1
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Shao DW, Zhao LJ, Sun JF. Synthesis and clinical application of representative small-molecule dipeptidyl Peptidase-4 (DPP-4) inhibitors for the treatment of type 2 diabetes mellitus (T2DM). Eur J Med Chem 2024; 272:116464. [PMID: 38704940 DOI: 10.1016/j.ejmech.2024.116464] [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: 03/26/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Diabetes mellitus is a chronic metabolic disorder characterized by high blood glucose levels, which can cause many diseases, including osteoporosis, fractures, arthritis, and foot complications. The inhibitors of dipeptidyl peptidase-4 (DPP-4), an enzyme involved in glucose metabolism regulation, are essential for managing Type 2 Diabetes Mellitus (T2DM). The inhibition of DPP-4 has become a promising treatment approach for T2DM because it can increase levels of active glucagon-like peptide-1 (GLP-1), leading to improved insulin secretion in response to glucose and reduced release of glucagon. The review commences by elucidating the role of DPP-4 in glucose homeostasis and its significance in T2DM pathophysiology. Furthermore, it presents the mechanism of action, preclinical pharmacodynamics, clinical efficacy, and toxicity profiles of small-molecule DPP-4 inhibitors across various clinical stages. This comprehensive review provides valuable insights into the synthesis and clinical application of DPP-4 inhibitors, serving as an invaluable resource for researchers, clinicians, and pharmaceutical professionals interested in diabetes therapeutics and drug development.
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Affiliation(s)
- Dong-Wei Shao
- First People's Hospital of Shangqiu, Henan Province, Shangqiu, 476100, China.
| | - Li-Jie Zhao
- The Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, United States.
| | - Jin-Feng Sun
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, College of Pharmacy, Yanji, Jilin, 133002, China; Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000, Leuven, Belgium.
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2
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Ni S, Takada Y, Ando T, Yu S, Yamashita Y, Takahashi Y, Sawada M, Oba M, Itoh Y, Suzuki T. Identification of a novel histone H2A mono-ubiquitination-inhibiting cell-active small molecule. Bioorg Med Chem Lett 2024; 105:129759. [PMID: 38636717 DOI: 10.1016/j.bmcl.2024.129759] [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: 02/27/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Histone H2A mono-ubiquitination plays important roles in epigenetic gene expression and is also involved in tumorigenesis. Small molecules controlling H2A ubiquitination are of interest as potential chemical tools and anticancer drugs. To identify novel small molecule inhibitors of H2A ubiquitination, we synthesized and evaluated several compounds designed based on PRT4165 (1), which is a reported histone ubiquitin ligase RING1A inhibitor. We found that compound 11b strongly inhibited the viability and reduced histone H2A mono-ubiquitination in human osteosarcoma U2OS cells. Therefore, compound 11b is a promising lead compound for the development of H2A histone ubiquitination-inhibiting small molecules.
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Affiliation(s)
- Siyao Ni
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takaaki Ando
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shengwang Yu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Yukari Takahashi
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miho Sawada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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3
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Hildebrandt ER, Hussain SA, Sieburg MA, Ravishankar R, Asad N, Gore S, Ito T, Hougland JL, Dore TM, Schmidt WK. Targeted genetic and small molecule disruption of N-Ras CaaX cleavage alters its localization and oncogenic potential. Bioorg Chem 2024; 147:107316. [PMID: 38583246 PMCID: PMC11098683 DOI: 10.1016/j.bioorg.2024.107316] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
Ras GTPases and other CaaX proteins undergo multiple post-translational modifications at their carboxyl-terminus. These events initiate with prenylation of a cysteine and are followed by endoproteolytic removal of the 'aaX' tripeptide and carboxylmethylation. Some CaaX proteins are only subject to prenylation, however, due to the presence of an uncleavable sequence. In this study, uncleavable sequences were used to stage Ras isoforms in a farnesylated and uncleaved state to address the impact of CaaX proteolysis on protein localization and function. This targeted strategy is more specific than those that chemically inhibit the Rce1 CaaX protease or delete the RCE1 gene because global abrogation of CaaX proteolysis impacts the entire CaaX protein proteome and effects cannot be attributed to any specific CaaX protein of the many concurrently affected. With this targeted strategy, clear mislocalization and reduced activity of farnesylated and uncleaved Ras isoforms was observed. In addition, new peptidomimetics based on cleavable Ras CaaX sequences and the uncleavable CAHQ sequence were synthesized and tested as Rce1 inhibitors using in vitro and cell-based assays. Consistently, these non-hydrolyzable peptidomimetic Rce1 inhibitors recapitulate Ras mislocalization effects when modeled on cleavable but not uncleavable CaaX sequences. These findings indicate that a prenylated and uncleavable CaaX sequence, which can be easily applied to a wide range of mammalian CaaX proteins, can be used to probe the specific impact of CaaX proteolysis on CaaX protein properties under conditions of an otherwise normally processed CaaX protein proteome.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Shaneela A Hussain
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | | | - Rajani Ravishankar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Nadeem Asad
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Sangram Gore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Takahiro Ito
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY, USA; Department of Biology, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse, Syracuse University, Syracuse, NY, USA
| | - Timothy M Dore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE; Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Walter K Schmidt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
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4
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Xu C, Sun Z, Zhang X, Zang Q, Yang Z, Li L, Yang X, He Y, Ma Z, Chen J. Discovery of 4-phenyl-1H-indazole derivatives as novel small-molecule inhibitors targeting the PD-1/PD-L1 interaction. Bioorg Chem 2024; 147:107376. [PMID: 38640722 DOI: 10.1016/j.bioorg.2024.107376] [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: 01/29/2024] [Revised: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The inhibition of the programmed cell death-1 (PD-1)/programmed cell death-ligand 1 (PD-L1) pathway with small molecules is a promising approach for cancer immunotherapy. Herein, novel small molecules compounds bearing various scaffolds including thiophene, thiazole, tetrahydroquinoline, benzimidazole and indazole were designed, synthesized and evaluated for their inhibitory activity against the PD-1/PD-L1 interaction. Among them, compound Z13 exhibited the most potent activity with IC50 of 189.6 nM in the homogeneous time-resolved fluorescence (HTRF) binding assay. Surface plasmon resonance (SPR) assay demonstrated that Z13 bound to PD-L1 with high affinity (KD values of 231 nM and 311 nM for hPD-L1 and mPD-L1, respectively). In the HepG2/Jurkat T co-culture cell model, Z13 decreased the viability rate of HepG2 cells in a concentration-dependent manner. In addition, Z13 showed significant in vivo antitumor efficacy (TGI = 52.6 % at 40 mg/kg) without obvious toxicity in the B16-F10 melanoma model. Furthermore, flow cytometry analysis demonstrated that Z13 inhibited tumor growth in vivo by activating the tumor immune microenvironment. These findings indicate that Z13 is a promising PD-1/PD-L1 inhibitor deserving further investigation.
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Affiliation(s)
- Chenglong Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhiqiang Sun
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xuewen Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qinru Zang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zichao Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ling Li
- The Eighth Affiliated Hospital, Sun Yat sen University, Shenzhen 518033, China
| | - Xixiang Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yueyu He
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zeli Ma
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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5
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Balsollier C, Bijkerk S, de Smit A, van Eekelen K, Bozovičar K, Husstege D, Tomašič T, Anderluh M, Pieters RJ. Discovery of two non-UDP-mimic inhibitors of O-GlcNAc transferase by screening a DNA-encoded library. Bioorg Chem 2024; 147:107321. [PMID: 38604018 DOI: 10.1016/j.bioorg.2024.107321] [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: 01/29/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
Finding potent inhibitors of O-GlcNAc transferase (OGT) has proven to be a challenge, especially because the diversity of published inhibitors is low. The large majority of available OGT inhibitors are uridine-based or uridine-like compounds that mimic the main interactions of glycosyl donor UDP-GlcNAc with the enzyme. Until recently, screening of DNA-encoded libraries for discovering hits against protein targets was dedicated to a few laboratories around the world, but has become accessible to wider public with the recent launch of the DELopen platform. Here we report the results and follow-up of a DNA-encoded library screening by using the DELopen platform. This led to the discovery of two new hits with structural features not resembling UDP. Small focused libraries bearing those two scaffolds were made, leading to low micromolar inhibition of OGT and elucidation of their structure-activity relationship.
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Affiliation(s)
- Cyril Balsollier
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Simon Bijkerk
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Arjan de Smit
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Kevin van Eekelen
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Krištof Bozovičar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Dirk Husstege
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Roland J Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht NL-3508 TB, The Netherlands.
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6
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Zhang DJ, Chen R, Zhang YX, Li CC, Ning RN, Jiang M, Qiu WW. Synthesis of Heterocyclic Ring-Fused Bisnoralcohol Derivatives as Novel Small-Molecule Antiosteoporosis Agents. J Med Chem 2024; 67:8271-8295. [PMID: 38717088 DOI: 10.1021/acs.jmedchem.4c00349] [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: 05/24/2024]
Abstract
A series of heterocyclic ring-fused derivatives of bisnoralcohol (BA) were synthesized and evaluated for their inhibitory effects on RANKL-induced osteoclastogenesis. Most of these derivatives possessed potent antiosteoporosis activities in a dose-dependent manner. Among these compounds, 31 (SH442, IC50 = 0.052 μM) exhibited the highest potency, displaying 100% inhibition at 1.0 μM and 82.8% inhibition at an even lower concentration of 0.1 μM, which was much more potent than the lead compound BA (IC50 = 2.325 μM). Cytotoxicity tests suggested that the inhibitory effect of these compounds on RANKL-induced osteoclast differentiation did not result from their cytotoxicity. Mechanistic studies revealed that SH442 inhibited the expression of osteoclastogenesis-related marker genes and proteins, including TRAP, TRAF6, c-Fos, CTSK, and MMP9. Especially, SH442 could significantly attenuate bone loss of ovariectomy mouse in vivo. Therefore, these BA derivatives could be used as promising leads for the development of a new type of antiosteoporosis agent.
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Affiliation(s)
- De-Jie Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Rong Chen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yu-Xin Zhang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine,197 Ruijin second Road, Shanghai 200025, China
| | - Chen-Chen Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Ruo-Nan Ning
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine,197 Ruijin second Road, Shanghai 200025, China
| | - Min Jiang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine,197 Ruijin second Road, Shanghai 200025, China
| | - Wen-Wei Qiu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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7
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Jia Y, Oyken M, Kim RQ, Tjokrodirijo RTN, de Ru AH, Janssen APA, Hacker SM, van Veelen PA, Geurink PP, Sapmaz A. Development of Inhibitors, Probes, and PROTAC Provides a Complete Toolbox to Study PARK7 in the Living Cell. J Med Chem 2024; 67:7935-7953. [PMID: 38713163 DOI: 10.1021/acs.jmedchem.3c02410] [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: 05/08/2024]
Abstract
The integration of diverse chemical tools like small-molecule inhibitors, activity-based probes (ABPs), and proteolysis targeting chimeras (PROTACs) advances clinical drug discovery and facilitates the exploration of various biological facets of targeted proteins. Here, we report the development of such a chemical toolbox for the human Parkinson disease protein 7 (PARK7/DJ-1) implicated in Parkinson's disease and cancers. By combining structure-guided design, miniaturized library synthesis, and high-throughput screening, we identified two potent compounds, JYQ-164 and JYQ-173, inhibiting PARK7 in vitro and in cells by covalently and selectively targeting its critical residue, Cys106. Leveraging JYQ-173, we further developed a cell-permeable Bodipy probe, JYQ-196, for covalent labeling of PARK7 in living cells and a first-in-class PARK7 degrader JYQ-194 that selectively induces its proteasomal degradation in human cells. Our study provides a valuable toolbox to enhance the understanding of PARK7 biology in cellular contexts and opens new opportunities for therapeutic interventions.
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Affiliation(s)
- Yuqing Jia
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich CH-8093, Switzerland
| | - Merve Oyken
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Rayman T N Tjokrodirijo
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Stephan M Hacker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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8
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Yang Z, Liu Z, Wan S, Xu J, Huang Y, He H, Liu T, Li L, Ren Y, Zhang J, Chen J. Discovery of Novel Small-Molecule-Based Potential PD-L1/EGFR Dual Inhibitors with High Druggability for Glioblastoma Immunotherapy. J Med Chem 2024; 67:7995-8019. [PMID: 38739112 DOI: 10.1021/acs.jmedchem.4c00128] [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: 05/14/2024]
Abstract
Based on the close relationship between programmed death protein ligand 1 (PD-L1) and epidermal growth factor receptor (EGFR) in glioblastoma (GBM), we designed and synthesized a series of small molecules as potential dual inhibitors of EGFR and PD-L1. Among them, compound EP26 exhibited the highest inhibitory activity against EGFR (IC50 = 37.5 nM) and PD-1/PD-L1 interaction (IC50 = 1.77 μM). In addition, EP26 displayed superior in vitro antiproliferative activities and in vitro immunomodulatory effects by promoting U87MG cell death in a U87MG/Jurkat cell coculture model. Furthermore, EP26 possessed favorable pharmacokinetic properties (F = 22%) and inhibited tumor growth (TGI = 92.0%) in a GBM mouse model more effectively than Gefitinib (77.2%) and NP19 (82.8%). Moreover, EP26 increased CD4+ cells and CD8+ cells in tumor microenvironment. Collectively, these results suggest that EP26 represents the first small-molecule-based PD-L1/EGFR dual inhibitor deserving further investigation as an immunomodulating agent for cancer treatment.
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Affiliation(s)
- Zichao Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ziqing Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianwei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yaqi Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haiqi He
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ting Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Ling Li
- The Eighth Affiliated Hospital, Sun Yat sen University, Shenzhen 518033, China
| | - Yichang Ren
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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9
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Stevens R, Thompson JDF, Fournier JCL, Burley GA, Battersby DJ, Miah AH. Innovative, combinatorial and high-throughput approaches to degrader synthesis. Chem Soc Rev 2024; 53:4838-4861. [PMID: 38596888 DOI: 10.1039/d3cs01127e] [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: 04/11/2024]
Abstract
Targeted protein degraders such as PROTACs and molecular glues are a rapidly emerging therapeutic modality within industry and academia. Degraders possess unique mechanisms of action that lead to the removal of specific proteins by co-opting the cell's natural degradation mechanisms via induced proximity. Their optimisation thus far has often been largely empirical, requiring the synthesis and screening of a large number of analogues. In addition, the synthesis and development of degraders is often challenging, leading to lengthy optimisation campaigns to deliver candidate-quality compounds. This review highlights how the synthesis of degraders has evolved in recent years, in particular focusing on means of applying high-throughput chemistry and screening approaches to expedite these timelines, which we anticipate to be valuable in shaping the future of degrader optimisation campaigns.
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Affiliation(s)
- Rebecca Stevens
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | | | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | - Afjal H Miah
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
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10
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Zaino AM, Dash RC, James SJ, MacGilvary N, Crompton A, McPherson KS, Stanzione M, Korzhnev DM, Dyson NJ, Chatterjee N, Cantor SB, Hadden MK. Lead compound profiling for small molecule inhibitors of the REV1-CT/RIR Translesion synthesis Protein-Protein interaction. Bioorg Med Chem 2024; 106:117755. [PMID: 38749343 DOI: 10.1016/j.bmc.2024.117755] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Translesion synthesis (TLS) is a cellular mechanism through which actively replicating cells recruit specialized, low-fidelity DNA polymerases to damaged DNA to allow for replication past these lesions. REV1 is one of these TLS DNA polymerases that functions primarily as a scaffolding protein to organize the TLS heteroprotein complex and ensure replication occurs in the presence of DNA lesions. The C-Terminal domain of REV1 (REV1-CT) forms many protein-protein interactions (PPIs) with other TLS polymerases, making it essential for TLS function and a promising drug target for anti-cancer drug development. We utilized several lead identification strategies to identify various small molecules capable of disrupting the PPI between REV1-CT and the REV1 Interacting Regions (RIR) present in several other TLS polymerases. These lead compounds were profiled in several in vitro potency and PK assays to identify two scaffolds (1 and 6) as the most promising for further development. Both 1 and 6 synergized with cisplatin in a REV1-dependent fashion and demonstrated promising in vivo PK and toxicity profiles.
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Affiliation(s)
- Angela M Zaino
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Radha Charan Dash
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Stephy J James
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA
| | - Nathan MacGilvary
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew Crompton
- University of Vermont Cancer Center and Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Kerry S McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, 149 13th Street Charlestown, Boston, MA, 02129, USA
| | - Nimrat Chatterjee
- University of Vermont Cancer Center and Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Sharon B Cantor
- Molecular Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT 06269-3092, USA.
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11
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Yu S, Huang W, Zhang H, Guo Y, Zhang B, Zhang G, Lei J. Discovery of the small molecular inhibitors against sclerostin loop3 as potential anti-osteoporosis agents by structural based virtual screening and molecular design. Eur J Med Chem 2024; 271:116414. [PMID: 38677061 DOI: 10.1016/j.ejmech.2024.116414] [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: 01/14/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Sclerostin is a secreted glycoprotein that expresses predominantly in osteocytes and inhibits bone formation by antagonizing the Wnt/β-catenin signaling pathway, and the loop3 region of sclerostin has recently discovered as a novel therapeutic target for bone anabolic treatment without increasing cardiovascular risk. Herein, we used a structural based virtual screening to search for small molecular inhibitors selectively targeting sclerostin loop3. A novel natural product hit ZINC4228235 (THFA) was identified as the sclerostin loop3-selective inhibitor with a Kd value of 42.43 nM against sclerostin loop3. The simplification and derivation of THFA using molecular modeling-guided modification allowed the discovery of an effective and loop3-selective small molecular inhibitor, compound (4-(3-acetamidoprop-1-yn-1-yl)benzoyl)glycine (AACA), with improved binding affinity (Kd = 15.4 nM) compared to the hit THFA. Further in-vitro experiment revealed that compound AACA could attenuate the suppressive effect of transfected sclerostin on Wnt signaling and bone formation. These results make AACA as a potential candidate for development of anti-osteoporosis agents without increasing cardiovascular risk.
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Affiliation(s)
- Sifan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong SAR, China.
| | - Weifeng Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hao Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yinfeng Guo
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Baoting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Hong Kong SAR, China.
| | - Jinping Lei
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China; State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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12
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Wang W, Qiu S, Zhang T, Zheng Z, Zhu K, Gao X, Zhao F, Ma X, Lin H, He Y, Zheng C. Quantum chemistry calculation-aided discovery of potent small-molecule mimics of glutathione peroxidases for the treatment of cisplatin-induced hearing loss. Eur J Med Chem 2024; 271:116404. [PMID: 38631262 DOI: 10.1016/j.ejmech.2024.116404] [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: 01/24/2024] [Revised: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Hearing loss (HL) is a health burden that seriously affects the quality of life of cancer patients receiving platinum-based chemotherapy, and few FDA-approved treatment specifically targets this condition. The main mechanisms that contribute to cisplatin-induced hearing loss are oxidative stress and subsequent cell death, including ferroptosis revealed by us as a new mechanism recently. In this study, we employed the frontier molecular orbital (FMO) theory approach as a convenient prediction method for the glutathione peroxidase (GPx)-like activity of isoselenazolones and discovered new isoselenazolones with great GPx-like activity. Notably, compound 19 exhibited significant protective effects against cisplatin-induced hair cell (HC) damage in vitro and in vivo and effectively reverses cisplatin-induced hearing loss through oral administration. Further investigations revealed that this compound effectively alleviated hair cell oxidative stress, apoptosis and ferroptosis. This research highlights the potential of GPx mimics as a therapeutic strategy against cisplatin-induced hearing loss. The application of quantum chemistry (QC) calculations in the study of GPx mimics sheds light on the development of new, innovative treatments for hearing loss.
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Affiliation(s)
- Wentao Wang
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Siyu Qiu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200031, China
| | - Tianyi Zhang
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Zhiwei Zheng
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200031, China
| | - Kongkai Zhu
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xing Gao
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Fengping Zhao
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China
| | - Xinyuan Ma
- School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200031, China
| | - Hongyan Lin
- School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200031, China
| | - Yingzi He
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200031, China.
| | - Canhui Zheng
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai, 200433, China.
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13
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Sanghai N, Vuong B, Burak Berk A, Afridi MSK, Tranmer GK. Current Small Molecule-Based Medicinal Chemistry Approaches for Neurodegeneration Therapeutics. ChemMedChem 2024; 19:e202300705. [PMID: 38329887 DOI: 10.1002/cmdc.202300705] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Neurodegenerative diseases (NDDs) like Alzheimer's disease (AD), Parkinson's disease (PD), and Amyotrophic lateral sclerosis (ALS) possess multifactorial aetiologies. In recent years, our understanding of the biochemical and molecular pathways across NDDs has increased, however, new advances in small molecule-based therapeutic strategies targeting NDDs are obscure and scarce. Moreover, NDDs have been studied for more than five decades, however, there is a paucity of drugs that can treat NDDs. Further, the highly lipoidal blood-brain barrier (BBB) limits the uptake of many therapeutic molecules into the brain and is a complicating factor in the development of new agents to treat neurodegeneration. Considering the highly complex nature of NDDs, the association of multiple risk factors, and the challenges to overcome the BBB junction, medicinal chemists have developed small organic molecule-based novel approaches to target NDDs over the last few decades, such as designing lipophilic molecules and applying prodrug strategies. Attempts have been made to utilize a multitarget approach to modulate different biochemical molecular pathways involved in NDDs, in addition to, medicinal chemists making better decisions in identifying optimized drug candidates for the central nervous system (CNS) by using web-based computational tools. To increase the clinical success of these drug candidates, an in vitro assay modeling the BBB has been utilized by medicinal chemists in the pre-clinical phase as a further screening measure of small organic molecules. Herein, we examine some of the intriguing strategies taken by medicinal chemists to design small organic molecules to combat NDDs, with the intention of increasing our awareness of neurodegenerative therapeutics.
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Affiliation(s)
- Nitesh Sanghai
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Billy Vuong
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Ahmet Burak Berk
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | | | - Geoffrey K Tranmer
- College of Pharmacy, Rady Faculty of Health Science, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
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14
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Xu C, Cui K, Ye Z, Feng Y, Wang H, Liu HW. Recent Advances of Aminopeptidases-Responsive Small-Molecular Probes for Bioimaging. Chem Asian J 2024; 19:e202400052. [PMID: 38436107 DOI: 10.1002/asia.202400052] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 03/05/2024]
Abstract
Aminopeptidases, enzymes with critical roles in human body, are emerging as vital biomarkers for metabolic processes and diseases. Aberrant aminopeptidase levels are often associated with diseases, particularly cancer. Small-molecule probes, such as fluorescent, fluorescent/photoacoustics, bioluminescent, and chemiluminescent probes, are essential tools in the study of aminopeptidases-related diseases. The fluorescent probes provide real-time insights into protein activities, offering high sensitivity in specific locations, and precise spatiotemporal results. Additionally, photoacoustic probes offer signals that are able to penetrate deeper tissues. Bioluminescent and chemiluminescent probes can enhance in vivo imaging abilities by reducing the background. This comprehensive review is focused on small-molecule probes that respond to four key aminopeptidases: aminopeptidase N, leucine aminopeptidase, Pyroglutamate aminopeptidase 1, and Prolyl Aminopeptidase, and their utilization in imaging tumors and afflicted regions. In this review, the design strategy of small-molecule probes, the variety of designs from previous studies, and the opportunities of future bioimaging applications are discussed, serving as a roadmap for future research, sparking innovations in aminopeptidase-responsive probe development, and enhancing our understanding of these enzymes in disease diagnostics and treatment.
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Affiliation(s)
- Chengyan Xu
- Department of Medicine, Shizhen College of Guizhou University of Traditional Chinese Medicine, Guiyang, 550200, China
| | - Kaixi Cui
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, 44106, United States
| | - Zhifei Ye
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yurong Feng
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Huabin Wang
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Hong-Wen Liu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, 410081, China
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15
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Shah Zaib Saleem R, Schwalm MP, Knapp S. Expanding the ligand spaces for E3 ligases for the design of protein degraders. Bioorg Med Chem 2024; 105:117718. [PMID: 38621319 DOI: 10.1016/j.bmc.2024.117718] [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: 01/24/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Targeted protein degradation (TPD) has recently emerged as an exciting new drug modality. However, the strategy of developing small molecule-based protein degraders has evolved over the past two decades and has now established molecular tags that are already in clinical use, as well as chimeric molecules, PROteolysis TArgeting Chimeras (PROTACs), based mainly on ligand systems developed for the two E3 ligases CRBN and VHL. The large size of the human E3 ligase family suggests that PROTACs can be developed by targeting a large diversity of E3 ligases, some of which have restricted expression patterns with the potential to design disease- or tissue-specific degraders. Indeed, many new E3 ligands have been published recently, confirming the druggability of E3 ligases. This review summarises recent data on E3 ligases and highlights the challenges in developing these molecules into efficient PROTACs rivalling the established degrader systems.
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Affiliation(s)
- Rahman Shah Zaib Saleem
- Department of Chemistry & Chemical Engineering, SBA School of Sciences & Engineering, LUMS, Pakistan
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.
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16
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Lim VJY, Gerber HD, Schihada H, Trinh VT, Hilger D, Vázquez O, Kolb P. A virtual library of small molecules mimicking dipeptides. Arch Pharm (Weinheim) 2024; 357:e2300636. [PMID: 38332463 DOI: 10.1002/ardp.202300636] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
Virtual combinatorial libraries are prevalent in drug discovery due to improvements in the prediction of synthetic reactions that can be performed. This has gone hand in hand with the development of virtual screening capabilities to effectively screen the large chemical spaces spanned by exhaustive enumeration of reaction products. In this study, we generated a small-molecule dipeptide mimic library to target proteins binding small peptides. The library was created based on the general idea of peptide synthesis, that is, amino acid mimics were reacted in silico to form the dipeptide mimics, yielding 2,036,819 unique compounds. After docking calculations, two compounds from the library were synthesized and tested against WD repeat-containing protein 5 (WDR5) and histamine receptors H1-H4 to evaluate whether these molecules are viable in assays. The compounds showed the highest potency at the histamine H3 receptor, with Ki values in the two-digit micromolar range.
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Affiliation(s)
- Victor Jun Yu Lim
- Pharmaceutical Chemistry, Department of Pharmacy, University of Marburg, Marburg, Germany
| | - Hans-Dieter Gerber
- Pharmaceutical Chemistry, Department of Pharmacy, University of Marburg, Marburg, Germany
| | - Hannes Schihada
- Pharmaceutical Chemistry, Department of Pharmacy, University of Marburg, Marburg, Germany
| | - Van Tuan Trinh
- Chemical Biology, Department of Chemistry, University of Marburg, Marburg, Germany
| | - Daniel Hilger
- Pharmaceutical Chemistry, Department of Pharmacy, University of Marburg, Marburg, Germany
| | - Olalla Vázquez
- Chemical Biology, Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
| | - Peter Kolb
- Pharmaceutical Chemistry, Department of Pharmacy, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, Germany
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17
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Zheng BX, Long W, Zheng W, Zeng Y, Guo XC, Chan KH, She MT, Leung ASL, Lu YJ, Wong WL. Mitochondria-Selective Dicationic Small-Molecule Ligand Targeting G-Quadruplex Structures for Human Colorectal Cancer Therapy. J Med Chem 2024; 67:6292-6312. [PMID: 38624086 DOI: 10.1021/acs.jmedchem.3c02240] [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: 04/17/2024]
Abstract
Mitochondria are important drug targets for anticancer and other disease therapies. Certain human mitochondrial DNA sequences capable of forming G-quadruplex structures (G4s) are emerging drug targets of small molecules. Despite some mitochondria-selective ligands being reported for drug delivery against cancers, the ligand design is mostly limited to the triphenylphosphonium scaffold. The ligand designed with lipophilic small-sized scaffolds bearing multipositive charges targeting the unique feature of high mitochondrial membrane potential (MMP) is lacking and most mitochondria-selective ligands are not G4-targeting. Herein, we report a new small-sized dicationic lipophilic ligand to target MMP and mitochondrial DNA G4s to enhance drug delivery for anticancer. The ligand showed marked alteration of mitochondrial gene expression and substantial induction of ROS production, mitochondrial dysfunction, DNA damage, cellular senescence, and apoptosis. The ligand also exhibited high anticancer activity against HCT116 cancer cells (IC50, 3.4 μM) and high antitumor efficacy in the HCT116 tumor xenograft mouse model (∼70% tumor weight reduction).
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Affiliation(s)
- Bo-Xin Zheng
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Wei Long
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Wende Zheng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Yaoxun Zeng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Xiao-Chun Guo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Ka-Hin Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Meng-Ting She
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
| | - Alan Siu-Lun Leung
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518057, P. R. China
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18
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Zhang J, Liu J, Zhang G, He X, Xiong F, Fan X, Li Y, Li Y. Synthesis of Diacylhydrazine Derivatives Based on Tetrazole-Focused DNA-Encoded Library. Org Lett 2024; 26:1094-1099. [PMID: 38277138 DOI: 10.1021/acs.orglett.3c04374] [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: 01/27/2024]
Abstract
Utilizing already existing DNA-encoded libraries (DELs) for the generation of a distinct DEL represents an expedited strategy for expanding the chemical space. Herein, we leverage the unique photoreactivity of tetrazoles to synthesize diacylhydrazines on DNA. Widely available carboxylic acids serving as building blocks were employed under the mild photomediated reaction conditions, affording diverse DNA-conjugated diacylhydrazines. This methodology also demonstrates robustness in DEL-compatible synthesis and facilitates the preparation of oligonucleotide-based chemical probes.
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Affiliation(s)
- Juan Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jinlu Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xun He
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Feng Xiong
- Shenzhen Innovation Center for Small Molecule Drug Discovery Co., Ltd., Shenzhen 518110, China
| | - Xiaohong Fan
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing 404100, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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19
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Testa C, Papini AM, Zeidler R, Vullo D, Carta F, Supuran CT, Rovero P. First studies on tumor associated carbonic anhydrases IX and XII monoclonal antibodies conjugated to small molecule inhibitors. J Enzyme Inhib Med Chem 2022; 37:592-596. [PMID: 35057692 PMCID: PMC8786240 DOI: 10.1080/14756366.2021.2004593] [Citation(s) in RCA: 6] [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: 10/13/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
We report for the first time Antibody-Drug-Conjugates (ADCs) containing human (h) Carbonic Anhydrase (CA; EC 4.2.1.1) directed Monoclonal Antibodies (MAbs) linked to low molecular weight inhibitors of the same enzymes by means of hydrophilic peptide spacers. In agreement with the incorporated CA directed MAb fragments, in vitro inhibition data of the obtained ADCs showed sub-nanomolar KI values for the tumour associated CAs IX and XII which were up to 10-fold more potent when compared to the corresponding unconjugated MAbs. In addition, the introduction of the CA inhibitor (CAI) benzenesulfonamide allowed the ADCs to potently inhibit the housekeeping tumoral off-target human CA II isoform. Such results are supporting the definition of an unprecedented reported class of ADCs able to hit simultaneously multiple hCAs physiologically cooperative in maintaining altered cellular metabolic pathways, and therefore ideal for the treatment of chronic diseases such as cancers and inflammation diseases.
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Affiliation(s)
- Chiara Testa
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology”, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology”, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Reinhard Zeidler
- Research Group Therapeutic Antibodies, Helmholtz Centre Munich German Research Centre for Environmental Health, Munich, Germany
- Department of Otorhinolaryngology, Klinikum der Universitaet, Munich, Germany
| | - Daniela Vullo
- NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, via Ugo Schff 6, Sesto Fiorentino (Florence), 50019Italy
| | - Fabrizio Carta
- NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, via Ugo Schff 6, Sesto Fiorentino (Florence), 50019Italy
| | - Claudiu T. Supuran
- NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, via Ugo Schff 6, Sesto Fiorentino (Florence), 50019Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology”, Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
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20
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Wang Q, Wang L, Zhang Y, Zhang X, Zhang L, Shang W, Bai F. Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications. J Med Chem 2022; 65:2827-2835. [PMID: 34415156 PMCID: PMC8409148 DOI: 10.1021/acs.jmedchem.1c00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/02/2021] [Indexed: 12/21/2022]
Abstract
The receptor recognition of the novel coronavirus SARS-CoV-2 relies on the "down-to-up" conformational change in the receptor-binding domain (RBD) of the spike (S) protein. Therefore, understanding the process of this change at the molecular level facilitates the design of therapeutic agents. With the help of coarse-grained molecular dynamic simulations, we provide evidence showing that the conformational dynamics of the S protein are globally cooperative. Importantly, an allosteric path was discovered that correlates the motion of the RBD with the motion of the junction between the subdomain 1 (SD1) and the subdomain 2 (SD2) of the S protein. Building on this finding, we designed non-RBD binding modulators to inhibit SARS-CoV-2 by prohibiting the conformational change of the S protein. Their inhibition effect and function stages at inhibiting SARS-CoV-2 were evaluated experimentally. In summary, our studies establish a molecular basis for future therapeutic agent design through allosteric effects.
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Affiliation(s)
- Qian Wang
- Hefei National Laboratory for Physical Sciences at the
Microscale and Department of Physics, University of Science and Technology of
China, Hefei, Anhui 230026, China
| | - Lin Wang
- School of Life Science and Technology and Shanghai
Institute for Advanced Immunochemical Studies, ShanghaiTech
University, Shanghai 201210, China
| | - Yumin Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071,
China
| | - XiangLei Zhang
- School of Life Science and Technology and Shanghai
Institute for Advanced Immunochemical Studies, ShanghaiTech
University, Shanghai 201210, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071,
China
| | - Weijuan Shang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071,
China
| | - Fang Bai
- School of Life Science and Technology and Shanghai
Institute for Advanced Immunochemical Studies, ShanghaiTech
University, Shanghai 201210, China
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21
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Basu S, Middya S, Banerjee M, Ghosh R, Pryde DC, Yadav DB, Shrivastava R, Surya A. The discovery of potent small molecule cyclic urea activators of STING. Eur J Med Chem 2022; 229:114087. [PMID: 34998056 DOI: 10.1016/j.ejmech.2021.114087] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/25/2021] [Accepted: 12/26/2021] [Indexed: 01/08/2023]
Abstract
STING mediates innate immune responses that are triggered by the presence of cytosolic DNA. Activation of STING to boost antigen recognition is a therapeutic modality that is currently being tested in cancer patients using nucleic-acid based macrocyclic STING ligands. We describe here the discovery of 3,4-dihydroquinazolin-2(1H)-one based 6,6-bicyclic heterocyclic agonists of human STING that activate all known human variants of STING with high potency.
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Affiliation(s)
- Sourav Basu
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - Sandip Middya
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - Monali Banerjee
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - Rajib Ghosh
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - David C Pryde
- Curadev Pharma Ltd., Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent, CT13 9ND, UK
| | - Dharmendra B Yadav
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - Ritesh Shrivastava
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India
| | - Arjun Surya
- Curadev Pharma Pvt. Ltd., B-87, Sector 83, Noida, 201305, Uttar Pradesh, India.
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22
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Ji H, Wang W, Li X, Han X, Zhang X, Wang J, Liu C, Huang L, Gao W. Natural Small Molecules Enabled Efficient Immunotherapy through Supramolecular Self-Assembly in P53-Mutated Colorectal Cancer. ACS Appl Mater Interfaces 2022; 14:2464-2477. [PMID: 35045602 DOI: 10.1021/acsami.1c16737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanomedicine, constructed from therapeutics, presents an advantage in drug delivery for cancer therapies. However, nanocarrier-based treatment systems have problems such as interbatch variability, multicomponent complexity, poor drug delivery, and carrier-related toxicity. To solve these issues, the natural molecule honokiol (HK), an anticancer agent in a phase I clinical trial (CTR20170822), was used to form a self-assembly nanoparticle (SA) through hydrogen bonding and hydrophobicity. The preparation of SA needs no molecular precursors or excipients in aqueous solution, and 100% drug-loaded SA exhibited superior tumor-targeting ability due to the enhanced permeability and retention (EPR) effect. Moreover, SA significantly enhanced the antitumor immunity relative to free HK, and the mechanism has notable selectivity to the p53 pathway. Furthermore, SA exhibited excellent physiological stability and inappreciable toxicity. Taken together, this supramolecular self-assembly strategy provides a safe and "molecular economy" model for rational design of clinical therapies and is expected to promote targeted therapy of HK, especially in colorectal cancer patients with obvious p53 status.
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Affiliation(s)
- Haixia Ji
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Wenzhe Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Xia Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Xiaoying Han
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Xinyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
| | - Changxiao Liu
- Tianjin Pharmaceutical Research Institute, Tianjin 300193, P.R. China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P.R. China
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23
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Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Identification and validation of selective deubiquitinase inhibitors. Cell Chem Biol 2021; 28:1758-1771.e13. [PMID: 34129829 PMCID: PMC9473745 DOI: 10.1016/j.chembiol.2021.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/18/2020] [Revised: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a class of isopeptidases that regulate ubiquitin dynamics through catalytic cleavage of ubiquitin from protein substrates and ubiquitin precursors. Despite growing interest in DUB biological function and potential as therapeutic targets, few selective small-molecule inhibitors and no approved drugs currently exist. To identify chemical scaffolds targeting specific DUBs and establish a broader framework for future inhibitor development across the gene family, we performed high-throughput screening of a chemically diverse small-molecule library against eight different DUBs, spanning three well-characterized DUB families. Promising hit compounds were validated in a series of counter-screens and orthogonal assays, as well as further assessed for selectivity across expanded panels of DUBs. Through these efforts, we have identified multiple highly selective DUB inhibitors and developed a roadmap for rapidly identifying and validating selective inhibitors of related enzymes.
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Affiliation(s)
- Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dominick Casalena
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Douglas Auld
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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24
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Kim T, Morshed MN, Londhe AM, Lim JW, Lee HE, Cho S, Cho SJ, Hwang H, Lim SM, Lee JY, Lee J, Pae AN. The translocator protein ligands as mitochondrial functional modulators for the potential anti-Alzheimer agents. J Enzyme Inhib Med Chem 2021; 36:831-846. [PMID: 33752569 PMCID: PMC7996082 DOI: 10.1080/14756366.2021.1900158] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/06/2022] Open
Abstract
Small molecule modulators of mitochondrial function have been attracted much attention in recent years due to their potential therapeutic applications for neurodegenerative diseases. The mitochondrial translocator protein (TSPO) is a promising target for such compounds, given its involvement in the formation of the mitochondrial permeability transition pore in response to mitochondrial stress. In this study, we performed a ligand-based pharmacophore design and virtual screening, and identified a potent hit compound, 7 (VH34) as a TSPO ligand. After validating its biological activity against amyloid-β (Aβ) induced mitochondrial dysfunction and in acute and transgenic Alzheimer's disease (AD) model mice, we developed a library of analogs, and we found two most active compounds, 31 and 44, which restored the mitochondrial membrane potential, ATP production, and cell viability under Aβ-induced mitochondrial toxicity. These compounds recovered learning and memory function in acute AD model mice with improved pharmacokinetic properties.
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Affiliation(s)
- TaeHun Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Mohammad N. Morshed
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
- Center for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Ashwini M. Londhe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Ji W. Lim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Ha E. Lee
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Suengmok Cho
- Department of Food Science and Technology, Pukyong National University, Pusan, Republic of Korea
| | - Sung J. Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, Republic of Korea
| | - Hayoung Hwang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, Republic of Korea
| | - Sang M. Lim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Jae Y. Lee
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science, Sungshin University, Seoul, Republic of Korea
| | - Ae N. Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
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25
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Ding L, Wei F, Wang N, Sun Y, Wang Q, Fan X, Qi L, Wang S. Tertiary sulphonamide derivatives as dual acting small molecules that inhibit LSD1 and suppress tubulin polymerisation against liver cancer. J Enzyme Inhib Med Chem 2021; 36:1563-1572. [PMID: 34281464 PMCID: PMC8291071 DOI: 10.1080/14756366.2021.1917564] [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: 02/07/2021] [Revised: 03/11/2021] [Accepted: 04/01/2021] [Indexed: 01/14/2023] Open
Abstract
A series of tertiary sulphonamide derivatives were synthesised and evaluated for their antiproliferative activity against liver cancer cell lines (SNU-475, HepG-2, and Bel-7402). Among these tertiary sulphonamides, compound 17a displayed the best anti-liver cancer activity against Bel-7402 cells with an IC50 value of 0.32 μM. Compound 17a could effectively inhibit tubulin polymerisation with an IC50 value of 1.27 μM. Meanwhile, it selectively suppressed LSD1 with an IC50 value of 63 nM. It also concentration-dependently inhibited migration against Bel-7402 cells. Importantly, tertiary sulphonamide 17a exhibited the potent antitumor activity in vivo. All these findings revealed that compound 17a might be a tertiary sulphonamide-based dual inhibitor of tubulin polymerisation and LSD1 to treat liver cancer.
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Affiliation(s)
- Lijuan Ding
- The First Hospital of Jilin University, Changchun, China
| | - Feng Wei
- The First Hospital of Jilin University, Changchun, China
| | - Nanya Wang
- The First Hospital of Jilin University, Changchun, China
| | - Yue Sun
- The First Hospital of Jilin University, Changchun, China
| | - Qiang Wang
- The First Hospital of Jilin University, Changchun, China
| | - Xia Fan
- The First Hospital of Jilin University, Changchun, China
| | - Ling Qi
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
| | - Shudong Wang
- The First Hospital of Jilin University, Changchun, China
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26
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Abstract
Cyclin-dependent kinase 9 (CDK9) plays a vital role in transcription through regulation of short-lived anti-apoptotic genes required for cancer cell survival. Therefore, targeting CDK9 with small molecule inhibitors has emerged as a potential cancer therapy. This article reviews the most recent CDK9 patent literature (2012-2020) related to small molecule inhibitors in cancer along with their selectivity profile and biological results in preclinical studies.
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Affiliation(s)
- Aisha Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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27
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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.
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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.
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28
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Abstract
Chromosome region maintenance 1 (CRM1) is a major nuclear export receptor protein and contributes to cell homeostasis by mediating the transport of cargo from the nucleus to the cytoplasm. CRM1 is a therapeutic target comprised of several tumor types, including osteosarcoma, multiple myeloma, gliomas, and pancreatic cancer. In the past decade, dozens of CRM1 inhibitors have been discovered and developed, including KPT-330, which received FDA approval for multiple myeloma (MM) and diffuse large B-cell lymphoma (DLBCL) in 2019 and 2020, respectively. This review summarizes the biological functions of CRM1, the current understanding of the role CRM1 plays in cancer, the discovery of CRM1 small-molecule inhibitors, preclinical and clinical studies on KPT-330, and other recently developed inhibitors. A new CRM1 inhibition mechanism and structural dynamics are discussed. Through this review, we hope to guide the future design and optimization of CRM1 inhibitors.
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Affiliation(s)
- Song Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qingxiang Sun
- State Key Laboratory of Biotherapy, Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
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29
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Li XP, Harijan RK, Cao B, Kahn JN, Pierce M, Tsymbal AM, Roberge JY, Augeri D, Tumer NE. Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2021; 64:15334-15348. [PMID: 34648707 PMCID: PMC10704857 DOI: 10.1021/acs.jmedchem.1c01370] [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] [Indexed: 11/30/2022]
Abstract
Ricin toxin A subunit (RTA) is the catalytic subunit of ricin, which depurinates an adenine from the sarcin/ricin loop in eukaryotic ribosomes. There are no approved inhibitors against ricin. We used a new strategy to disrupt RTA-ribosome interactions by fragment screening using surface plasmon resonance. Here, using a structure-guided approach, we improved the affinity and inhibitory activity of small-molecular-weight lead compounds and obtained improved compounds with over an order of magnitude higher efficiency. Four advanced compounds were characterized by X-ray crystallography. They bind at the RTA-ribosome binding site as the original compound but in a distinctive manner. These inhibitors bind remotely from the catalytic site and cause local conformational changes with no alteration of the catalytic site geometry. Yet they inhibit depurination by ricin holotoxin and inhibit the cytotoxicity of ricin in mammalian cells. They are the first agents that protect against ricin holotoxin by acting directly on RTA.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Bin Cao
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jennifer N Kahn
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - David Augeri
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
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30
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Xie Z, Xiang C, Li X, Fan C, Chen T, Liu M, Ma Y, Bai F, Tang W, Hu Y. Discovery of Potent Antiallergic Agents Based on an o-Aminopyridinyl Alkynyl Scaffold. J Med Chem 2021; 64:13588-13603. [PMID: 34476950 DOI: 10.1021/acs.jmedchem.1c00976] [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: 11/29/2022]
Abstract
Effective therapeutic agents are highly desired for immune-mediated allergic diseases. Herein, we report the design, synthesis, and structure-activity relationship of an o-aminopyridinyl alkyne series as novel orally bioavailable antiallergic agents, which was identified through phenotypic screening. Compound optimization yielded a highly potent compound 36, which effectively suppressed mast cell degranulation in a dose-dependent manner (IC50, 2.54 nM for RBL-2H3 cells; 48.28 nM for peritoneal mast cells (PMCs)) with a good therapeutic index. It also regulated the activation of FcεRI-mediated downstream signaling proteins in IgE/Ag-stimulated RBL-2H3 cells. In addition, 36 exhibited excellent in vivo pharmacokinetic properties and antiallergic efficacy in both passive systemic anaphylaxis (PSA) and house dust mite (HDM)-induced murine models of pulmonary allergic inflammation. Furthermore, preliminary analysis of the kinases profile identified Src-family kinases as potential targets for 36. Compound 36 may serve as a new valuable lead compound for future antiallergic drug discovery.
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Affiliation(s)
- Zhicheng Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Caigui Xiang
- Laboratory of Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xin Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Chen Fan
- Laboratory of Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Taiwen Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Moting Liu
- Laboratory of Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanjie Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Fang Bai
- Laboratory of Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wei Tang
- Laboratory of Immunopharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Youhong Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No. 555 Zu-Chong-Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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Signorello MG, Rapetti F, Meta E, Sidibè A, Bruno O, Brullo C. New Series of Pyrazoles and Imidazo-Pyrazoles Targeting Different Cancer and Inflammation Pathways. Molecules 2021; 26:molecules26195735. [PMID: 34641279 PMCID: PMC8510017 DOI: 10.3390/molecules26195735] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
(1) Background: different previously synthesized pyrazoles and imidazo-pyrazoles showed interesting anti-angiogenic action, being able to interfere with ERK1/2, AKT and p38MAPK phosphorylation in different manners and with different potency; (2) Methods: here, a new small compound library, endowed with the same differently decorated chemical scaffolds, has been synthetized to obtain new agents able to inhibit different pathways involved in inflammation, cancer and human platelet aggregation. (3) Results: most of the new synthesized derivatives resulted able to block ROS production, platelet aggregation and p38MAPK phosphorylation both in platelets and Human Umbilical Vein Endothelial cells (HUVEC). This paves the way for the development of new agents with anti-angiogenic activity.
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Affiliation(s)
- Maria Grazia Signorello
- Biochemistry Lab., Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy;
| | - Federica Rapetti
- Section of Medicinal Chemistry, Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy; (F.R.); (O.B.)
| | - Elda Meta
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, Vlaams Instituut Voor Biotechnologie, 3000 Leuven, Belgium;
| | - Adama Sidibè
- Department of Cell Physiology and Metabolism, University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland;
| | - Olga Bruno
- Section of Medicinal Chemistry, Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy; (F.R.); (O.B.)
| | - Chiara Brullo
- Section of Medicinal Chemistry, Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, I-16132 Genova, Italy; (F.R.); (O.B.)
- Correspondence: ; Tel.: +39-010-353-8368
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32
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Walter I, Adam S, Gentilini MV, Kany AM, Brengel C, Thomann A, Sparwasser T, Köhnke J, Hartmann RW. Structure-Activity Relationship and Mode-Of-Action Studies Highlight 1-(4-Biphenylylmethyl)-1H-imidazole-Derived Small Molecules as Potent CYP121 Inhibitors. ChemMedChem 2021; 16:2786-2801. [PMID: 34010508 PMCID: PMC8519103 DOI: 10.1002/cmdc.202100283] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Indexed: 11/29/2022]
Abstract
CYP121 of Mycobacterium tuberculosis (Mtb) is an essential target for the development of novel potent drugs against tuberculosis (TB). Besides known antifungal azoles, further compounds of the azole class were recently identified as CYP121 inhibitors with antimycobacterial activity. Herein, we report the screening of a similarity-oriented library based on the former hit compound, the evaluation of affinity toward CYP121, and activity against M. bovis BCG. The results enabled a comprehensive SAR study, which was extended through the synthesis of promising compounds and led to the identification of favorable features for affinity and/or activity and hit compounds with 2.7-fold improved potency. Mode of action studies show that the hit compounds inhibit substrate conversion and highlighted CYP121 as the main antimycobacterial target of our compounds. Exemplified complex crystal structures of CYP121 with three inhibitors reveal a common binding site. Engaging in both hydrophobic interactions as well as hydrogen bonding to the sixth iron ligand, our compounds block a solvent channel leading to the active site heme. Additionally, we report the first CYP inhibitors that are able to reduce the intracellular replication of M. bovis BCG in macrophages, emphasizing their potential as future drug candidates against TB.
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Affiliation(s)
- Isabell Walter
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Sebastian Adam
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Maria Virginia Gentilini
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Andreas M. Kany
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Christian Brengel
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Andreas Thomann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
| | - Tim Sparwasser
- Institute of Infection Immunology, TWINCORECentre for Experimental and Clinical Infection ResearchA Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI)HannoverGermany
| | - Jesko Köhnke
- Workgroup Structural Biology of Biosynthetic EnzymesHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland UniversitySaarbrückenGermany
| | - Rolf W. Hartmann
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research SaarlandCampus E8.166123SaarbrückenGermany
- Department of PharmacyPharmaceutical and Medicinal ChemistrySaarland UniversityCampus C2.366123SaarbrückenGermany
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Cuzzucoli Crucitti V, Contreas L, Taresco V, Howard SC, Dundas AA, Limo MJ, Nisisako T, Williams PM, Williams P, Alexander MR, Wildman RD, Muir BW, Irvine DJ. Generation and Characterization of a Library of Novel Biologically Active Functional Surfactants (Surfmers) Using Combined High-Throughput Methods. ACS Appl Mater Interfaces 2021; 13:43290-43300. [PMID: 34464079 DOI: 10.1021/acsami.1c08662] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report the first successful combination of three distinct high-throughput techniques to deliver the accelerated design, synthesis, and property screening of a library of novel, bio-instructive, polymeric, comb-graft surfactants. These three-dimensional, surface-active materials were successfully used to control the surface properties of particles by forming a unimolecular deep layer on the surface of the particles via microfluidic processing. This strategy deliberately utilizes the surfactant to both create the stable particles and deliver a desired cell-instructive behavior. Therefore, these specifically designed, highly functional surfactants are critical to promoting a desired cell response. This library contained surfactants constructed from 20 molecularly distinct (meth)acrylic monomers, which had been pre-identified by HT screening to exhibit specific, varied, and desirable bacterial biofilm inhibitory responses. The surfactant's self-assembly properties in water were assessed by developing a novel, fully automated, HT method to determine the critical aggregation concentration. These values were used as the input data to a computational-based evaluation of the key molecular descriptors that dictated aggregation behavior. Thus, this combination of HT techniques facilitated the rapid design, generation, and evaluation of further novel, highly functional, cell-instructive surfaces by application of designed surfactants possessing complex molecular architectures.
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Affiliation(s)
- Valentina Cuzzucoli Crucitti
- Centre for Additive Manufacturing and Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD U.K
| | - Leonardo Contreas
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD U.K
| | - Vincenzo Taresco
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD U.K
| | | | - Adam A Dundas
- Centre for Additive Manufacturing and Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD U.K
| | - Marion J Limo
- Interface and Surface Analysis Centre, University of Nottingham, Nottingham, NG7 2RD U.K
| | - Takasi Nisisako
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Philip M Williams
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD U.K
| | - Paul Williams
- Biodiscovery Institute, National Biofilms Innovation Centre and School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD U.K
| | | | - Ricky D Wildman
- Centre for Additive Manufacturing and Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD U.K
| | | | - Derek J Irvine
- Centre for Additive Manufacturing and Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, Nottingham, NG7 2RD U.K
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Yıldız M, Bayrak N, Yıldırım H, Mataracı-Kara E, Shilkar D, Jayaprakash V, Fatih Tuyun A. Exploration of brominated Plastoquinone analogs: Discovery and structure-activity relationships of small antimicrobial lead molecules. Bioorg Chem 2021; 116:105316. [PMID: 34509796 DOI: 10.1016/j.bioorg.2021.105316] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/04/2021] [Accepted: 08/28/2021] [Indexed: 11/19/2022]
Abstract
In the fight with the antimicrobial resistance, our continuous effort to find quinone analogs with higher inhibitory activity has previously led us to the promising Plastoquinone analogs. The 1,4-quinone moiety substituted with alkoxy substituent(s) plays an important role in the field of antimicrobial and anticancer drug discovery and development. Thus, an extensive series of 1,4-quinones, substituted in different positions with a variety of alkoxy substituents, has been designed, synthesized, and evaluated for their antimicrobial activity. Here, we describe the synthesis of brominated Plastoquinone analogs (BrPQ1-15) based on the dimethyl-1,4-quinone scaffold by employing two different paths. We also present here the in vitro antimicrobial activity of these analogs (BrPQ1-15) against a panel of pathogenic organisms. These studies resulted in several new selective antibacterial inhibitors and gave valuable insights into the structure-activity relationships. Among all the analogs studied, two analogs BrPQ1 with a methoxy substituent and BrPQ14 with a cyclic dioxy stand out as the most promising antibacterial molecules against Staphylococcus aureus and Staphylococcus epidermidis. Afterwards, two analogs were selected for a further investigation for biofilm evaluation. Finally, molecular docking studies for BrPQ1 and BrPQ14 with probable target S. aureus PNPase (5XEX) and predictive ADMET studies were also carried out.
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Affiliation(s)
- Mahmut Yıldız
- Department of Chemistry, Gebze Technical University, Gebze 41400, Kocaeli, Turkey
| | - Nilüfer Bayrak
- Department of Chemistry, Engineering Faculty, Istanbul University-Cerrahpasa, Avcilar 34320, Istanbul, Turkey
| | - Hatice Yıldırım
- Department of Chemistry, Engineering Faculty, Istanbul University-Cerrahpasa, Avcilar 34320, Istanbul, Turkey
| | - Emel Mataracı-Kara
- Department of Pharmaceutical Microbiology, Pharmacy Faculty, Istanbul University, Beyazit 34116, Istanbul, Turkey
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Amaç Fatih Tuyun
- Department of Chemistry, Faculty of Science, Istanbul University, Fatih, Istanbul, Turkey.
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35
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Elkamhawy A, Ammar UM, Paik S, Abdellattif MH, Elsherbeny MH, Lee K, Roh EJ. Scaffold Repurposing of In-House Small Molecule Candidates Leads to Discovery of First-in-Class CDK-1/HER-2 Dual Inhibitors: In Vitro and In Silico Screening. Molecules 2021; 26:molecules26175324. [PMID: 34500757 PMCID: PMC8433807 DOI: 10.3390/molecules26175324] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, multitargeted drugs are considered a potential approach in treating cancer. In this study, twelve in-house indole-based derivatives were preliminary evaluated for their inhibitory activities over VEGFR-2, CDK-1/cyclin B and HER-2. Compound 15l showed the most inhibitory activities among the tested derivatives over CDK-1/cyclin B and HER-2. Compound 15l was tested for its selectivity in a small kinase panel. It showed dual selectivity for CDK-1/cyclin B and HER-2. Moreover, in vitro cytotoxicity assay was assessed for the selected series against nine NCI cell lines. Compound 15l showed the most potent inhibitory activities among the tested compounds. A deep in silico molecular docking study was conducted for compound 15l to identify the possible binding modes into CDK-1/cyclin B and HER-2. The docking results revealed that compound 15l displayed interesting binding modes with the key amino acids in the binding sites of both kinases. In vitro and in silico studies demonstrate the indole-based derivative 15l as a selective dual CDK-1 and HER-2 inhibitor. This emphasizes a new challenge in drug development strategies and signals a significant milestone for further structural and molecular optimization of these indole-based derivatives in order to achieve a drug-like property.
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Affiliation(s)
- Ahmed Elkamhawy
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Korea
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Correspondence: or (A.E.); (K.L.); (E.J.R.)
| | - Usama M. Ammar
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0NR, UK;
| | - Sora Paik
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (S.P.); (M.H.E.)
| | - Magda H. Abdellattif
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Mohamed H. Elsherbeny
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (S.P.); (M.H.E.)
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12566, Egypt
| | - Kyeong Lee
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Korea
- Correspondence: or (A.E.); (K.L.); (E.J.R.)
| | - Eun Joo Roh
- Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea; (S.P.); (M.H.E.)
- Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea
- Correspondence: or (A.E.); (K.L.); (E.J.R.)
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36
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Li Y, Zhang Y, Wu X, Gao Y, Guo J, Tian Y, Lin Z, Wang X. Discovery of natural 15-LOX small molecule inhibitors from Chinese herbal medicine using virtual Screening, biological evaluation and molecular dynamics studies. Bioorg Chem 2021; 115:105197. [PMID: 34426159 DOI: 10.1016/j.bioorg.2021.105197] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Chinese herbal medicines (CHM) are frequently used to treat different types of inflammatory diseases and 15-Lipoxygenase (15-LOX) is a critical target enzyme for treating various inflammatory diseases. In this study, natural 15-LOX inhibitors were identified in CHM using an approach of virtual screening combined with the biological assays. First, an in-house Chinese medicine database containing 360 compounds was screened using a virtual screening approach based on pharmacophore and molecular docking to uncover several novel potential 15-LOX inhibitors. Secondly, the inhibitory effect of virtual screening hits against the 15-LOX enzyme was validated in an in vitro enzyme inhibition assay. Then, a tumor necrosis factor-α (TNF-α) release assay was carried out to explore the anti-inflammatory response of the active compounds. Furthermore, molecular dynamics (MD) simulation and binding free energy calculation were applied to analyze the process of inhibitors binding and also compared the mode of binding of the inhibitors by using the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) method. Finally, licochalcone B and eriodictyol were confirmed as inhibitors of the 15-LOX enzyme with IC50 values of 9.67 and 18.99 μM, respectively. In vitro cell-based assay showed that licochalcone B and eriodictyol inhibited the release of TNF-α factor in RAW264.7 cells stimulated by lipopolysaccharides (LPS) in a dose-dependent manner. Molecular dynamics and binding free energy analysis showed that the two 15-LOX-ligand systems immediately attained equilibrium with almost 1 Å fluctuation, the calculated binding free energies were found around -18.89 and -12.96 kcal/mol for licochalcone B and eriodictyol, respectively. Thr412, Arg415, Val420, Thr429, Ile602 and Trp606 were the main amino acid residues for the inhibition of 15-LOX enzyme activity. The current study confirms that licochalcone B and eriodictyol are 15-LOX inhibitors and can suppress the release of the TNF-α factor in RAW264.7 cells stimulated by LPS, thus providing a basis for the follow-up research and development for 15-LOX inhibitors.
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Affiliation(s)
- Yatong Li
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine, School of Pharmacy, Ministry of Education, Minzu University of China, Haidian District, Beijing 100081, China
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Junfang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yulang Tian
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ziyue Lin
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China.
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37
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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.
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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
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38
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Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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39
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Parsons WH, Rutland NT, Crainic JA, Cardozo JM, Chow AS, Andrews CL, Sheehan BK. Development of succinimide-based inhibitors for the mitochondrial rhomboid protease PARL. Bioorg Med Chem Lett 2021; 49:128290. [PMID: 34311087 DOI: 10.1016/j.bmcl.2021.128290] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
While the biochemistry of rhomboid proteases has been extensively studied since their discovery two decades ago, efforts to define the physiological roles of these enzymes are ongoing and would benefit from chemical probes that can be used to manipulate the functions of these proteins in their native settings. Here, we describe the use of activity-based protein profiling (ABPP) technology to conduct a targeted screen for small-molecule inhibitors of the mitochondrial rhomboid protease PARL, which plays a critical role in regulating mitophagy and cell death. We synthesized a series of succinimide-containing sulfonyl esters and sulfonamides and discovered that these compounds serve as inhibitors of PARL with the most potent sulfonamides having submicromolar affinity for the enzyme. A counterscreen against the bacterial rhomboid protease GlpG demonstrates that several of these compounds display selectivity for PARL over GlpG by as much as two orders of magnitude. Both the sulfonyl ester and sulfonamide scaffolds exhibit reversible binding and are able to engage PARL in mammalian cells. Collectively, our findings provide encouraging precedent for the development of PARL-selective inhibitors and establish N-[(arylsulfonyl)oxy]succinimides and N-arylsulfonylsuccinimides as new molecular scaffolds for inhibiting members of the rhomboid protease family.
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Affiliation(s)
- William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States.
| | - Nicholas T Rutland
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Jennifer A Crainic
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Joaquin M Cardozo
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Alyssa S Chow
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Charlotte L Andrews
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Brendan K Sheehan
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
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40
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Chapagai D, Ramamoorthy G, Varghese J, Nurmemmedov E, McInnes C, Wyatt MD. Nonpeptidic, Polo-Box Domain-Targeted Inhibitors of PLK1 Block Kinase Activity, Induce Its Degradation and Target-Resistant Cells. J Med Chem 2021; 64:9916-9925. [PMID: 34210138 PMCID: PMC10451095 DOI: 10.1021/acs.jmedchem.1c00133] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PLK1, polo-like kinase 1, is a central player regulating mitosis. Inhibition of the subcellular localization and kinase activity of PLK1 through the PBD, polo-box domain, is a viable alternative to ATP-competitive inhibitors, for which the development of resistance and inhibition of related PLK family members are concerns. We describe novel nonpeptidic PBD-binding inhibitors, termed abbapolins, identified through successful application of the REPLACE strategy and demonstrate their potent antiproliferative activity in prostate tumors and other cell lines. Furthermore, abbapolins show PLK1-specific binding and inhibitory activity, as measured by a cellular thermal shift assay and an ability to block phosphorylation of TCTP, a validated target of PLK1-mediated kinase activity. Additional evidence for engagement of PLK1 was obtained through the unique observation that abbapolins induce PLK1 degradation in a manner that closely matches antiproliferative activity. Moreover, abbapolins demonstrate antiproliferative activity in cells that are dramatically resistant to ATP-competitive PLK1 inhibitors.
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Affiliation(s)
- Danda Chapagai
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gurusankar Ramamoorthy
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Jessy Varghese
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute and Pacific Neuroscience Institute at Providence Saint John's Health Center, Santa Monica, California 90404-2312, United States
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Michael D Wyatt
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, South Carolina 29208, United States
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Shukla S, Ying W, Gray F, Yao Y, Simes ML, Zhao Q, Miao H, Cho HJ, González-Alonso P, Winkler A, Lund G, Purohit T, Kim E, Zhang X, Ray JM, He S, Nikolaidis C, Ndoj J, Wang J, Jaremko Ł, Jaremko M, Ryan RJH, Guzman ML, Grembecka J, Cierpicki T. Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Nat Chem Biol 2021; 17:784-793. [PMID: 34155404 PMCID: PMC8238916 DOI: 10.1038/s41589-021-00815-5] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-modifying complex that monoubiquitinates histone H2A and is involved in maintaining the repressed chromatin state. Emerging evidence suggests PRC1 activity in various cancers, rationalizing the need for small-molecule inhibitors with well-defined mechanisms of action. Here, we describe the development of compounds that directly bind to RING1B-BMI1, the heterodimeric complex constituting the E3 ligase activity of PRC1. These compounds block the association of RING1B-BMI1 with chromatin and inhibit H2A ubiquitination. Structural studies demonstrate that these inhibitors bind to RING1B by inducing the formation of a hydrophobic pocket in the RING domain. Our PRC1 inhibitor, RB-3, decreases the global level of H2A ubiquitination and induces differentiation in leukemia cell lines and primary acute myeloid leukemia (AML) samples. In summary, we demonstrate that targeting the PRC1 RING domain with small molecules is feasible, and RB-3 represents a valuable chemical tool to study PRC1 biology.
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Affiliation(s)
- Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Weijiang Ying
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Felicia Gray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yiwu Yao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Miranda L Simes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Qingjie Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Alyssa Winkler
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - George Lund
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - EunGi Kim
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaotian Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua M Ray
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shihan He
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jingya Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- MedImmune, LLC, Gaithersburg, MD, USA
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Russell J H Ryan
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Monica L Guzman
- Division of Hematology and Medical Oncology, Leukemia Program, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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42
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Sultani HN, Morgan I, Hussain H, Roos AH, Haeri HH, Kaluđerović GN, Hinderberger D, Westermann B. Access to New Cytotoxic Triterpene and Steroidal Acid-TEMPO Conjugates by Ugi Multicomponent-Reactions. Int J Mol Sci 2021; 22:ijms22137125. [PMID: 34281176 PMCID: PMC8268079 DOI: 10.3390/ijms22137125] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/30/2022] Open
Abstract
Multicomponent reactions, especially the Ugi-four component reaction (U-4CR), provide powerful protocols to efficiently access compounds having potent biological and pharmacological effects. Thus, a diverse library of betulinic acid (BA), fusidic acid (FA), cholic acid (CA) conjugates with TEMPO (nitroxide) have been prepared using this approach, which also makes them applicable in electron paramagnetic resonance (EPR) spectroscopy. Moreover, convertible amide modified spin-labelled fusidic acid derivatives were selected for post-Ugi modification utilizing a wide range of reaction conditions which kept the paramagnetic center intact. The nitroxide labelled betulinic acid analogue 6 possesses cytotoxic effects towards two investigated cell lines: prostate cancer PC3 (IC50 7.4 ± 0.7 μM) and colon cancer HT29 (IC50 9.0 ± 0.4 μM). Notably, spin-labelled fusidic acid derivative 8 acts strongly against these two cancer cell lines (PC3: IC50 6.0 ± 1.1 μM; HT29: IC50 7.4 ± 0.6 μM). Additionally, another fusidic acid analogue 9 was also found to be active towards HT29 with IC50 7.0 ± 0.3 μM (CV). Studies on the mode of action revealed that compound 8 increased the level of caspase-3 significantly which clearly indicates induction of apoptosis by activation of the caspase pathway. Furthermore, the exclusive mitochondria targeting of compound 18 was successfully achieved, since mitochondria are the major source of ROS generation.
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Affiliation(s)
- Haider N. Sultani
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany; (H.N.S.); (I.M.); (H.H.); (G.N.K.)
| | - Ibrahim Morgan
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany; (H.N.S.); (I.M.); (H.H.); (G.N.K.)
| | - Hidayat Hussain
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany; (H.N.S.); (I.M.); (H.H.); (G.N.K.)
| | - Andreas H. Roos
- Physical Chemistry—Complex Self-Organizing Systems, Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany; (A.H.R.); (H.H.H.); (D.H.)
| | - Haleh H. Haeri
- Physical Chemistry—Complex Self-Organizing Systems, Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany; (A.H.R.); (H.H.H.); (D.H.)
| | - Goran N. Kaluđerović
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany; (H.N.S.); (I.M.); (H.H.); (G.N.K.)
- Department of Engineering and Natural Sciences, University of Applied Sciences Merseburg, Eberhard-Leibnitz-Strasse 2, 06217 Merseburg, Germany
| | - Dariush Hinderberger
- Physical Chemistry—Complex Self-Organizing Systems, Institute of Chemistry, Martin Luther University Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle, Germany; (A.H.R.); (H.H.H.); (D.H.)
| | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany; (H.N.S.); (I.M.); (H.H.); (G.N.K.)
- Organic Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120 Halle, Germany
- Correspondence: ; Tel.: +49-345-5582-1340; Fax: +49-345-5582-1309
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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.
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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.
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44
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Zhang W, Yu C, Yang M, Wen S, Zhang J. Characterization of a Hg 2+-Selective Fluorescent Probe Based on Rhodamine B and Its Imaging in Living Cells. Molecules 2021; 26:3385. [PMID: 34205046 PMCID: PMC8199853 DOI: 10.3390/molecules26113385] [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: 04/18/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
A small organic molecule P was synthesized and characterized as a fluorometric and colorimetric dual-modal probe for Hg2+. The sensing characteristics of the proposed probe for Hg2+ were studied in detail. A fluorescent enhancing property at 583 nm (>30 fold) accompanied with a visible colorimetric change, from colorless to pink, was observed with the addition of Hg2+ to P in an ethanol-water solution (8:2, v/v, 20 mM HEPES, pH 7.0), which would be helpful to fabricate Hg2+-selective probes with "naked-eye" and fluorescent detection. Meanwhile, cellular experimental results demonstrated its low cytotoxicity and good biocompatibility, and the application of P for imaging of Hg2+ in living cells was satisfactory.
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Affiliation(s)
- Wenting Zhang
- Laboratory of Environmental Monitoring, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou 571199, China; (W.Z.); (C.Y.); (S.W.)
- School of Public Health, Hainan Medical University, Haikou 571101, China;
| | - Chunwei Yu
- Laboratory of Environmental Monitoring, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou 571199, China; (W.Z.); (C.Y.); (S.W.)
| | - Mei Yang
- School of Public Health, Hainan Medical University, Haikou 571101, China;
| | - Shaobai Wen
- Laboratory of Environmental Monitoring, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou 571199, China; (W.Z.); (C.Y.); (S.W.)
| | - Jun Zhang
- Laboratory of Environmental Monitoring, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou 571199, China; (W.Z.); (C.Y.); (S.W.)
- Laboratory of Tropical Biomedicine and Biotechnology, Hainan Medical University, Haikou 571101, China
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45
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Rasheed OK, Buhl C, Evans JT, Ryter KT. Design of Trehalose-Based Amide/Sulfonamide C-type Lectin Receptor Signaling Compounds. ChemMedChem 2021; 16:1246-1251. [PMID: 33415819 PMCID: PMC8068603 DOI: 10.1002/cmdc.202000775] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/06/2021] [Indexed: 02/06/2023]
Abstract
Mincle agonists have been shown to induce inflammatory cytokine production, such as tumor necrosis factor-alpha (TNF) and promote the development of a Th1/Th17 immune response that might be crucial to development of effective vaccination against pathogens such as Mycobacterium tuberculosis. As an expansion of our previous work, a library of 6,6'-amide and sulfonamide α,α-d-trehalose compounds with various substituents on the aromatic ring was synthesized efficiently in good to excellent yields. These compounds were evaluated for their ability to activate the human C-type lectin receptor Mincle by the induction of cytokines from human peripheral blood mononuclear cells. A preliminary structure-activity relationship (SAR) of these novel trehalose diamides and sulfonamides revealed that aryl amide-linked trehalose compounds demonstrated improved activity and relatively high potency cytokine production compared to the Mincle ligand trehalose dibehenate adjuvant (TDB) and the natural ligand trehalose dimycolate (TDM) inducing dose-dependent and human-Mincle-specific stimulation in a HEK reporter cell line.
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Affiliation(s)
- Omer K Rasheed
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
- Inimmune Corp., 1121 E. Broadway, Suite 121, Missoula, MT 59802, USA
| | - Cassandra Buhl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Jay T Evans
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
- Center for Translational Medicine, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Kendal T Ryter
- Department of Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
- Center for Translational Medicine, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, 32 Campus Dr., Missoula, MT 59812, USA
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46
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Gaur NK, Goyal VD, Kulkarni K, Makde RD. Machine learning classifiers aid virtual screening for efficient design of mini-protein therapeutics. Bioorg Med Chem Lett 2021; 38:127852. [PMID: 33609660 DOI: 10.1016/j.bmcl.2021.127852] [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: 12/12/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/15/2022]
Abstract
De novo design of mini-proteins (4-12 kDa) has recently been shown to produce new candidates for protein therapeutics. They are temperature stable molecules that bind to the drug target with high affinity for inhibiting its interactions. The development of mini-protein binders requires laboratory screening of tens of thousands of molecules for effective target binding. In this study we trained machine learning classifiers which can distinguish, with 90% accuracy and 80% precision, mini-protein binders from non-binding molecules designed for a particular target; this significantly reduces the number of mini protein candidates for experimental screening. Further, on the basis of our results we propose a multi-stage protocol where a small dataset (few hundred experimentally verified target-specific mini-proteins) can be used to train classifiers for improving the efficiency of mini-protein design for any specific target.
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Affiliation(s)
- Neeraj K Gaur
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India; Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India.
| | - Venuka Durani Goyal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ravindra D Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
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47
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Long S, Loureiro JB, Carvalho C, Gales L, Saraiva L, Pinto MMM, Puthongking P, Sousa E. Semi-Synthesis of Small Molecules of Aminocarbazoles: Tumor Growth Inhibition and Potential Impact on p53. Molecules 2021; 26:molecules26061637. [PMID: 33804175 PMCID: PMC7998292 DOI: 10.3390/molecules26061637] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/22/2022] Open
Abstract
The tumor suppressor p53 is inactivated by mutation in approximately 50% of human cancers. Small molecules that bind and stabilize those mutants may represent effective anticancer drugs. Herein, we report the tumor cell growth inhibitory activity of carbazole alkaloids and amino derivatives, as well as their potential activation of p53. Twelve aminocarbazole alkaloids were semi-synthesized from heptaphylline (1), 7-methoxy heptaphylline (2), and 7-methoxymukonal (3), isolated from Clausena harmandiana, using a reductive amination protocol. Naturally-occurring carbazoles 1–3 and their amino derivatives were evaluated for their potential effect on wild-type and mutant p53 activity using a yeast screening assay and on human tumor cell lines. Naturally-occurring carbazoles 1–3 showed the most potent growth inhibitory effects on wild-type p53-expressing cells, being heptaphylline (1) the most promising in all the investigated cell lines. However, compound 1 also showed growth inhibition against non-tumor cells. Conversely, semi-synthetic aminocarbazole 1d showed an interesting growth inhibitory activity in tumor cells expressing both wild-type and mutant p53, exhibiting low growth inhibition on non-tumor cells. The yeast assay showed a potential reactivation of mutant p53 by heptaphylline derivatives, including compound 1d. The results obtained indicate that carbazole alkaloids may represent a promising starting point to search for new mutp53-reactivating agents with promising applications in cancer therapy.
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Affiliation(s)
- Solida Long
- Laboratory of Organic and Pharmaceutical Chemistry (LQOF), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; or (M.M.M.P.)
| | - Joana B. Loureiro
- Laboratory of Microbiology (LAQV/REQUIMTE), Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.B.L.); (C.C.)
| | - Carla Carvalho
- Laboratory of Microbiology (LAQV/REQUIMTE), Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.B.L.); (C.C.)
| | - Luís Gales
- Institute for the Biomedical Science Abel Salazar (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Instituto de Biologia Molecular e Celular (i3S-IBMC), University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Lucília Saraiva
- Laboratory of Microbiology (LAQV/REQUIMTE), Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.B.L.); (C.C.)
- Correspondence: (L.S.); (E.S.); Tel.: +351-2-2042-8689 (E.S.)
| | - Madalena M. M. Pinto
- Laboratory of Organic and Pharmaceutical Chemistry (LQOF), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; or (M.M.M.P.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Matosinhos, Portugal
| | - Ploenthip Puthongking
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Khon Kean University, Khon Kean 40002, Thailand;
| | - Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry (LQOF), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; or (M.M.M.P.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), 4450-208 Matosinhos, Portugal
- Correspondence: (L.S.); (E.S.); Tel.: +351-2-2042-8689 (E.S.)
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Golosov AA, Flyer AN, Amin J, Babu C, Gampe C, Li J, Liu E, Nakajima K, Nettleton D, Patel TJ, Reid PC, Yang L, Monovich LG. Design of Thioether Cyclic Peptide Scaffolds with Passive Permeability and Oral Exposure. J Med Chem 2021; 64:2622-2633. [PMID: 33629858 DOI: 10.1021/acs.jmedchem.0c01505] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 12/15/2022]
Abstract
Advances in the design of permeable peptides and in the synthesis of large arrays of macrocyclic peptides with diverse amino acids have evolved on parallel but independent tracks. Less precedent combines their respective attributes, thereby limiting the potential to identify permeable peptide ligands for key targets. Herein, we present novel 6-, 7-, and 8-mer cyclic peptides (MW 774-1076 g·mol-1) with passive permeability and oral exposure that feature the amino acids and thioether ring-closing common to large array formats, including DNA- and RNA-templated synthesis. Each oral peptide herein, selected from virtual libraries of partially N-methylated peptides using in silico methods, reflects the subset consistent with low energy conformations, low desolvation penalties, and passive permeability. We envision that, by retaining the backbone N-methylation pattern and consequent bias toward permeability, one can generate large peptide arrays with sufficient side chain diversity to identify permeability-biased ligands to a variety of protein targets.
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Affiliation(s)
- Andrei A Golosov
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alec N Flyer
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jakal Amin
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charles Babu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christian Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jingzhou Li
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eugene Liu
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Katsumasa Nakajima
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David Nettleton
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Tajesh J Patel
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Patrick C Reid
- PeptiDream, Inc., 3-25-23 Tonomachi, Kawasaki-Ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Lihua Yang
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lauren G Monovich
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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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.
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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
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50
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Ben Khalaf N, Pham S, Romeo G, Abdelghany S, Intagliata S, Sedillo P, Salerno L, Gonzales J, Fathallah DM, Perkins DJ, Hurwitz I, Pittalà V. A computer-aided approach to identify novel Leishmania major protein disulfide isomerase inhibitors for treatment of leishmaniasis. J Comput Aided Mol Des 2021; 35:297-314. [PMID: 33615401 DOI: 10.1007/s10822-021-00374-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/15/2021] [Indexed: 12/19/2022]
Abstract
Leishmaniasis is an infectious disease caused by parasites of the genus Leishmania and transmitted by the bite of a sand fly. To date, most available drugs for treatment are toxic and beyond the economic means of those affected by the disease. Protein disulfide isomerase (PDI) is a chaperone protein that plays a major role in the folding of newly synthesized proteins, specifically assisting in disulfide bond formation, breakage, or rearrangement in all non-native proteins. In previous work, we demonstrated that Leishmania major PDI (LmPDI) has an essential role in pathogen virulence. Furthermore, inhibition of LmPDI further blocked parasite infection in macrophages. In this study, we utilized a computer-aided approach to design a series of LmPDI inhibitors. Fragment-based virtual screening allowed for the understanding of the inhibitors' modes of action on LmPDI active sites. The generated compounds obtained after multiple rounds of virtual screening were synthesized and significantly inhibited target LmPDI reductase activity and were shown to decrease in vitro parasite growth in human monocyte-derived macrophages. This novel cheminformatics and synthetic approach led to the identification of a new series of compounds that might be optimized into novel drugs, likely more specific and less toxic for the treatment of leishmaniasis.
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Affiliation(s)
- Noureddine Ben Khalaf
- Department of Life Sciences, Health Biotechnology Program, College of Graduates Studies, King Fahd Chair for Health Biotechnology, Arabian Gulf University, Road 2904 Building 293, Manama, 329, Kingdom of Bahrain.
| | - Susie Pham
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Giuseppe Romeo
- Department of Drug Sciences, University of Catania, V.le A. Doria 6, 95125, Catania, Italy
| | - Sara Abdelghany
- Department of Molecular Medicine, Princess Al-Jawhara Center for Genetics and Inherited Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Sebastiano Intagliata
- Department of Drug Sciences, University of Catania, V.le A. Doria 6, 95125, Catania, Italy
| | - Peter Sedillo
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Loredana Salerno
- Department of Drug Sciences, University of Catania, V.le A. Doria 6, 95125, Catania, Italy
| | - Jessica Gonzales
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Dahmani M Fathallah
- Department of Life Sciences, Health Biotechnology Program, College of Graduates Studies, King Fahd Chair for Health Biotechnology, Arabian Gulf University, Road 2904 Building 293, Manama, 329, Kingdom of Bahrain
| | - Douglas J Perkins
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ivy Hurwitz
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Valeria Pittalà
- Department of Drug Sciences, University of Catania, V.le A. Doria 6, 95125, Catania, Italy
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