMID: 32812371 DOI: 10.1002/cmdc.202000543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/16/2022]
Abstract
Combined photochemical arylation, "nuisance effect" (SN Ar) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein-ligand structure determination. Reactions were deliberately allowed to run "out of control" in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with SN Ar processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.
Collapse
Affiliation(s)
- Raysa Khan Tareque
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Storm Hassell-Hart
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Tobias Krojer
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Anthony Bradley
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Romain Talon
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Michael Fairhead
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iain J Day
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Kamlesh Bala
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Robert Felix
- Bio-Techne (Tocris Bioscience), The Watkins Building, Atlantic Road Avonmouth, Bristol, BS11 9QD, UK
| | - Paul D Kemmitt
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB10 1XL, UK
| | - Paul Brennan
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Frank von Delft
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot, Oxford, OX11 0DE, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, Auckland Park, 2006, South Africa
| | - Laura Díaz Sáez
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kilian Huber
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - John Spencer
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| |
Collapse
|
44
|
Sadybekov AA, Brouillette RL, Marin E, Sadybekov AV, Luginina A, Gusach A, Mishin A, Besserer-Offroy É, Longpré JM, Borshchevskiy V, Cherezov V, Sarret P, Katritch V. Structure-Based Virtual Screening of Ultra-Large Library Yields Potent Antagonists for a Lipid GPCR. Biomolecules 2020; 10:E1634. [PMID: 33287369 PMCID: PMC7761830 DOI: 10.3390/biom10121634] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Cysteinyl leukotriene G protein-coupled receptors, CysLT1R and CysLT2R, regulate bronchoconstrictive and pro-inflammatory effects and play a key role in allergic disorders, cardiovascular diseases, and cancer. CysLT1R antagonists have been widely used to treat asthma disorders, while CysLT2R is a potential target against uveal melanoma. However, very few selective antagonist chemotypes for CysLT receptors are available, and the design of such ligands has proved to be challenging. To overcome this obstacle, we took advantage of recently solved crystal structures of CysLT receptors and an ultra-large Enamine REAL library, representing a chemical space of 680 M readily available compounds. Virtual ligand screening employed 4D docking models comprising crystal structures of CysLT1R and CysLT2R and their corresponding ligand-optimized models. Functional assessment of the candidate hits yielded discovery of five novel antagonist chemotypes with sub-micromolar potencies and the best Ki = 220 nM at CysLT1R. One of the hits showed inverse agonism at the L129Q constitutively active mutant of CysLT2R, with potential utility against uveal melanoma.
Collapse
Affiliation(s)
- Arman A. Sadybekov
- Michelson Center for Convergent Biosciences, Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA;
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; (A.V.S.); (V.C.)
| | - Rebecca L. Brouillette
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (R.L.B.); (É.B.-O.); (J.-M.L.); (P.S.)
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
| | - Anastasiia V. Sadybekov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; (A.V.S.); (V.C.)
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
| | - Élie Besserer-Offroy
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (R.L.B.); (É.B.-O.); (J.-M.L.); (P.S.)
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jean-Michel Longpré
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (R.L.B.); (É.B.-O.); (J.-M.L.); (P.S.)
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; (A.V.S.); (V.C.)
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (E.M.); (A.L.); (A.G.); (A.M.); (V.B.)
| | - Philippe Sarret
- Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (R.L.B.); (É.B.-O.); (J.-M.L.); (P.S.)
| | - Vsevolod Katritch
- Michelson Center for Convergent Biosciences, Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA;
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; (A.V.S.); (V.C.)
| |
Collapse
|
45
|
Serrán-Aguilera L, Mariotto E, Rubbini G, Castro Navas FF, Marco C, Carrasco-Jiménez MP, Ballarotto M, Macchiarulo A, Hurtado-Guerrero R, Viola G, Lopez-Cara LC. Synthesis, biological evaluation, in silico modeling and crystallization of novel small monocationic molecules with potent antiproliferative activity by dual mechanism. Eur J Med Chem 2020; 207:112797. [PMID: 32977218 DOI: 10.1016/j.ejmech.2020.112797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 12/28/2022]
Abstract
Seeking for new anticancer drugs with strong antiproliferative activity and simple molecular structure, we designed a novel series of compounds based on our previous reported pharmacophore model composed of five moieties. Antiproliferative assays on four tumoral cell lines and evaluation of Human Choline Kinase CKα1 enzymatic activity was performed for these compounds. Among tested molecules, those ones with biphenyl spacer showed betters enzymatic and antiproliferative activities (n-v). Docking and crystallization studies validate the hypothesis and confirm the results. The most active compound (t) induces a significant arrest of the cell cycle in G0/G1 phase that ultimately lead to apoptosis, following the mitochondrial pathway, as demonstrated for other choline kinase inhibitors. However additional assays reveal that the inhibition of choline uptake could also be involved in the antiproliferative outcome of this class of compounds.
Collapse
Affiliation(s)
- Lucía Serrán-Aguilera
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, 35128, Padova, Italy
| | - Gianluca Rubbini
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Francisco Fermín Castro Navas
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, 18071, Granada, Spain
| | | | - Marco Ballarotto
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo 1, Perugia, 06123, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo 1, Perugia, 06123, Italy
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzada (LMA), Mariano Esquillor S/n, Campus Rio Ebro, Edificio I+D; Fundacion ARAID, 50018, Zaragoza, Spain; Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, 35128, Padova, Italy
| | - Luisa Carlota Lopez-Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain.
| |
Collapse
|
46
|
Abstract
Catalytic C-H oxyfunctionalization reactions have garnered significant attention in recent years with their ability to streamline synthetic routes toward complex molecules. Consequently, there have been significant strides in the design and development of catalysts that enable diversification through C-H functionalization reactions. Enzymatic C-H oxygenation reactions are often complementary to small molecule based synthetic approaches, providing a powerful tool when deployable on preparative-scale. This review highlights key advances in scalable biocatalytic C-H oxyfunctionalization reactions developed within the past decade.
Collapse
Affiliation(s)
- Suman Chakrabarty
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | | | | | | |
Collapse
|
47
|
Caciolla J, Picone G, Farruggia G, Valenti D, Rampa A, Malucelli E, Belluti F, Trezza A, Spiga O, Iotti S, Gobbi S, Cappadone C, Bisi A. Multifaceted activity of polyciclic MDR revertant agents in drug-resistant leukemic cells: Role of the spacer. Bioorg Chem 2020; 106:104460. [PMID: 33229118 DOI: 10.1016/j.bioorg.2020.104460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022]
Abstract
A small library of derivatives carrying a polycyclic scaffold recently identified by us as a new privileged structure in medicinal chemistry was designed and synthesized, aiming at obtaining potent MDR reverting agents also endowed with antitumor properties. In particular, as a follow-up of our previous studies, attention was focused on the role of the spacer connecting the polycyclic core with a properly selected nitrogen-containing group. A relevant increase in reverting potency was observed, going from the previously employed but-2-ynyl- to a pent-3-ynylamino moiety, as in compounds 3d and 3e, while the introduction of a triazole ring proved to differently impact on the activity of the compounds. The docking results supported the data obtained by biological tests, showing, for the most active compounds, the ability to establish specific bonds with P-glycoprotein. Moreover, a multifaceted anticancer profile and dual in vitro activity was observed for all compounds, showing both revertant and antitumor effects on leukemic cells. In this respect, 3c emerged as a "triple-target" agent, endowed with a relevant reverting potency, a considerable antiproliferative activity and a collateral sensitivity profile.
Collapse
Affiliation(s)
- Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Giovanna Picone
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via S. Donato 19/2, 40127 Bologna, Italy
| | - Giovanna Farruggia
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via S. Donato 19/2, 40127 Bologna, Italy; National Institute of Biostructures and Biosystems, Via delle Medaglie D'oro, 305, 00136 Roma, Italy
| | - Dario Valenti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Emil Malucelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via S. Donato 19/2, 40127 Bologna, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy
| | - Stefano Iotti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via S. Donato 19/2, 40127 Bologna, Italy; National Institute of Biostructures and Biosystems, Via delle Medaglie D'oro, 305, 00136 Roma, Italy
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Concettina Cappadone
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via S. Donato 19/2, 40127 Bologna, Italy.
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
| |
Collapse
|
48
|
Goracci L, Desantis J, Valeri A, Castellani B, Eleuteri M, Cruciani G. Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications. J Med Chem 2020; 63:11615-11638. [PMID: 33026811 PMCID: PMC8015227 DOI: 10.1021/acs.jmedchem.0c00793] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Indexed: 12/15/2022]
Abstract
Hetero-bifunctional PROteolysis TArgeting Chimeras (PROTACs) represent a new emerging class of small molecules designed to induce polyubiquitylation and proteasomal-dependent degradation of a target protein. Despite the increasing number of publications about the synthesis, biological evaluation, and mechanism of action of PROTACs, the characterization of the pharmacokinetic properties of this class of compounds is still minimal. Here, we report a study on the metabolism of a series of 40 PROTACs in cryopreserved human hepatocytes at multiple time points. Our results indicated that the metabolism of PROTACs could not be predicted from that of their constituent ligands. Their linkers' chemical nature and length resulted in playing a major role in the PROTACs' liability. A subset of compounds was also tested for metabolism by human cytochrome P450 3A4 (CYP3A4) and human aldehyde oxidase (hAOX) for more in-depth data interpretation, and both enzymes resulted in active PROTAC metabolism.
Collapse
Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Jenny Desantis
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Beatrice Castellani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Michela Eleuteri
- Montelino
Therapeutics, LLC, 7
Powdermill Lane, Southborough, Massachusetts 01772 Unites States
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| |
Collapse
|
49
|
Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P, Brandão-Neto J, Carbery A, Davison G, Dias A, Downes TD, Dunnett L, Fairhead M, Firth JD, Jones SP, Keeley A, Keserü GM, Klein HF, Martin MP, Noble MEM, O'Brien P, Powell A, Reddi RN, Skyner R, Snee M, Waring MJ, Wild C, London N, von Delft F, Walsh MA. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 2020; 11:5047. [PMID: 33028810 PMCID: PMC7542442 DOI: 10.1038/s41467-020-18709-w] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
Collapse
Affiliation(s)
- Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Paul Gehrtz
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anna Carbery
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Gemma Davison
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Thomas D Downes
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael Fairhead
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - James D Firth
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - S Paul Jones
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - György M Keserü
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Hanna F Klein
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Mathew P Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Martin E M Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Ailsa Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rambabu N Reddi
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Matthew Snee
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Conor Wild
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
| |
Collapse
|
50
|
Sarin H. Pressure regulated basis for gene transcription by delta-cell micro-compliance modeled in silico: Biphenyl, bisphenol and small molecule ligand models of cell contraction-expansion. PLoS One 2020; 15:e0236446. [PMID: 33021979 PMCID: PMC7537880 DOI: 10.1371/journal.pone.0236446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular diameter, lipophilicity and hydrophilicity exclusion affinity limits exist for small molecule carrier-mediated diffusion or transport through channel pores or interaction with the cell surface glycocalyx. The molecular structure lipophilicity limit for non-specific carrier-mediated transmembrane diffusion through polarity-selective transport channels of the cell membrane is Lexternal structure ∙ Hpolar group-1 of ≥ 1.07. The cell membrane channel pore size is > 0.752 and < 0.758 nm based on a 3-D ellipsoid model (biphenyl), and within the molecular diameter size range 0.744 and 0.762 nm based on a 2-D elliptical model (alkanol). The adjusted van der Waals diameter (vdWD, adj; nm) for the subset of halogenated vapors is predictive of the required MAC for anesthetic potency at an initial (-) Δ Cmicro effect. The molecular structure L ∙ Hpolar group-1 for Neu5Ac is 0.080, and the L ∙ Hpolar group-1 interval range for the cell surface glycocalyx hydrophilicity barrier interaction is 0.101 (Saxitoxin, Stx; Linternal structure ∙ Hpolar group-1) - 0.092 (m-xylenediamine, Lexternal structure · Hpolar group). Differential predictive effective pressure mapping of gene activation or repression reveals that p-dioxin exposure results in activation of AhR-Erβ (Arnt)/Nrf-2, Pparδ, Errγ (LxRα), Dio3 (Dio2) and Trα limbs, and due to high affinity Dio2 and Dio3 (OH-TriCDD, Lext · H-1: 1.91–4.31) exothermy-antagonism (Δ contraction) with high affinity T4/rT3-TRα-mediated agonism (Δ expansion). co-planar PCB metabolite exposure (Lext · H-1: 1.95–3.91) results in activation of AhR (Erα/β)/Nrf2, Rev-Erbβ, Errα, Dio3 (Dio2) and Trα limbs with a Δ Cmicro contraction of 0.89 and Δ Cmicro expansion of 1.05 as compared to p-dioxin. co-, ortho-planar PCB metabolite exposure results in activation of Car/PxR, Pparα (Srebf1,—Lxrβ), Arnt (AhR-Erβ), AR, Dio1 (Dio2) and Trβ limbs with a Δ Cmicro contraction of 0.73 and Δ Cmicro expansion of 1.18 (as compared to p-dioxin). Bisphenol A exposure (Lext struct ∙ H-1: 1.08–1.12, BPA–BPE, Errγ; BPAF, Lext struct ∙ H-1: 1.23, CM Erα, β) results in increased duration at Peff for Timm8b (Peff 0.247) transcription and in indirect activation of the AhR/Nrf-2 hybrid pathway with decreased duration at Peff 0.200 (Nrf1) and increased duration at Peff 0.257 (Dffa). The Bpa/Bpaf convergent pathway Cmicro contraction-expansion response increase in the lower Peff interval is 0.040; in comparison, small molecule hormone Δ Cmicro contraction-expansion response increases in the lower Peff intervals for gene expression ≤ 0.168 (Dex· GR) ≥ 0.156 (Dht · AR), with grade of duration at Peff (min·count) of 1.33x105 (Dex/Cort) and 1.8–2.53x105 (Dht/R1881) as compared to the (-) coupled (+) Δ CmicroPeff to 0.136 (Wnt5a, Esr2) with applied DES (1.86x106). The subtype of trans-differentiated cell as a result of an applied toxin or toxicant is predictable by delta-Cmicro determined by Peff mapping. Study findings offer additional perspective on the basis for pressure regulated gene transcription by alterations in cell micro-compliance (Δ contraction-expansion, Cmicro), and are applicable for the further predictive modeling of gene to gene transcription interactions, and small molecule modulation of cell effective pressure (Peff) and its potential.
Collapse
Affiliation(s)
- Hemant Sarin
- Freelance Investigator in Translational Science and Medicine, Charleston, West Virginia, United States of America
- * E-mail:
| |
Collapse
|