1
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Wasilewicz A, Bojkova D, Beniddir MA, Cinatl J, Rabenau HF, Grienke U, Rollinger JM, Kirchweger B. Molecular networking unveils anti-SARS-CoV-2 constituents from traditionally used remedies. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117206. [PMID: 37783406 DOI: 10.1016/j.jep.2023.117206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plants and fungi have a long tradition in ethnopharmacology for the treatment of infectious diseases including viruses. Many of these natural products have also been used to combat SARS-CoV-2 infections or symptoms of the post- and long-COVID form, owing to the scarcity of clinically approved therapeutics. AIM OF THE STUDY The ongoing threat posed by SARS-CoV-2, along with the rapidly evolving new variants, requires the development of new antiviral compounds. The aim of this study was to identify anti-SARS-CoV-2 herbal and fungal extracts used in traditional medicine against acute respiratory infection, inflammation, and related symptoms. Additionally, we sought to characterize their bioactive constituents. MATERIALS AND METHODS The antiviral activity and cell cytotoxicity of 179 herbal and fungal extracts were evaluated using two SARS-CoV-2 infection assays in Caco-2 cells. 19 plant extracts with and without anti-SARS-CoV-2 activity underwent detailed dereplication using molecular networking. RESULTS Extracts from Angelica sinensis (Oliv.) Diels roots, Annona squamosa L. seeds, Azadirachta indica A. Juss. fruits, Buddleja officinalis Maxim. flowers, Burkea africana Hook. bark and Clinopodium menthifolium (Host) Stace aerial parts showed a potent anti SARS-CoV-2 activity (IC50 < 5 μg/ml) with only moderate cytotoxicity (CC50 > 60 μg/ml, Caco-2). By performing the dereplication with a bioactivity-featured molecular network (MN) on the extract library level, rather than on the level of individual extracts, we could pinpoint compounds characteristic for active extracts. Thus, a straight-forward identification of potential anti-SARS-CoV-2 natural compounds was achieved prior to any fractionation or isolation efforts. CONCLUSIONS A sophisticated hyphenation of empirical knowledge with MS-based bioinformatics and automated compound annotation was applied to decipher the chemical space of the investigated extracts. The correlation with experimentally assessed anti-SARS-CoV-2 activities helped in predicting compound classes and structural elements relevant for the antiviral activities. Consequently, this accelerated the identification of constituents from the investigated mixtures with inhibitory effects against SARS-CoV-2.
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Affiliation(s)
- Andreas Wasilewicz
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria; Vienna Doctoral School of Pharmaceutical, and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
| | - Denisa Bojkova
- Institute of Medical Virology, University Hospital Frankfurt, Paul-Ehrlich-Straβe 40, 60596, Frankfurt am Main, Germany.
| | - Mehdi A Beniddir
- Équipe Chimie des Substances Naturelles, BioCIS, CNRS, Université Paris-Saclay, 17 Avenue des Sciences, 91400, Orsay, France.
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital Frankfurt, Paul-Ehrlich-Straβe 40, 60596, Frankfurt am Main, Germany.
| | - Holger F Rabenau
- Institute of Medical Virology, University Hospital Frankfurt, Paul-Ehrlich-Straβe 40, 60596, Frankfurt am Main, Germany.
| | - Ulrike Grienke
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
| | - Judith M Rollinger
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
| | - Benjamin Kirchweger
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
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2
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Turrin G, Lo Cascio E, Giacon N, Fantinati A, Cristofori V, Illuminati D, Preti D, Morciano G, Pinton P, Agyapong ED, Trapella C, Arcovito A. Spiropiperidine-Based Oligomycin-Analog Ligands To Counteract the Ischemia-Reperfusion Injury in a Renal Cell Model. J Med Chem 2024; 67:586-602. [PMID: 37991993 PMCID: PMC10789258 DOI: 10.1021/acs.jmedchem.3c01792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023]
Abstract
Finding a therapy for ischemia-reperfusion injury, which consists of cell death following restoration of blood flowing into the artery affected by ischemia, is a strong medical need. Nowadays, only the use of broad-spectrum molecular therapies has demonstrated a partial efficacy in protecting the organs following reperfusion, while randomized clinical trials focused on more specific drug targets have failed. In order to overcome this problem, we applied a combination of molecular modeling and chemical synthesis to identify novel spiropiperidine-based structures active in mitochondrial permeability transition pore opening inhibition as a key process to enhance cell survival after blood flow restoration. Our results were confirmed by biological assay on an in vitro cell model on HeLa and human renal proximal tubular epithelial cells and pave the way to further investigation on an in vivo model system.
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Affiliation(s)
- Giulia Turrin
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari,46, 44121 Ferrara, Italy
| | - Ettore Lo Cascio
- Dipartimento
di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Noah Giacon
- Dipartimento
di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Anna Fantinati
- Department
of Environmental and Prevention Sciences, University of Ferrara, Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Virginia Cristofori
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari,46, 44121 Ferrara, Italy
| | - Davide Illuminati
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari,46, 44121 Ferrara, Italy
| | - Delia Preti
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari,46, 44121 Ferrara, Italy
| | - Giampaolo Morciano
- Department
of Medical Sciences, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy
- Laboratory
for Technologies of Advanced Therapies (LTTA), Via Fossato di Mortara,70, 44121 Ferrara, Italy
| | - Paolo Pinton
- Department
of Medical Sciences, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy
- Laboratory
for Technologies of Advanced Therapies (LTTA), Via Fossato di Mortara,70, 44121 Ferrara, Italy
| | - Esther Densu Agyapong
- Department
of Medical Sciences, University of Ferrara, Via Fossato di Mortara 70, 44121 Ferrara, Italy
| | - Claudio Trapella
- Department
of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari,46, 44121 Ferrara, Italy
- Laboratory
for Technologies of Advanced Therapies (LTTA), Via Fossato di Mortara,70, 44121 Ferrara, Italy
| | - Alessandro Arcovito
- Dipartimento
di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
- Fondazione
Policlinico Universitario “A. Gemelli”, IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
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3
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Pham L, Jiang R, Liu Z, Nguyen M, Nguyen Y, Gong Y, Bi Y, Kim HR, Kim YR, Kim G. Synthesis of 9-Cinnamyl-9 H-purine Derivatives as Novel TLR4/MyD88/NF-κB Pathway Inhibitors for Anti-inflammatory Effects. ACS Med Chem Lett 2023; 14:1839-1847. [PMID: 38116448 PMCID: PMC10726439 DOI: 10.1021/acsmedchemlett.3c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
The novel 9-cinnamyl-9H-purine skeleton, inspired by resveratrol and curcumin, was developed to avoid a pan-assay interference compound (PAINS) related to invalid metabolic pancreas activity (IMPS). It replaced the phenol group with purine analogues, the building blocks of DNA and RNA. Alterations to the hydroxyl group in the cinnamyl group, such as H, Me, or F substitutions, were made to impede its oxidation to a PAINS-associated quinone. Among the compounds tested, 5e significantly inhibited nitric oxide production in LPS-induced macrophages (IC50: 6.4 vs 26.4 μM for resveratrol). 5e also reduced pro-inflammatory cytokine levels (IL-6, TNF-α, IL-1β) and lowered iNOS and COX-2 protein levels. Mechanistically, 5e disrupted the TLR4-MyD88 protein interaction, leading to the suppression of the NF-κB signaling pathway suppression. In an atopic dermatitis mouse model, 5e reduced ear edema and inflammation. These findings indicate that the novel 9-cinnamyl-9H-purine skeleton provides therapeutic insight into treating various human diseases by regulating inflammation.
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Affiliation(s)
- Linh Pham
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Rui Jiang
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Zijing Liu
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Mai Nguyen
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yen Nguyen
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yue Gong
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yanran Bi
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Hong-Rae Kim
- Department
of Biomedical Sciences, College of Medicine, Korea University, Seoul 02708, Korea
| | - Young Ran Kim
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Gyudong Kim
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
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4
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Li L, Wu H, Wang J, Ji Z, Fang T, Lu H, Yan L, Shen F, Zhang D, Jiang Y, Ni T. Discovery of Novel 8-Hydroxyquinoline Derivatives with Potent In Vitro and In Vivo Antifungal Activity. J Med Chem 2023; 66:16364-16376. [PMID: 37975824 DOI: 10.1021/acs.jmedchem.3c01771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal pathogens can cause life-threatening infections, yet current antifungals are inadequate at treating many of these, highlighting the importance of novel drug discovery. Here, we report hit compound L14, a novel 8-hydroxyquinoline derivative with potent and broad-spectrum antifungal activity. In vitro experiments exhibited that L14 had better activity and lower cytotoxicity than that of clioquinol and showed synergy in combination with fluconazole (FLC). In a Candida albicans-infected murine model, L14 at 2 mg/kg showed better in vivo efficacy than clioquinol at reducing fungal burden and extending the survival of C. albicans-infected mice. In addition, L14 alone or in combination with FLC had significant inhibitory activity against hypha and biofilm formation. Overall, our data indicated that 8-hydroxyquinoline derivative L14 has favorable pharmacokinetics and acceptable safety profiles and could be further investigated as a promising antifungal hit compound.
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Affiliation(s)
- Liping Li
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Hao Wu
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Jiayin Wang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Fuzhou 350112, China
| | - Zhe Ji
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Ting Fang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Hui Lu
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Lan Yan
- School of Pharmacy, Naval Medical University, PLA, No. 325 Guohe Road, Shanghai 200433, China
| | - Fuming Shen
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Dazhi Zhang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
- School of Pharmacy, Naval Medical University, PLA, No. 325 Guohe Road, Shanghai 200433, China
| | - Yuanying Jiang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
| | - Tingjunhong Ni
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, No. 1239 Siping Road, Shanghai 200092, China
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5
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Gleixner J, Gattor AO, Humphrys LJ, Brunner T, Keller M. [ 3H]UR-JG102-A Radiolabeled Cyclic Peptide with High Affinity and Excellent Selectivity for the Neuropeptide Y Y 4 Receptor. J Med Chem 2023; 66:13788-13808. [PMID: 37773891 DOI: 10.1021/acs.jmedchem.3c01224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The family of human neuropeptide Y receptors (YRs) comprises four subtypes (Y1R, Y2R, Y4R, and Y5R) that are involved in the regulation of numerous physiological processes. Until now, Y4R binding studies have been predominantly performed in hypotonic sodium-free buffers using 125I-labeled derivatives of the endogenous YR agonists pancreatic polypeptide or peptide YY. A few tritium-labeled Y4R ligands have been reported; however, when used in buffers containing sodium at a physiological concentration, their Y4R affinities are insufficient. Based on the cyclic hexapeptide UR-AK86C, we developed a new tritium-labeled Y4R radioligand ([3H]UR-JG102, [3H]20). In sodium-free buffer, [3H]20 exhibits a very low Y4R dissociation constant (Kd 0.012 nM). In sodium-containing buffer (137 mM Na+), the Y4R affinity is lower (Kd 0.11 nM) but still considerably higher compared to previously reported tritiated Y4R ligands. Therefore, [3H]20 represents a useful tool compound for the determination of Y4R binding affinities under physiological-like conditions.
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Affiliation(s)
- Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Laura J Humphrys
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Thomas Brunner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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6
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Feoli A, Iannelli G, Cipriano A, Milite C, Shen L, Wang Z, Hadjikyriacou A, Lowe TL, Safaeipour C, Viviano M, Sarno G, Morretta E, Monti MC, Yang Y, Clarke SG, Cosconati S, Castellano S, Sbardella G. Identification of a Protein Arginine Methyltransferase 7 (PRMT7)/Protein Arginine Methyltransferase 9 (PRMT9) Inhibitor. J Med Chem 2023; 66:13665-13683. [PMID: 37560786 PMCID: PMC10578352 DOI: 10.1021/acs.jmedchem.3c01030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 08/11/2023]
Abstract
Less studied than the other protein arginine methyltransferase isoforms, PRMT7 and PRMT9 have recently been identified as important therapeutic targets. Yet, most of their biological roles and functions are still to be defined, as well as the structural requirements that could drive the identification of selective modulators of their activity. We recently described the structural requirements that led to the identification of potent and selective PRMT4 inhibitors spanning both the substrate and the cosubstrate pockets. The reanalysis of the data suggested a PRMT7 preferential binding for shorter derivatives and prompted us to extend these structural studies to PRMT9. Here, we report the identification of the first potent PRMT7/9 inhibitor and its binding mode to the two PRMT enzymes. Label-free quantification mass spectrometry confirmed significant inhibition of PRMT activity in cells. We also report the setup of an effective AlphaLISA assay to screen small molecule inhibitors of PRMT9.
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Affiliation(s)
- Alessandra Feoli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giulia Iannelli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Alessandra Cipriano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Ciro Milite
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Lei Shen
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Zhihao Wang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Andrea Hadjikyriacou
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Troy L. Lowe
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Cyrus Safaeipour
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Monica Viviano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giuliana Sarno
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Elva Morretta
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Maria Chiara Monti
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Yanzhong Yang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Castellano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Gianluca Sbardella
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
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7
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Ciulla DA, Xu Z, Pezzullo JL, Dranchak P, Wang C, Giner JL, Inglese J, Callahan BP. Paracatalytic induction: Subverting specificity in hedgehog protein autoprocessing with small molecules. Methods Enzymol 2023; 685:1-41. [PMID: 37245899 PMCID: PMC10294009 DOI: 10.1016/bs.mie.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Paracatalytic inducers are antagonists that shift the specificity of biological catalysts, resulting in non-native transformations. In this Chapter we describe methods to discover paracatalytic inducers of Hedgehog (Hh) protein autoprocessing. Native autoprocessing uses cholesterol as a substrate nucleophile to assist in cleaving an internal peptide bond within a precursor form of Hh. This unusual reaction is brought about by HhC, an enzymatic domain that resides within the C-terminal region of Hh precursor proteins. Recently, we reported paracatalytic inducers as a novel class of Hh autoprocessing antagonists. These small molecules bind HhC and tilt the substrate specificity away from cholesterol in favor of solvent water. The resulting cholesterol-independent autoproteolysis of the Hh precursor generates a non-native Hh side product with substantially reduced biological signaling activity. Protocols are provided for in vitro FRET-based and in-cell bioluminescence assays to discover and characterize paracatalytic inducers of Drosophila and human hedgehog protein autoprocessing, respectively.
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Affiliation(s)
- Daniel A Ciulla
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY, United States
| | - John L Pezzullo
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - José-Luis Giner
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY, United States
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8
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Felicetti T, Gwee CP, Burali MS, Chan KWK, Alonso S, Pismataro MC, Sabatini S, Barreca ML, Cecchetti V, Vasudevan SG, Manfroni G. Functionalized sulfonyl anthranilic acid derivatives inhibit replication of all the four dengue serotypes. Eur J Med Chem 2023; 252:115283. [PMID: 36965228 DOI: 10.1016/j.ejmech.2023.115283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023]
Abstract
Dengue virus (DENV), a mosquito-borne flavivirus, continues to be a major public health threat in many countries and no approved antiviral therapeutics are available yet. In this work, we designed and synthesized a series of sulfonyl anthranilic acid (SAA) derivatives using a ligand-based scaffold morphing approach of the 2,1-benzothiazine 2,2-dioxide core, previously used by us to develop DENV polymerase inhibitors resulting devoid of any cell-based antiviral activity. Several derivatives based on the new SAA chemotype exhibited potent inhibition against DENV infection in the cell-based assay but did not inhibit DENV NS5 polymerase activity in the in vitro de novo initiation and elongation assays. Notably, best compounds 26 and 39 showed EC50 values in the range of 0.54-1.36 μM against cells infected with the four dengue serotypes (DENV-1-4). Time-of-drug-addition assay revealed that analogue 26 is a post-entry replication inhibitor that appears to be specific for cells of primate origin, implicating a host target with a high barrier to resistance. In conclusion, SAA derivatives offer a valuable starting point for developing effective Dengue antiviral therapeutics.
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Affiliation(s)
- Tommaso Felicetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Chin Piaw Gwee
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Maria Sole Burali
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Sylvie Alonso
- Infectious Diseases Translational Research Programme, Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, Singapore; Immunology programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Maria Chiara Pismataro
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Stefano Sabatini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Maria Letizia Barreca
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Violetta Cecchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Institute for Glycomics, Griffith University, Queensland, 4222, Australia.
| | - Giuseppe Manfroni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via Del Liceo, 1-06123, Perugia, Italy.
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9
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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10
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Yang X, Childs-Disney JL, Disney MD. A meditation on accelerating the development of small molecule medicines targeting RNA. Expert Opin Drug Discov 2023; 18:115-117. [PMID: 35658797 PMCID: PMC9878438 DOI: 10.1080/17460441.2022.2084528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Xueyi Yang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | | | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
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11
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Alov P, Stoimenov H, Lessigiarska I, Pencheva T, Tzvetkov NT, Pajeva I, Tsakovska I. In Silico Identification of Multi-Target Ligands as Promising Hit Compounds for Neurodegenerative Diseases Drug Development. Int J Mol Sci 2022; 23:13650. [PMID: 36362434 PMCID: PMC9655539 DOI: 10.3390/ijms232113650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 09/29/2023] Open
Abstract
The conventional treatment of neurodegenerative diseases (NDDs) is based on the "one molecule-one target" paradigm. To combat the multifactorial nature of NDDs, the focus is now shifted toward the development of small-molecule-based compounds that can modulate more than one protein target, known as "multi-target-directed ligands" (MTDLs), while having low affinity for proteins that are irrelevant for the therapy. The in silico approaches have demonstrated a potential to be a suitable tool for the identification of MTDLs as promising drug candidates with reduction in cost and time for research and development. In this study more than 650,000 compounds were screened by a series of in silico approaches to identify drug-like compounds with predicted activity simultaneously towards three important proteins in the NDDs symptomatic treatment: acetylcholinesterase (AChE), histone deacetylase 2 (HDAC2), and monoamine oxidase B (MAO-B). The compounds with affinities below 5.0 µM for all studied targets were additionally filtered to remove known non-specifically binding or unstable compounds. The selected four hits underwent subsequent refinement through in silico blood-brain barrier penetration estimation, safety evaluation, and molecular dynamics simulations resulting in two hit compounds that constitute a rational basis for further development of multi-target active compounds against NDDs.
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Affiliation(s)
- Petko Alov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Hristo Stoimenov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Iglika Lessigiarska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Tania Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Nikolay T. Tzvetkov
- Institute of Molecular Biology “Acad. Roumen Tsanev”, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| | - Ilza Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
| | - Ivanka Tsakovska
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria
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12
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Antolin AA, Sanfelice D, Crisp A, Villasclaras Fernandez E, Mica IL, Chen Y, Collins I, Edwards A, Müller S, Al-Lazikani B, Workman P. The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use. Nucleic Acids Res 2022; 51:D1492-D1502. [PMID: 36268860 PMCID: PMC9825478 DOI: 10.1093/nar/gkac909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 01/30/2023] Open
Abstract
We describe the Chemical Probes Portal (https://www.chemicalprobes.org/), an expert review-based public resource to empower chemical probe assessment, selection and use. Chemical probes are high-quality small-molecule reagents, often inhibitors, that are important for exploring protein function and biological mechanisms, and for validating targets for drug discovery. The publication, dissemination and use of chemical probes provide an important means to accelerate the functional annotation of proteins, the study of proteins in cell biology, physiology, and disease pathology, and to inform and enable subsequent pioneering drug discovery and development efforts. However, the widespread use of small-molecule compounds that are claimed as chemical probes but are lacking sufficient quality, especially being inadequately selective for the desired target or even broadly promiscuous in behaviour, has resulted in many erroneous conclusions in the biomedical literature. The Chemical Probes Portal was established as a public resource to aid the selection and best-practice use of chemical probes in basic and translational biomedical research. We describe the background, principles and content of the Portal and its technical development, as well as examples of its applications and use. The Chemical Probes Portal is a community resource and we therefore describe how researchers can be involved in its content and development.
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Affiliation(s)
- Albert A Antolin
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Domenico Sanfelice
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Alisa Crisp
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Eloy Villasclaras Fernandez
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Ioan L Mica
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Yi Chen
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK,Centre for Cancer Drug Discovery, The Institute of Cancer Research, London, SM2 5NG, UK,Chemical Probes Portal, www.chemicalprobes.org
| | - Aled Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, ONM5G 1L7, Canada,Chemical Probes Portal, www.chemicalprobes.org
| | | | | | - Paul Workman
- To whom correspondence should be addressed. Tel: +44 2087224580;
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13
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a “good” hit in the course of a screening campaign still rely on a lot of luck – which is within the reach of academics –, that the hit to lead process requires a lot of chemistry and that if public–private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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14
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Zhou X, Pan Y, Qu Y, Ke X. Tideglusib Inhibits Pif1 Helicase of Bacteroides sp. via an Irreversible and Cys-380-Dependent Mechanism. ACS OMEGA 2022; 7:31289-31298. [PMID: 36092604 PMCID: PMC9453980 DOI: 10.1021/acsomega.2c03546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Pif1 helicase plays multiple roles in maintaining genome stability, which is an attractive therapeutic target for helicase-related diseases, while small molecules targeting Pif1 are not yet available. In this study, we performed a fluorescence polarization-based high-throughput screening and identified that an FDA-approved drug, Tideglusib (TD), could inhibit the DNA-binding activity (IC50 = 6.2 ± 0.4 μM) and ATPase and helicase activity (IC50 = 2-4 μM) of Bacteroides sp. Pif1 (BaPif1), which was also confirmed with human Pif1. In addition, the TD analogue TDZD-8 displayed similar inhibitory effects on Pif1 activities. Notably, TD irreversibly inhibited BaPif1 and severely induced BaPif1 aggregation. Furthermore, inhibition of BaPif1 by TD was significantly attenuated in the presence of dithiothreitol, indicating that TD could be a thiol-reactive compound. We also identified that Cys-380 of BaPif1 is critical for the inhibition by TD, suggesting that TD inhibits BaPif1 via an irreversible and Cys-380-dependent mechanism.
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15
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Bajusz D, Keserű GM. Maximizing the integration of virtual and experimental screening in hit discovery. Expert Opin Drug Discov 2022; 17:629-640. [PMID: 35671403 DOI: 10.1080/17460441.2022.2085685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Experimental and virtual screening contributes to the discovery of more than 50% of clinical candidates. Considering the similar concept and goals, early-phase drug discovery would benefit from the effective integration of these approaches. AREAS COVERED After reviewing the recent trends in both experimental and virtual screening, the authors discuss different integration strategies from parallel, focused, sequential, and iterative screening. Strategic considerations are demonstrated in a number of real-life case studies. EXPERT OPINION Experimental and virtual screening are complementary approaches that should be integrated in lead discovery settings. Virtual screening can access extremely large synthetically feasible chemical space that can be effectively searched on GPU clusters or cloud architectures. Experimental screening provides reliable datasets by quantitative HTS applications, and DNA-encoded libraries (DEL) have enlarged the chemical space covered by these technologies. These developments, together with the use of artificial intelligence methods, represent new options for their efficient integration. The case studies discussed here demonstrate the benefits of complementary strategies, such as focused and iterative screening.
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Affiliation(s)
- Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
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16
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Chuang ST, Papp H, Kuczmog A, Eells R, Condor Capcha JM, Shehadeh LA, Jakab F, Buchwald P. Methylene Blue Is a Nonspecific Protein-Protein Interaction Inhibitor with Potential for Repurposing as an Antiviral for COVID-19. Pharmaceuticals (Basel) 2022; 15:621. [PMID: 35631447 PMCID: PMC9144480 DOI: 10.3390/ph15050621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/07/2023] Open
Abstract
We have previously identified methylene blue, a tricyclic phenothiazine dye approved for clinical use for the treatment of methemoglobinemia and for other medical applications as a small-molecule inhibitor of the protein-protein interaction (PPI) between the spike protein of the SARS-CoV-2 coronavirus and ACE2, the first critical step of the attachment and entry of this coronavirus responsible for the COVID-19 pandemic. Here, we show that methylene blue concentration dependently inhibits this PPI for the spike protein of the original strain as well as for those of variants of concern such as the D614G mutant and delta (B.1.617.2) with IC50 in the low micromolar range (1-5 μM). Methylene blue also showed promiscuous activity and inhibited several other PPIs of viral proteins (e.g., HCoV-NL63-ACE2, hepatitis C virus E-CD81) as well as others (e.g., IL-2-IL-2Rα) with similar potency. This nonspecificity notwithstanding, methylene blue inhibited the entry of pseudoviruses bearing the spike protein of SARS-CoV-2 in hACE2-expressing host cells, both for the original strain and the delta variant. It also blocked SARS-CoV-2 (B.1.5) virus replication in Vero E6 cells with an IC50 in the low micromolar range (1.7 μM) when assayed using quantitative PCR of the viral RNA. Thus, while it seems to be a promiscuous PPI inhibitor with low micromolar activity and has a relatively narrow therapeutic index, methylene blue inhibits entry and replication of SARS-CoV-2, including several of its mutant variants, and has potential as a possible inexpensive, broad-spectrum, orally bioactive small-molecule antiviral for the prevention and treatment of COVID-19.
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Affiliation(s)
- Sung-Ting Chuang
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Henrietta Papp
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Anett Kuczmog
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | | | - Jose M. Condor Capcha
- Division of Cardiology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (J.M.C.C.); (L.A.S.)
- Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Lina A. Shehadeh
- Division of Cardiology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; (J.M.C.C.); (L.A.S.)
- Interdisciplinary Stem Cell Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ferenc Jakab
- National Laboratory of Virology, University of Pécs, 7622 Pécs, Hungary; (H.P.); (A.K.); (F.J.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7622 Pécs, Hungary
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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17
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Iannelli G, Milite C, Marechal N, Cura V, Bonnefond L, Troffer-Charlier N, Feoli A, Rescigno D, Wang Y, Cipriano A, Viviano M, Bedford MT, Cavarelli J, Castellano S, Sbardella G. Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J Med Chem 2022; 65:11574-11606. [PMID: 35482954 PMCID: PMC9469100 DOI: 10.1021/acs.jmedchem.2c00252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Protein arginine
methyltransferases (PRMTs) are important therapeutic
targets, playing a crucial role in the regulation of many cellular
processes and being linked to many diseases. Yet, there is still much
to be understood regarding their functions and the biological pathways
in which they are involved, as well as on the structural requirements
that could drive the development of selective modulators of PRMT activity.
Here we report a deconstruction–reconstruction approach that,
starting from a series of type I PRMT inhibitors previously identified
by us, allowed for the identification of potent and selective inhibitors
of PRMT4, which regardless of the low cell permeability show an evident
reduction of arginine methylation levels in MCF7 cells and a marked
reduction of proliferation. We also report crystal structures with
various PRMTs supporting the observed specificity and selectivity.
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Affiliation(s)
| | | | - Nils Marechal
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Vincent Cura
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Luc Bonnefond
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Nathalie Troffer-Charlier
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | | | | | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | | | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jean Cavarelli
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
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18
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Rullo M, Cipolloni M, Catto M, Colliva C, Miniero DV, Latronico T, de Candia M, Benicchi T, Linusson A, Giacchè N, Altomare CD, Pisani L. Probing Fluorinated Motifs onto Dual AChE-MAO B Inhibitors: Rational Design, Synthesis, Biological Evaluation, and Early-ADME Studies. J Med Chem 2022; 65:3962-3977. [PMID: 35195417 DOI: 10.1021/acs.jmedchem.1c01784] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bioisosteric H/F or CH2OH/CF2H replacement was introduced in coumarin derivatives previously characterized as dual AChE-MAO B inhibitors to probe the effects on both inhibitory potency and drug-likeness. Along with in vitro screening, we investigated early-ADME parameters related to solubility and lipophilicity (Sol7.4, CHI7.4, log D7.4), oral bioavailability and central nervous system (CNS) penetration (PAMPA-HDM and PAMPA-blood-brain barrier (BBB) assays, Caco-2 bidirectional transport study), and metabolic liability (half-lives and clearance in microsomes, inhibition of CYP3A4). Both specific and nonspecific tissue toxicities were determined in SH-SY5Y and HepG2 lines, respectively. Compound 15 bearing a -CF2H motif emerged as a water-soluble, orally bioavailable CNS-permeant potent inhibitor of both human AChE (IC50 = 550 nM) and MAO B (IC50 = 8.2 nM, B/A selectivity > 1200). Moreover, 15 behaved as a safe and metabolically stable neuroprotective agent, devoid of cytochrome liability.
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Affiliation(s)
- Mariagrazia Rullo
- Department of Pharmacy─Pharmaceutical Sciences, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | | | - Marco Catto
- Department of Pharmacy─Pharmaceutical Sciences, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | | | - Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", via Orabona, 4, 70125 Bari, Italy
| | - Tiziana Latronico
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", via Orabona, 4, 70125 Bari, Italy
| | - Modesto de Candia
- Department of Pharmacy─Pharmaceutical Sciences, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | | | - Anna Linusson
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nicola Giacchè
- TES Pharma s.r.l., Corso Vannucci 47, 06121 Perugia, Italy
| | - Cosimo Damiano Altomare
- Department of Pharmacy─Pharmaceutical Sciences, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
| | - Leonardo Pisani
- Department of Pharmacy─Pharmaceutical Sciences, University of Bari "Aldo Moro", via Orabona 4, 70125 Bari, Italy
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19
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Wang M, Tang T, Li R, Huang Z, Ling D, Zheng L, Ding Y, Liu T, Xu W, Zhu F, Min H, Boonhok R, Mao F, Zhu J, Li X, Jiang L, Li J. Drug Repurposing of Quisinostat to Discover Novel Plasmodium falciparum HDAC1 Inhibitors with Enhanced Triple-Stage Antimalarial Activity and Improved Safety. J Med Chem 2022; 65:4156-4181. [PMID: 35175762 DOI: 10.1021/acs.jmedchem.1c01993] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our previous work found that the clinical histone deacetylase (HDAC) inhibitor quisinostat exhibited a significant antimalarial effect but with severe toxicity. In this work, 35 novel derivatives were designed and synthesized based on quisinostat as the lead compound, and their in vitro antimalarial activities and cytotoxicities were systematically evaluated. Among them, JX35 showed potent inhibition against both wild-type and multidrug-resistant parasite strains and displayed a significant in vivo killing effect against all life cycles of parasites, including the blood stage, liver stage, and gametocyte stage, indicating its potential for the simultaneous treatment, chemoprevention, and blockage of malaria transmission. Compared with quisinostat, JX35 exhibited stronger antimalarial efficacy, more adequate safety, and good pharmacokinetic properties. Additionally, mechanistic studies via molecular docking studies, induced PfHDAC1/2 knockdown assays, and PfHDAC1 enzyme inhibition assays jointly indicated that the antimalarial target of JX35 was PfHDAC1. In summary, we discovered the promising candidate PfHDAC1 inhibitor JX35, which showed stronger triple-stage antimalarial effects and lower toxicity than quisinostat.
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Affiliation(s)
- Manjiong Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tongke Tang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, P.R. China
| | - Ruoxi Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhenghui Huang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dazheng Ling
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lulu Zheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Ding
- Department of Pathogenic Biology, Army Medical University, Chongqing 400038, China
| | - Taiping Liu
- Department of Pathogenic Biology, Army Medical University, Chongqing 400038, China
| | - Wenyue Xu
- Department of Pathogenic Biology, Army Medical University, Chongqing 400038, China
| | - Feng Zhu
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Hui Min
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Rachasak Boonhok
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Fei Mao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jin Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaokang Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lubin Jiang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, P.R. China
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.,College of Pharmacy and Chemistry, Dali University, 5 Xue Ren Road, Dali 671000, China.,Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China
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20
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Konieczny A, Conrad M, Ertl FJ, Gleixner J, Gattor AO, Grätz L, Schmidt MF, Neu E, Horn AHC, Wifling D, Gmeiner P, Clark T, Sticht H, Keller M. N-Terminus to Arginine Side-Chain Cyclization of Linear Peptidic Neuropeptide Y Y 4 Receptor Ligands Results in Picomolar Binding Constants. J Med Chem 2021; 64:16746-16769. [PMID: 34748345 DOI: 10.1021/acs.jmedchem.1c01574] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The family of neuropeptide Y (NPY) receptors comprises four subtypes (Y1R, Y2R, Y4R, Y5R), which are addressed by at least three endogenous peptides, i.e., NPY, peptide YY, and pancreatic polypeptide (PP), the latter showing a preference for Y4R. A series of cyclic oligopeptidic Y4R ligands were prepared by applying a novel approach, i.e., N-terminus to arginine side-chain cyclization. Most peptides acted as Y4R partial agonists, showing up to 60-fold higher Y4R affinity compared to the linear precursor peptides. Two cyclic hexapeptides (18, 24) showed higher Y4R potency (Ca2+ aequorin assay) and, with pKi values >10, also higher Y4R affinity compared to human pancreatic polypeptide (hPP). Compounds such as 18 and 24, exhibiting considerably lower molecular weight and considerably more pronounced Y4R selectivity than PP and previously described dimeric peptidic ligands with high Y4R affinity, represent promising leads for the preparation of labeled tool compounds and might support the development of drug-like Y4R ligands.
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Affiliation(s)
- Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Marcus Conrad
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Lukas Grätz
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Maximilian F Schmidt
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Eduard Neu
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, D-91052 Erlangen, Germany
| | - Anselm H C Horn
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - David Wifling
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany.,Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, D-91052 Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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21
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Paysant H, Hedir S, Justaud F, Weiswald LB, El Dine AN, Soulieman A, Hachem A, Elie N, Brotin E, Denoyelle C, Bignon J, Roussi F, Jouanne M, Tasseau O, Roisnel T, Voisin-Chiret AS, Grée R, Levoin N, Poulain L. Structural revision of the Mcl-1 inhibitor MIM1: synthesis and biological studies on ovarian cancer cells with evaluation of designed analogues. Org Biomol Chem 2021; 19:8968-8987. [PMID: 34596646 DOI: 10.1039/d1ob01521d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the area of cancer research, the development of new and potent inhibitors of anti-apoptotic proteins is a very active and promising topic. The small molecule MIM1 has been reported earlier as one of the first selective inhibitors of the anti-apoptotic protein Mcl-1. In the present paper, we first revised the structure of this molecule based on extensive physicochemical analyses. Then we designed and synthesized a focused library of analogues for the corrected structure of MIM1. Next, these molecules were subjected to a panel of in cellulo biological studies, allowing the identification of dual Bcl-xL/Mcl-1 inhibitors, as well as selective Mcl-1 inhibitors. These results have been complemented by fluorescence polarization assays with the Mcl-1 protein. Preliminary structure-activity relationships were discussed and extensive molecular modelling studies allowed us to propose a rationale for the biological activity of this series of new inhibitors, in particular for the selectivity of inhibition of Mcl-1 versus Bcl-xL.
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Affiliation(s)
- Hippolyte Paysant
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Siham Hedir
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Frédéric Justaud
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France.
| | - Louis Bastien Weiswald
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Assaad Nasr El Dine
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France. .,Laboratoire de Chimie Médicinale et de Produits Naturels, Université Libanaise, Faculté des Sciences et PRASE-EDST, Hadath, Beyrouth, Liban
| | - Ali Soulieman
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France. .,Laboratoire de Chimie Médicinale et de Produits Naturels, Université Libanaise, Faculté des Sciences et PRASE-EDST, Hadath, Beyrouth, Liban
| | - Ali Hachem
- Laboratoire de Chimie Médicinale et de Produits Naturels, Université Libanaise, Faculté des Sciences et PRASE-EDST, Hadath, Beyrouth, Liban
| | - Nicolas Elie
- Normandie Univ, UNICAEN, SF 4206 ICORE, CMABIO3, Caen, France
| | - Emilie Brotin
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France.,Normandie Univ, UNICAEN, SF 4206 ICORE, CMABIO3, Caen, France.,Normandie Univ, UNICAEN, SF4206 ICORE, Plateforme ImpedanCELL, Caen, France
| | - Christophe Denoyelle
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France.,Normandie Univ, UNICAEN, SF 4206 ICORE, CMABIO3, Caen, France.,Normandie Univ, UNICAEN, SF4206 ICORE, Plateforme ImpedanCELL, Caen, France
| | - Jérôme Bignon
- Institut de Chimie des Substances Naturelles CNRS UPR 2301, Université Paris Saclay, Gif-sur-Yvette, France
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles CNRS UPR 2301, Université Paris Saclay, Gif-sur-Yvette, France
| | - Marie Jouanne
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France
| | - Olivier Tasseau
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France.
| | - Thierry Roisnel
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France.
| | - Anne Sophie Voisin-Chiret
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), 14000 Caen, France
| | - René Grée
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000, Rennes, France.
| | - Nicolas Levoin
- Bioprojet-Biotech, 4 rue du Chesnay Beauregard, BP 96205, 35762, Saint Grégoire, France
| | - Laurent Poulain
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE "Unité de Recherche Interdisciplinaire pour la Prévention et le Traitement des Cancers", Caen, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
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22
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Computationally Assisted Lead Optimization of Novel Potent and Selective MAO-B Inhibitors. Biomedicines 2021; 9:biomedicines9101304. [PMID: 34680421 PMCID: PMC8533211 DOI: 10.3390/biomedicines9101304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 12/24/2022] Open
Abstract
A series of dietary flavonoid acacetin 7-O-methyl ether derivatives were computationally designed aiming to improve the selectivity and potency profiles against monoamine oxidase (MAO) B. The designed compounds were evaluated for their potential to inhibit human MAO-A and -B. Compounds 1c, 2c, 3c, and 4c were the most potent with a Ki of 37 to 68 nM against MAO-B. Compounds 1c–4c displayed more than a thousand-fold selectivity index towards MAO-B compared with MAO-A. Moreover, compounds 1c and 2c showed reversible inhibition of MAO-B. These results provide a basis for further studies on the potential application of these modified flavonoids for the treatment of Parkinson’s Disease and other neurological disorders.
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23
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RNase P Inhibitors Identified as Aggregators. Antimicrob Agents Chemother 2021; 65:e0030021. [PMID: 33972249 DOI: 10.1128/aac.00300-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNase P is an essential enzyme responsible for tRNA 5'-end maturation. In most bacteria, the enzyme is a ribonucleoprotein consisting of a catalytic RNA subunit and a small protein cofactor termed RnpA. Several studies have reported small-molecule inhibitors directed against bacterial RNase P that were identified by high-throughput screenings. Using the bacterial RNase P enzymes from Thermotoga maritima, Bacillus subtilis, and Staphylococcus aureus as model systems, we found that such compounds, including RNPA2000 (and its derivatives), iriginol hexaacetate, and purpurin, induce the formation of insoluble aggregates of RnpA rather than acting as specific inhibitors. In the case of RNPA2000, aggregation was induced by Mg2+ ions. These findings were deduced from solubility analyses by microscopy and high-performance liquid chromatography (HPLC), RnpA-inhibitor co-pulldown experiments, detergent addition, and RnpA titrations in enzyme activity assays. Finally, we used a B. subtilis RNase P depletion strain, whose lethal phenotype could be rescued by a protein-only RNase P of plant origin, for inhibition zone analyses on agar plates. These cell-based experiments argued against RNase P-specific inhibition of bacterial growth by RNPA2000. We were also unable to confirm the previously reported nonspecific RNase activity of S. aureus RnpA itself. Our results indicate that high-throughput screenings searching for bacterial RNase P inhibitors are prone to the identification of "false positives" that are also termed pan-assay interference compounds (PAINS).
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24
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Cinnamic acid/β-ionone hybrids: synthesis and in vitro anticancer activity evaluation. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02799-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Hao L, Zhang M, Li X, Xin X, Lei F, Lai X, Zhao G, Wu H. Highly efficient whole-cell biosynthesis and cytotoxicity of esculin esters. J Biotechnol 2021; 337:46-56. [PMID: 34197823 DOI: 10.1016/j.jbiotec.2021.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022]
Abstract
Esculin is a polyphenol with multiple bioactivities and poor lipophilicity. Therefore, a whole-cell catalytic strategy for esculin acylation was developed to improve its lipophilicity. A total of 12 strains were tested, among which Pseudomonas stutzeri exhibited the highest catalytic activity and mono-acylated regioselectivity. The conversion reached the highest level of 92.7 % at 24 h under the optimal conditions, when vinyl acetate was used as an acyl donor. The catalytic ability of P. stutzeri remained above 60 % after three cycles. Subsequently, five esculin esters with different lengths of fatty chains were synthesized and structurally identified. Of them, esculin-6'-O-octanoate, esculin-6'-O-laurate, and esculin-6'-O-myristate exhibited cytotoxicity on LO2 cells by inducing apoptosis and necrosis. The cytotoxicity of these three esters may attribute to their membrane-disrupting properties. This study provides a novel whole-cell biocatalytic strategy for the acylation of esculin and insight for application of esculin esters as a food additive or drug.
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Affiliation(s)
- Lisha Hao
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Mengmeng Zhang
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Xiaofeng Li
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Xuan Xin
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Faling Lei
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Xueneng Lai
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Guanglei Zhao
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
| | - Hui Wu
- College of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong, 510640, China.
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26
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Bojadzic D, Alcazar O, Chen J, Chuang ST, Capcha JMC, Shehadeh LA, Buchwald P. Small-Molecule Inhibitors of the Coronavirus Spike: ACE2 Protein-Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2. ACS Infect Dis 2021; 7:1519-1534. [PMID: 33979123 PMCID: PMC8130611 DOI: 10.1021/acsinfecdis.1c00070] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Inhibitors of the protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and human ACE2 (hACE2), which acts as a ligand-receptor pair that initiates the viral attachment and cellular entry of this coronavirus causing the ongoing COVID-19 pandemic, are of considerable interest as potential antiviral agents. While blockade of such PPIs with small molecules is more challenging than that with antibodies, small-molecule inhibitors (SMIs) might offer alternatives that are less strain- and mutation-sensitive, suitable for oral or inhaled administration, and more controllable/less immunogenic. Here, we report the identification of SMIs of this PPI by screening our compound library focused around the chemical space of organic dyes. Among promising candidates identified, several dyes (Congo red, direct violet 1, Evans blue) and novel druglike compounds (DRI-C23041, DRI-C91005) inhibited the interaction of hACE2 with the spike proteins of SARS-CoV-2 as well as SARS-CoV with low micromolar activity in our cell-free ELISA-type assays (IC50's of 0.2-3.0 μM), whereas control compounds, such as sunset yellow FCF, chloroquine, and suramin, showed no activity. Protein thermal shift assays indicated that the SMIs of interest identified here bind SARS-CoV-2-S and not hACE2. While dyes seemed to be promiscuous inhibitors, DRI-C23041 showed some selectivity and inhibited the entry of two different SARS-CoV-2-S expressing pseudoviruses into hACE2-expressing cells in a concentration-dependent manner with low micromolar IC50's (6-7 μM). This provides proof-of-principle evidence for the feasibility of small-molecule inhibition of PPIs critical for SARS-CoV-2 attachment/entry and serves as a first guide in the search for SMI-based alternative antiviral therapies for the prevention and treatment of diseases caused by coronaviruses in general and COVID-19 in particular.
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Affiliation(s)
- Damir Bojadzic
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Oscar Alcazar
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jinshui Chen
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Sung-Ting Chuang
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Jose M. Condor Capcha
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
| | - Lina A. Shehadeh
- Division of Cardiology, University of Miami, Miami, Florida, USA
- Interdisciplinary Stem Cell Institute, University of Miami, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miami, Florida, USA
| | - Peter Buchwald
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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27
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Blaschke T, Bajorath J. Fine-tuning of a generative neural network for designing multi-target compounds. J Comput Aided Mol Des 2021; 36:363-371. [PMID: 34046745 PMCID: PMC9325839 DOI: 10.1007/s10822-021-00392-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/23/2021] [Indexed: 12/20/2022]
Abstract
Exploring the origin of multi-target activity of small molecules and designing new multi-target compounds are highly topical issues in pharmaceutical research. We have investigated the ability of a generative neural network to create multi-target compounds. Data sets of experimentally confirmed multi-target, single-target, and consistently inactive compounds were extracted from public screening data considering positive and negative assay results. These data sets were used to fine-tune the REINVENT generative model via transfer learning to systematically recognize multi-target compounds, distinguish them from single-target or inactive compounds, and construct new multi-target compounds. During fine-tuning, the model showed a clear tendency to increasingly generate multi-target compounds and structural analogs. Our findings indicate that generative models can be adopted for de novo multi-target compound design.
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Affiliation(s)
- Thomas Blaschke
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, 53115, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 6, 53115, Bonn, Germany.
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28
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Abstract
"There's plenty of room at the bottom" (Richard Feynman, 1959): an invitation for (metalla)carboranes to enter the (new) field of nanomedicine. For two decades, the number of publications on boron cluster compounds designed for potential applications in medicine has been constantly increasing. Hundreds of compounds have been screened in vitro or in vivo for a variety of biological activities (chemotherapeutics, radiotherapeutics, antiviral, etc.), and some have shown rather promising potential for further development. However, until now, no boron cluster compounds have made it to the clinic, and even clinical trials have been very sparse. This review introduces a new perspective in the field of medicinal boron chemistry, namely that boron-based drugs should be regarded as nanomedicine platforms, due to their peculiar self-assembly behaviour in aqueous solutions, and treated as such. Examples for boron-based 12- and 11-vertex clusters and appropriate comparative studies from medicinal (in)organic chemistry and nanomedicine, highlighting similarities, differences and gaps in physicochemical and biological characterisation methods, are provided to encourage medicinal boron chemists to fill in the gaps between chemistry laboratory and real applications in living systems by employing bioanalytical and biophysical methods for characterising and controlling the aggregation behaviour of the clusters in solution.
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Affiliation(s)
- Marta Gozzi
- Institute of Inorganic ChemistryFaculty of Chemistry and MineralogyLeipzig UniversityJohannisallee 2904103LeipzigGermany
- Institute of Analytical ChemistryFaculty of Chemistry and MineralogyLeipzig UniversityLinnéstr. 304103LeipzigGermany
- Institute of Medicinal Physics and BiophysicsFaculty of MedicineLeipzig UniversityHärtelstr. 16–1804107LeipzigGermany
| | - Benedikt Schwarze
- Institute of Medicinal Physics and BiophysicsFaculty of MedicineLeipzig UniversityHärtelstr. 16–1804107LeipzigGermany
| | - Evamarie Hey‐Hawkins
- Institute of Inorganic ChemistryFaculty of Chemistry and MineralogyLeipzig UniversityJohannisallee 2904103LeipzigGermany
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29
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Revuelto A, de Lucio H, García-Soriano JC, Sánchez-Murcia PA, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Efficient Dimerization Disruption of Leishmania infantum Trypanothione Reductase by Triazole-phenyl-thiazoles. J Med Chem 2021; 64:6137-6160. [PMID: 33945281 PMCID: PMC8480782 DOI: 10.1021/acs.jmedchem.1c00206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Indexed: 01/06/2023]
Abstract
Inhibition of Leishmania infantum trypanothione disulfide reductase (LiTryR) by disruption of its homodimeric interface has proved to be an alternative and unexploited strategy in the search for novel antileishmanial agents. Proof of concept was first obtained by peptides and peptidomimetics. Building on previously reported dimerization disruptors containing an imidazole-phenyl-thiazole scaffold, we now report a new 1,2,3-triazole-based chemotype that yields noncompetitive, slow-binding inhibitors of LiTryR. Several compounds bearing (poly)aromatic substituents dramatically improve the ability to disrupt LiTryR dimerization relative to reference imidazoles. Molecular modeling studies identified an almost unexplored hydrophobic region at the interfacial domain as the putative binding site for these compounds. A subsequent structure-based design led to a symmetrical triazole analogue that displayed even more potent inhibitory activity over LiTryR and enhanced leishmanicidal activity. Remarkably, several of these novel triazole-bearing compounds were able to kill both extracellular and intracellular parasites in cell cultures.
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Affiliation(s)
- Alejandro Revuelto
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Héctor de Lucio
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | | | - Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - Antonio Jiménez-Ruiz
- Departamento
de Biología de Sistemas, Universidad
de Alcalá, E-28805 Alcalá de Henares, Madrid, Spain
| | - María-José Camarasa
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Sonsoles Velázquez
- Instituto
de Química Médica (IQM-CSIC), c/ Juan de la Cierva 3, E-28006 Madrid, Spain
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30
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Wiedmann M, Dranchak PK, Aitha M, Queme B, Collmus CD, Kashipathy MM, Kanter L, Lamy L, Rogers JM, Tao D, Battaile KP, Rai G, Lovell S, Suga H, Inglese J. Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases. J Biol Chem 2021; 296:100628. [PMID: 33812994 PMCID: PMC8113725 DOI: 10.1016/j.jbc.2021.100628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 01/11/2023] Open
Abstract
Catalysis of human phosphoglycerate mutase is dependent on a 2,3-bisphosphoglycerate cofactor (dPGM), whereas the nonhomologous isozyme in many parasitic species is cofactor independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure–activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized Caenorhabditis elegans iPGM, measured as fold enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using cocrystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from Brugia malayi, Onchocerca volvulus, Dirofilaria immitis, and Escherichia coli, is achieved by a codependence between (1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn2+ in the iPGM phosphatase domain and (2) shape complementarity surrounding the macrocyclic core at the phosphotransferase–phosphatase domain interface. Our results show that the high-affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.
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Affiliation(s)
- Mareike Wiedmann
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Patricia K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Mahesh Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Bryan Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Christopher D Collmus
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Maithri M Kashipathy
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Liza Kanter
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Laurence Lamy
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Joseph M Rogers
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kevin P Battaile
- IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Scott Lovell
- Protein Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas, USA
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo, Japan.
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
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31
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Lak P, O'Donnell H, Du X, Jacobson MP, Shoichet BK. A Crowding Barrier to Protein Inhibition in Colloidal Aggregates. J Med Chem 2021; 64:4109-4116. [PMID: 33761256 DOI: 10.1021/acs.jmedchem.0c02253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small molecule colloidal aggregates adsorb and partially denature proteins, inhibiting them artifactually. Oddly, this inhibition is typically time-dependent. Two mechanisms might explain this: low concentrations of the colloid and enzyme might mean low encounter rates, or colloid-based protein denaturation might impose a kinetic barrier. These two mechanisms should have different concentration dependencies. Perplexingly, when enzyme concentration was increased, incubation times actually lengthened, inconsistent with both models and with classical chemical kinetics of solution species. We therefore considered molecular crowding, where colloids with lower protein surface density demand a shorter incubation time than more crowded colloids. To test this, we grew and shrank colloid surface area. As the surface area shrank, the incubation time lengthened, while as it increased, the converse was true. These observations support a crowding effect on protein binding to colloidal aggregates. Implications for drug delivery and for detecting aggregation-based inhibition will be discussed.
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Affiliation(s)
- Parnian Lak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Henry O'Donnell
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Xuewen Du
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2550, United States
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32
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Affiliation(s)
- Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
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33
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Dahlin JL, Auld DS, Rothenaigner I, Haney S, Sexton JZ, Nissink JWM, Walsh J, Lee JA, Strelow JM, Willard FS, Ferrins L, Baell JB, Walters MA, Hua BK, Hadian K, Wagner BK. Nuisance compounds in cellular assays. Cell Chem Biol 2021; 28:356-370. [PMID: 33592188 PMCID: PMC7979533 DOI: 10.1016/j.chembiol.2021.01.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Steve Haney
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park SK10 4TG, UK
| | | | | | | | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02140, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA
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34
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Calzaferri F, Narros-Fernández P, de Pascual R, de Diego AMG, Nicke A, Egea J, García AG, de Los Ríos C. Synthesis and Pharmacological Evaluation of Novel Non-nucleotide Purine Derivatives as P2X7 Antagonists for the Treatment of Neuroinflammation. J Med Chem 2021; 64:2272-2290. [PMID: 33560845 DOI: 10.1021/acs.jmedchem.0c02145] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ATP-gated P2X7 purinergic receptor (P2X7) is involved in the pathogenesis of many neurodegenerative diseases (NDDs). Several P2X7 antagonists have been developed, though none of them reached clinical trials for this indication. In this work, we designed and synthesized novel blood-brain barrier (BBB)-permeable derivatives as potential P2X7 antagonists. They comprise purine or xanthine cores linked to an aryl group through different short spacers. Compounds were tested in YO-PRO-1 uptake assays and intracellular calcium dynamics in a human P2X7-expressing HEK293 cell line, two-electrode voltage-clamp recordings in Xenopus laevis oocytes, and in interleukin 1β release assays in mouse peritoneal macrophages. BBB permeability was assessed by parallel artificial membrane permeability assays and P-glycoprotein ATPase activity. Dichloroarylpurinylethanones featured a certain P2X7 blockade, being compound 6 (2-(6-chloro-9H-purin-9-yl)-1-(2,4-dichlorophenyl)ethan-1-one), named ITH15004, the most potent, selective, and BBB-permeable antagonist. Compound 6 can be considered as a first non-nucleotide purine hit for future drug optimizations.
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Affiliation(s)
- Francesco Calzaferri
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
| | - Paloma Narros-Fernández
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, C/ Diego de León, 62-1a Planta, 28006 Madrid, Spain
| | - Ricardo de Pascual
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
| | - Antonio M G de Diego
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Javier Egea
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, C/ Diego de León, 62-1a Planta, 28006 Madrid, Spain
| | - Antonio G García
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, C/ Diego de León, 62-1a Planta, 28006 Madrid, Spain
| | - Cristóbal de Los Ríos
- Instituto-Fundación Teófilo Hernando and Departamento de Farmacología, Facultad de Medicina, Universidad Autónoma de Madrid, C/ Arzobispo Morcillo 4, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, C/ Diego de León, 62-1a Planta, 28006 Madrid, Spain
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35
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Zhang X, Chen H, Lei Y, Zhang X, Xu L, Liu W, Fan Z, Ma Z, Yin Z, Li L, Zhu C, Ma B. Multifunctional agents based on benzoxazolone as promising therapeutic drugs for diabetic nephropathy. Eur J Med Chem 2021; 215:113269. [PMID: 33588177 DOI: 10.1016/j.ejmech.2021.113269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/24/2021] [Accepted: 01/30/2021] [Indexed: 12/13/2022]
Abstract
Diabetic nephropathy (DN) is resulted from activations of polyol pathway and oxidative stress by abnormal metabolism of glucose, and no specific medication is available. We designed a novel class of benzoxazolone derivatives, and a number of individuals were found to have significant antioxidant activity and inhibition of aldose reductase of the key enzyme in the polyol pathway. The outstanding compound (E)-2-(7-(4-hydroxy-3-methoxystyryl)-2-oxobenzo[d]oxazol-3(2H)-yl)acetic acid was identified to reduce urinary proteins in diabetic mice suggesting an alleviation in the diabetic nephropathy, and this was confirmed by kidney hematoxylin-eosin staining. Further investigations showed blood glucose normalization, declined in the polyol pathway and lipid peroxides, and raised glutathione and superoxide dismutase activity. Thus, we suggest a therapeutic function of the compound for DN which could be attributed to the combination of hypoglycemic, aldose reductase inhibition and antioxidant.
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Affiliation(s)
- Xin Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Huan Chen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Yanqi Lei
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Xiaonan Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Long Xu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Wenchao Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Zhenya Fan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Zequn Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Zhechang Yin
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Lingyun Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Changjin Zhu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
| | - Bing Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081, Beijing, China.
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36
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Blaschke T, Feldmann C, Bajorath J. Prediction of Promiscuity Cliffs Using Machine Learning. Mol Inform 2021; 40:e2000196. [PMID: 32881355 PMCID: PMC7816223 DOI: 10.1002/minf.202000196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/03/2020] [Indexed: 12/22/2022]
Abstract
Compounds with the ability to interact with multiple targets, also called promiscuous compounds, provide the basis for polypharmacological drug discovery. In recent years, a plethora of structural analogs with different promiscuity has been identified. Nevertheless, the molecular origins of promiscuity remain to be elucidated. In this study, we systematically extracted different structural analogs with varying promiscuity using the matched molecular pair (MMP) formalism from public biological screening and medicinal chemistry data. Care was taken to eliminate all compounds with potential false-positive activity annotations from the analysis. Promiscuity predictions were then attempted at the level of compound pairs representing promiscuity cliffs (PCs; formed by analogs with large promiscuity differences) and corresponding non-PC MMPs (analog pairs without significant promiscuity differences). To address this prediction task, different machine learning models were generated and the results were compared with single compound predictions. PCs encoding promiscuity differences were found to contain more structure-promiscuity relationship information than sets of individual promiscuous compounds. In addition, feature analysis was carried out revealing key contributions to the correct prediction of PCs and non-PC MMPs via machine learning.
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Affiliation(s)
- Thomas Blaschke
- Department of Life Science InformaticsB-ITLIMES Program Unit Chemical Biology and Medicinal ChemistryRheinische Friedrich-Wilhelms-UniversitätEndenicher Allee 19cD-53115BonnGermany
| | - Christian Feldmann
- Department of Life Science InformaticsB-ITLIMES Program Unit Chemical Biology and Medicinal ChemistryRheinische Friedrich-Wilhelms-UniversitätEndenicher Allee 19cD-53115BonnGermany
| | - Jürgen Bajorath
- Department of Life Science InformaticsB-ITLIMES Program Unit Chemical Biology and Medicinal ChemistryRheinische Friedrich-Wilhelms-UniversitätEndenicher Allee 19cD-53115BonnGermany
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37
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Hatley RJD, Procopiou PA, McLachlan SP, Westendorf LE, Meanwell NA, Ewing WR, Macdonald SJF. Writing Your Next Medicinal Chemistry Article: Journal Bibliometrics and Guiding Principles for Industrial Authors. J Med Chem 2020; 63:14336-14356. [PMID: 33103431 DOI: 10.1021/acs.jmedchem.0c01159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Writing scientific articles is immensely rewarding but challenging. This Perspective provides the medicinal chemist with background and advice on the art and process of writing manuscripts and complements the instructions to authors provided by journals. Included are many tips that we wish we had known when we first started writing. Bibliometric data from seven medicinal chemistry journals between 2000 and 2019 are collated including Bioorganic and Medicinal Chemistry Letters and the Journal of Medicinal Chemistry. Although the overall number of articles has doubled, the output from 23 large pharma companies in the past decade has dropped significantly. Commentary is given on the entire process of writing original scientific articles, opinion articles, and reviews. Examples from our own papers and experience are shared including what typically motivates the writer, challenges commonly encountered, and how we find time to write. Finally, the benefits derived from much wider publishing of industrial medicinal chemistry are described.
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Affiliation(s)
- Richard J D Hatley
- RGDscience Ltd, 2nd Floor, 2 Walsworth Road, Hitchin, Herts SG4 9SP, U.K
| | - Panayiotis A Procopiou
- School of Cancer and Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, U.K
| | - Steven P McLachlan
- Data & Computational Science, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Laura E Westendorf
- Enterprise Information Management, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543-4000, United States
| | - William R Ewing
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543-4000, United States
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38
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Croppi G, Zhou Y, Yang R, Bian Y, Zhao M, Hu Y, Ruan BH, Yu J, Wu F. Discovery of an Inhibitor for Bacterial 3-Mercaptopyruvate Sulfurtransferase that Synergistically Controls Bacterial Survival. Cell Chem Biol 2020; 27:1483-1499.e9. [DOI: 10.1016/j.chembiol.2020.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 08/12/2020] [Accepted: 10/22/2020] [Indexed: 12/19/2022]
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39
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Sun D, Peyear TA, Bennett WFD, Holcomb M, He S, Zhu F, Lightstone FC, Andersen OS, Ingólfsson HI. Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays. J Med Chem 2020; 63:11809-11818. [PMID: 32945672 PMCID: PMC7586341 DOI: 10.1021/acs.jmedchem.0c00958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Indexed: 01/07/2023]
Abstract
Partitioning of bioactive molecules, including drugs, into cell membranes may produce indiscriminate changes in membrane protein function. As a guide to safe drug development, it therefore becomes important to be able to predict the bilayer-perturbing potency of hydrophobic/amphiphilic drugs candidates. Toward this end, we exploited gramicidin channels as molecular force probes and developed in silico and in vitro assays to measure drugs' bilayer-modifying potency. We examined eight drug-like molecules that were found to enhance or suppress gramicidin channel function in a thick 1,2-dierucoyl-sn-glycero-3-phosphocholine (DC22:1PC) but not in thin 1,2-dioleoyl-sn-glycero-3-phosphocholine (DC18:1PC) lipid bilayer. The mechanism underlying this difference was attributable to the changes in gramicidin dimerization free energy by drug-induced perturbations of lipid bilayer physical properties and bilayer-gramicidin interactions. The combined in silico and in vitro approaches, which allow for predicting the perturbing effects of drug candidates on membrane protein function, have implications for preclinical drug safety assessment.
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Affiliation(s)
- Delin Sun
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Thasin A. Peyear
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - W. F. Drew Bennett
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Matthew Holcomb
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Stewart He
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Fangqiang Zhu
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Felice C. Lightstone
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Olaf S. Andersen
- Department
of Physiology and Biophysics, Weill Cornell
Medicine, New York, New York 10065, United States
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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40
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Panknin O, Wagenfeld A, Bone W, Bender E, Nowak-Reppel K, Fernández-Montalván AE, Nubbemeyer R, Bäurle S, Ring S, Schmees N, Prien O, Schäfer M, Friedrich C, Zollner TM, Steinmeyer A, Mueller T, Langer G. Discovery and Characterization of BAY 1214784, an Orally Available Spiroindoline Derivative Acting as a Potent and Selective Antagonist of the Human Gonadotropin-Releasing Hormone Receptor as Proven in a First-In-Human Study in Postmenopausal Women. J Med Chem 2020; 63:11854-11881. [PMID: 32960053 DOI: 10.1021/acs.jmedchem.0c01076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The growth of uterine fibroids is sex hormone-dependent and commonly associated with highly incapacitating symptoms. Most treatment options consist of the control of these hormonal effects, ultimately blocking proliferative estrogen signaling (i.e., oral contraceptives/antagonization of human gonadotropin-releasing hormone receptor [hGnRH-R] activity). Full hGnRH-R blockade, however, results in menopausal symptoms and affects bone mineralization, thus limiting treatment duration or demanding estrogen add-back approaches. To overcome such issues, we aimed to identify novel, small-molecule hGnRH-R antagonists. This led to the discovery of compound BAY 1214784, an orally available, potent, and selective hGnRH-R antagonist. Altering the geminal dimethylindoline core of the initial hit compound to a spiroindoline system significantly improved GnRH-R antagonist potencies across several species, mandatory for a successful compound optimization in vivo. In a first-in-human study in postmenopausal women, once daily treatment with BAY 1214784 effectively lowered plasma luteinizing hormone levels by up to 49%, at the same time being associated with low pharmacokinetic variability and good tolerability.
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Affiliation(s)
- Olaf Panknin
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Andrea Wagenfeld
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Wilhelm Bone
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Eckhard Bender
- Research & Development, Pharmaceuticals, Bayer AG, Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Katrin Nowak-Reppel
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | | | - Reinhard Nubbemeyer
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Stefan Bäurle
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Sven Ring
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Norbert Schmees
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Olaf Prien
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Martina Schäfer
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Christian Friedrich
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Thomas M Zollner
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Andreas Steinmeyer
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
| | - Thomas Mueller
- Research & Development, Pharmaceuticals, Bayer AG, Aprather Weg 18a, 42113 Wuppertal, Germany
| | - Gernot Langer
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstrasse 170, 13342 Berlin, Germany
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41
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Ng S, Juang YC, Chandramohan A, Kaan HYK, Sadruddin A, Yuen TY, Ferrer-Gago FJ, Lee XC, Liew X, Johannes CW, Brown CJ, Kannan S, Aronica PG, Berglund NA, Verma CS, Liu L, Stoeck A, Sawyer TK, Partridge AW, Lane DP. De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits. ACS Med Chem Lett 2020; 11:1993-2001. [PMID: 33062184 DOI: 10.1021/acsmedchemlett.0c00022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/01/2020] [Indexed: 12/14/2022] Open
Abstract
Nonspecific promiscuous compounds can mislead researchers and waste significant resources. This phenomenon, though well-documented for small molecules, has not been widely explored for the peptide modality. Here we demonstrate that two purported peptide-based KRas inhibitors, SAH-SOS1 A and cyclorasin 9A5, exemplify false-positive molecules-in terms of both their binding affinities and cellular activities. Through multiple gold-standard biophysical techniques, we unambiguously show that both peptides lack specific binding to KRas and instead induce protein unfolding. Although these peptides inhibited cellular proliferation, the activities appeared to be off-target on the basis of a counterscreen with KRas-independent cell lines. We further demonstrate that their cellular activities are derived from membrane disruption. Accordingly, we propose that to de-risk false-positive molecules, orthogonal binding assays and cellular counterscreens are indispensable.
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Affiliation(s)
| | | | | | | | | | - Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | | | - Xue’Er Cheryl Lee
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | - Xi Liew
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | | | | | | | | | | | | | - Lijuan Liu
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Tomi K. Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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42
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Purgatorio R, Kulikova LN, Pisani L, Catto M, Candia M, Carrieri A, Cellamare S, De Palma A, Beloglazkin AA, Reza Raesi G, Voskressensky LG, Altomare CD. Scouting around 1,2,3,4‐Tetrahydrochromeno[3,2‐
c
]pyridin‐10‐ones for Single‐ and Multitarget Ligands Directed towards Relevant Alzheimer's Targets. ChemMedChem 2020; 15:1947-1955. [DOI: 10.1002/cmdc.202000468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Rosa Purgatorio
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Larisa N. Kulikova
- Organic Chemistry Department Peoples' Friendship University of Russia (RUDN) 6 Miklukho-Maklaya St. Moscow 117198 Russia
| | - Leonardo Pisani
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Marco Catto
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Modesto Candia
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Antonio Carrieri
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Saverio Cellamare
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Andrey A. Beloglazkin
- Organic Chemistry Department Peoples' Friendship University of Russia (RUDN) 6 Miklukho-Maklaya St. Moscow 117198 Russia
| | - Ghulam Reza Raesi
- Organic Chemistry Department Peoples' Friendship University of Russia (RUDN) 6 Miklukho-Maklaya St. Moscow 117198 Russia
| | - Leonid G. Voskressensky
- Organic Chemistry Department Peoples' Friendship University of Russia (RUDN) 6 Miklukho-Maklaya St. Moscow 117198 Russia
| | - Cosimo D. Altomare
- Department of Pharmacy-Drug Sciences University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
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43
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Nizi MG, Desantis J, Nakatani Y, Massari S, Mazzarella MA, Shetye G, Sabatini S, Barreca ML, Manfroni G, Felicetti T, Rushton-Green R, Hards K, Latacz G, Satała G, Bojarski AJ, Cecchetti V, Kolář MH, Handzlik J, Cook GM, Franzblau SG, Tabarrini O. Antitubercular polyhalogenated phenothiazines and phenoselenazine with reduced binding to CNS receptors. Eur J Med Chem 2020; 201:112420. [DOI: 10.1016/j.ejmech.2020.112420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/21/2020] [Accepted: 05/02/2020] [Indexed: 02/08/2023]
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44
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Yang T, Zhang T, Guan XN, Dong Z, Lan L, Yang S, Yang CG. Tideglusib and Its Analogues As Inhibitors of Staphylococcus aureus SrtA. J Med Chem 2020; 63:8442-8457. [PMID: 32639734 DOI: 10.1021/acs.jmedchem.0c00803] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sortase A (SrtA) anchors surface proteins to the cell wall envelope, and it has attracted increasing interesting as a potential antivirulence target. Several small-molecule inhibitors for SrtA have been developed, but target validation remains largely underexplored. Herein, we report a new class of SrtA inhibitors that supports antivirulence therapy through small-molecule targeting of SrtA. Tideglusib (TD), a drug candidate for myotonic dystrophy, was outstanding in high-throughput screening. A concise synthetic route quickly provided TD analogues, and the structure-activity relationships for SrtA inhibition have been established from those analogues. Several compounds largely retained the in vitro potency and exhibited a better solubility than TD. Additionally, TD attenuated virulence-related phenotypes in vitro and protected mice against lethal S. aureus USA300 bacteremia. Our study indicates that TD and its analogues could be new candidates as SrtA inhibitors with potential in the development of new antivirulence agents.
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Affiliation(s)
- Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guizhou 550025, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang-Na Guan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ze Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guizhou 550025, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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45
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Mugnaini C, Kostrzewa M, Bryk M, Mahmoud AM, Brizzi A, Lamponi S, Giorgi G, Ferlenghi F, Vacondio F, Maccioni P, Colombo G, Mor M, Starowicz K, Di Marzo V, Ligresti A, Corelli F. Design, Synthesis, and Physicochemical and Pharmacological Profiling of 7-Hydroxy-5-oxopyrazolo[4,3- b]pyridine-6-carboxamide Derivatives with Antiosteoarthritic Activity In Vivo. J Med Chem 2020; 63:7369-7391. [PMID: 32515588 DOI: 10.1021/acs.jmedchem.0c00595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hallmark of joint diseases, such as osteoarthritis (OA), is pain, originating from both inflammatory and neuropathic components, and compounds able to modulate the signal transduction pathways of the cannabinoid type-2 receptor (CB2R) can represent a helpful option in the treatment of OA. In this perspective, a set of 18 cannabinoid type-2 receptor (CB2R) ligands was developed based on an unprecedented structure. With the aim of improving the physicochemical properties of previously reported 4-hydroxy-2-quinolone-3-carboxamides, a structural optimization program led to the discovery of isosteric 7-hydroxy-5-oxopyrazolo[4,3-b]pyridine-6-carboxamide derivatives. These new compounds are endowed with high affinity for the CB2R and moderate to good selectivity over the cannabinoid type-1 receptor (CB1R), associated with good physicochemical characteristics. As to the functional activity at the CB2R, compounds able to act either as agonists or as inverse agonists/antagonists were discovered. Among them, compound 51 emerged as a potent CB2R agonist able to reduce pain in rats carrying OA induced by injection of monoiodoacetic acid (MIA).
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Affiliation(s)
- Claudia Mugnaini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Magdalena Kostrzewa
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy.,Institute of Genetics and Biophysics, National Research Council of Italy, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Marta Bryk
- Institute of Genetics and Biophysics, National Research Council of Italy, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Ali Mokhtar Mahmoud
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Antonella Brizzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Gianluca Giorgi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Francesca Ferlenghi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Paola Maccioni
- Institute of Neuroscience, National Research Council of Italy, S.S. 554, km 4,500, 09042 Monserrato, Cagliari, Italy
| | - Giancarlo Colombo
- Institute of Neuroscience, National Research Council of Italy, S.S. 554, km 4,500, 09042 Monserrato, Cagliari, Italy
| | - Marco Mor
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Katarzyna Starowicz
- Department of Neurochemistry, Institute of Pharmacology, Polish Academy of Sciences, ul. Smetna 12, 31-343 Cracow, Poland
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Alessia Ligresti
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Federico Corelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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46
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Li X, Himes RA, Prosser LC, Christie CF, Watt E, Edwards SF, Metcalf CS, West PJ, Wilcox KS, Chan SS, Chou CJ. Discovery of the First Vitamin K Analogue as a Potential Treatment of Pharmacoresistant Seizures. J Med Chem 2020; 63:5865-5878. [PMID: 32390424 PMCID: PMC7684765 DOI: 10.1021/acs.jmedchem.0c00168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite the availability of more than 25 antiseizure drugs on the market, approximately 30% of patients with epilepsy still suffer from seizures. Thus, the epilepsy therapy market has a great need for a breakthrough drug that will aid pharmacoresistant patients. In our previous study, we discovered a vitamin K analogue, 2h, which displayed modest antiseizure activity in zebrafish and mouse seizure models. However, there are limitations to this compound due to its pharmacokinetic profile. In this study, we develop a new series of vitamin K analogues by modifying the structure of 2h. Among these, compound 3d shows full protection in a rodent pharmacoresistant seizure model with limited rotarod motor toxicity and favorable pharmacokinetic properties. Furthermore, the brain/plasma concentration ratio of 3d indicates its excellent permeability into the brain. The resulting data shows that 3d can be further developed as a potential antiseizure drug in the clinic.
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Affiliation(s)
- Xiaoyang Li
- Ocean University of China, School of Medicine and Pharmacy, Qingdao, Shandong, 266071, China
| | - Richard A. Himes
- Department of Chemistry and Biochemistry, College of Charleston, 66 George Street,Charleston, South Carolina29424, USA
| | - Lyndsey C. Prosser
- Department of Chemistry and Biochemistry, College of Charleston, 66 George Street,Charleston, South Carolina29424, USA
| | | | - Emma Watt
- Department of Chemistry and Biochemistry, College of Charleston, 66 George Street,Charleston, South Carolina29424, USA
| | - Sharon F. Edwards
- Anticonvulsant Drug Development (ADD) Program, Department of Pharmacology & Toxicology, University of Utah, 84112, USA
| | - Cameron S. Metcalf
- Anticonvulsant Drug Development (ADD) Program, Department of Pharmacology & Toxicology, University of Utah, 84112, USA
| | - Peter J. West
- Anticonvulsant Drug Development (ADD) Program, Department of Pharmacology & Toxicology, University of Utah, 84112, USA
| | - Karen S. Wilcox
- Anticonvulsant Drug Development (ADD) Program, Department of Pharmacology & Toxicology, University of Utah, 84112, USA
| | - Sherine S.L. Chan
- Neuroene Therapeutics, Mount Pleasant, South Carolina 29464, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - C. James Chou
- Neuroene Therapeutics, Mount Pleasant, South Carolina 29464, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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47
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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48
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Srinivasan B, Kantae V, Robinson J. Resurrecting the phoenix: When an assay fails. Med Res Rev 2020; 40:1776-1793. [DOI: 10.1002/med.21670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/18/2020] [Accepted: 03/27/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Vasudev Kantae
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - James Robinson
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
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49
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She X, Pegoli A, Gruber CG, Wifling D, Carpenter J, Hübner H, Chen M, Wan J, Bernhardt G, Gmeiner P, Holliday ND, Keller M. Red-Emitting Dibenzodiazepinone Derivatives as Fluorescent Dualsteric Probes for the Muscarinic Acetylcholine M2 Receptor. J Med Chem 2020; 63:4133-4154. [PMID: 32233403 DOI: 10.1021/acs.jmedchem.9b02172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xueke She
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Andrea Pegoli
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Corinna G. Gruber
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - David Wifling
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Jessica Carpenter
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, U.K
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Mengya Chen
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Jianfei Wan
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Günther Bernhardt
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Nicholas D. Holliday
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Derby Road, Nottingham NG7 2UH, U.K
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
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50
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Bruder M, Polo G, Trivella DBB. Natural allosteric modulators and their biological targets: molecular signatures and mechanisms. Nat Prod Rep 2020; 37:488-514. [PMID: 32048675 DOI: 10.1039/c9np00064j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to 2018Over the last decade more than two hundred single natural products were confirmed as natural allosteric modulators (alloNPs) of proteins. The compounds are presented and discussed with the support of a chemical space, constructed using a principal component analysis (PCA) of molecular descriptors from chemical compounds of distinct databases. This analysis showed that alloNPs are dispersed throughout the majority of the chemical space defined by natural products in general. Moreover, a cluster of alloNPs was shown to occupy a region almost devoid of allosteric modulators retrieved from a dataset composed mainly of synthetic compounds, further highlighting the importance to explore the entire natural chemical space for probing allosteric mechanisms. The protein targets which alloNPs bind to comprised 81 different proteins, which were classified into 5 major groups, with enzymes, in particular hydrolases, being the main representative group. The review also brings a critical interpretation on the mechanisms by which alloNPs display their molecular action on proteins. In the latter analysis, alloNPs were classified according to their final effect on the target protein, resulting in 3 major categories: (i) local alteration of the orthosteric site; (ii) global alteration in protein dynamics that change function; and (iii) oligomer stabilisation or protein complex destabilisation via protein-protein interaction in sites distant from the orthosteric site. G-protein coupled receptors (GPCRs), which use a combination of the three types of allosteric regulation found, were also probed by natural products. In summary, the natural allosteric modulators reviewed herein emphasise their importance for exploring alternative chemotherapeutic strategies, potentially pushing the boundaries of the druggable space of pharmacologically relevant drug targets.
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Affiliation(s)
- Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), National Centre for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil.
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