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González-Álvarez H, Ensan D, Xin T, Wong JF, Zepeda-Velázquez CA, Cros J, Sweeney MN, Hoffer L, Kiyota T, Wilson BJ, Aman A, Roberts O, Isaac MB, Bullock AN, Smil D, Al-awar R. Discovery of Conformationally Constrained ALK2 Inhibitors. J Med Chem 2024; 67:4707-4725. [PMID: 38498998 PMCID: PMC10983009 DOI: 10.1021/acs.jmedchem.3c02308] [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: 12/07/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
Despite decades of research on new diffuse intrinsic pontine glioma (DIPG) treatments, little or no progress has been made on improving patient outcomes. In this work, we explored novel scaffold modifications of M4K2009, a 3,5-diphenylpyridine ALK2 inhibitor previously reported by our group. Here we disclose the design, synthesis, and evaluation of a first-in-class set of 5- to 7-membered ether-linked and 7-membered amine-linked constrained inhibitors of ALK2. This rigidification strategy led us to the discovery of the ether-linked inhibitors M4K2308 and M4K2281 and the amine-linked inhibitors M4K2304 and M4K2306, each with superior potency against ALK2. Notably, M4K2304 and M4K2306 exhibit exceptional selectivity for ALK2 over ALK5, surpassing the reference compound. Preliminary studies on their in vivo pharmacokinetics, including blood-brain barrier penetration, revealed that these constrained scaffolds have favorable exposure and do open a novel chemical space for further optimization and future evaluation in orthotopic models of DIPG.
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Affiliation(s)
- Héctor González-Álvarez
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Deeba Ensan
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Tao Xin
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Jong Fu Wong
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carlos A. Zepeda-Velázquez
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Julien Cros
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Melissa N. Sweeney
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Laurent Hoffer
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Taira Kiyota
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Brian J. Wilson
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Ahmed Aman
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Leslie
Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Owen Roberts
- M4K Pharma, 101 College Street, MaRS Centre,
South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Methvin B. Isaac
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Alex N. Bullock
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David Smil
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Rima Al-awar
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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2
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Qi J, Zheng Y, Li B, Ai Y, Chen M, Zheng X. Pyridoxal hydrochloride thiosemicarbazones with copper ions inhibit cell division via Topo-I and Topo-IIɑ. J Inorg Biochem 2022; 232:111816. [DOI: 10.1016/j.jinorgbio.2022.111816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/28/2022] [Accepted: 04/02/2022] [Indexed: 12/17/2022]
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3
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Srikanth D, Vinayak Joshi S, Ghouse Shaik M, Pawar G, Bujji S, Kanchupalli V, Chopra S, Nanduri S. A Comprehensive Review on Potential Therapeutic Inhibitors of Nosocomial Acinetobacter baumannii Superbugs. Bioorg Chem 2022; 124:105849. [DOI: 10.1016/j.bioorg.2022.105849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/20/2022]
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Narasimhan J, Letinski S, Jung SP, Gerasyuto A, Wang J, Arnold M, Chen G, Hedrick J, Dumble M, Ravichandran K, Levitz T, Cui C, Drennan CL, Stubbe J, Karp G, Branstrom A. Ribonucleotide reductase, a novel drug target for gonorrhea. eLife 2022; 11:e67447. [PMID: 35137690 PMCID: PMC8865847 DOI: 10.7554/elife.67447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic-resistant Neisseria gonorrhoeae (Ng) are an emerging public health threat due to increasing numbers of multidrug resistant (MDR) organisms. We identified two novel orally active inhibitors, PTC-847 and PTC-672, that exhibit a narrow spectrum of activity against Ng including MDR isolates. By selecting organisms resistant to the novel inhibitors and sequencing their genomes, we identified a new therapeutic target, the class Ia ribonucleotide reductase (RNR). Resistance mutations in Ng map to the N-terminal cone domain of the α subunit, which we show here is involved in forming an inhibited α4β4 state in the presence of the β subunit and allosteric effector dATP. Enzyme assays confirm that PTC-847 and PTC-672 inhibit Ng RNR and reveal that allosteric effector dATP potentiates the inhibitory effect. Oral administration of PTC-672 reduces Ng infection in a mouse model and may have therapeutic potential for treatment of Ng that is resistant to current drugs.
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Affiliation(s)
| | | | | | | | - Jiashi Wang
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | | | - Jean Hedrick
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | - Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Talya Levitz
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Gary Karp
- PTC Therapeutics, IncSouth PlainfieldUnited States
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5
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Ouvry G. Recent applications of seven-membered rings in drug design. Bioorg Med Chem 2022; 57:116650. [PMID: 35123178 DOI: 10.1016/j.bmc.2022.116650] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/28/2023]
Abstract
This short review aims at highlighting recent design strategies hinged on using seven-membered rings. Analyses of the different selected examples coupled with torsion profiles derived from the CCDC suggest some of these strategies could have broad applications.
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Affiliation(s)
- Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
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6
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Ohuchi S, Koyama H, Shigehisa H. Catalytic Synthesis of Cyclic Guanidines via Hydrogen Atom Transfer and Radical-Polar Crossover. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shunya Ohuchi
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Koyama
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Shigehisa
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
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Song F, Li Z, Bian Y, Huo X, Fang J, Shao L, Zhou M. Indole/isatin-containing hybrids as potential antibacterial agents. Arch Pharm (Weinheim) 2020; 353:e2000143. [PMID: 32667714 DOI: 10.1002/ardp.202000143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022]
Abstract
The emergence and worldwide spread of drug-resistant bacteria have already posed a serious threat to human life, creating the urgent need to develop potent and novel antibacterial drug candidates with high efficacy. Indole and isatin (indole-2,3-dione) present a wide structural and mechanistic diversity, so their derivatives possess various pharmacological properties and occupy a salient place in the development of new drugs. Indole/isatin-containing hybrids, which demonstrate a promising activity against a panel of clinically important Gram-positive and Gram-negative bacteria, are privileged scaffolds for the discovery of novel antibacterial candidates. This review, covering articles published between January 2015 and May 2020, focuses on the development and structure-activity relationship (SAR) of indole/isatin-containing hybrids with potential application for fighting bacterial infections, to facilitate further rational design of novel drug candidates.
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Affiliation(s)
- Feng Song
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, China.,School of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Zhenghua Li
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, China
| | - Yunqiang Bian
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, China
| | - Xiankai Huo
- Department of Medical Imaging, Dezhou People's Hospital, Dezhou, Shandong, China
| | - Junman Fang
- School of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Linlin Shao
- School of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Meng Zhou
- School of Life Sciences, Dezhou University, Dezhou, Shandong, China
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Ivanenkov YA, Yamidanov RS, Osterman IA, Sergiev PV, Aladinskiy VA, Aladinskaya AV, Terentiev VA, Veselov MS, Ayginin AA, Skvortsov DA, Komarova KS, Chemeris AV, Baimiev AK, Sofronova AA, Malyshev AS, Machulkin AE, Petrov RA, Bezrukov DS, Filkov GI, Puchinina MM, Zainullina LF, Maximova MA, Zileeva ZR, Vakhitova YV, Dontsova OA. Identification of N-Substituted Triazolo-azetidines as Novel Antibacterials using pDualrep2 HTS Platform. Comb Chem High Throughput Screen 2019; 22:346-354. [DOI: 10.2174/1386207322666190412165316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 12/17/2022]
Abstract
Aim and Objective:
Antibiotic resistance is a serious constraint to the development of new
effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main
challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with
antibacterial activity.
Materials and Methods:
Using our unique double-reporter system, in-house large-scale HTS campaign
was conducted for the identification of antibacterial potency of small-molecule compounds. The
construction allows us to visually assess the underlying mechanism of action. After the initial HTS and
rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were
carried out.
Results:
HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted
triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary
hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation
blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high
concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not
demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of
direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an
improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the
same strain. In contrast to the parent hit, this compound was more active and selective, and provided a
robust IP position.
Conclusion:
N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the
development of novel active and selective antibacterial compounds.
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Affiliation(s)
- Yan A. Ivanenkov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Renat S. Yamidanov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Ilya A. Osterman
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | - Petr V. Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
| | | | | | - Victor A. Terentiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Mark S. Veselov
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Andrey A. Ayginin
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Dmitry A. Skvortsov
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Katerina S. Komarova
- Lomonosov Moscow State University, Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russian Federation
| | - Alexey V. Chemeris
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Alexey Kh. Baimiev
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Alina A. Sofronova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | | | - Alexey E. Machulkin
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Rostislav A. Petrov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Dmitry S. Bezrukov
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
| | - Gleb I. Filkov
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Maria M. Puchinina
- Moscow Institute of Physics and Technology (State University), 9 Institutskiy lane, Dolgoprudny City, Moscow Region, 141700, Russian Federation
| | - Liana F. Zainullina
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Marina A. Maximova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Zulfiya R. Zileeva
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Yulia V. Vakhitova
- Institute of Biochemistry and Genetics Russian Academy of Science (IBG RAS) Ufa Scientific Centre, Oktyabrya Prospekt 71, 450054, Ufa, Russian Federation
| | - Olga A. Dontsova
- Lomonosov Moscow State University, Chemistry Dept, Leninskie gory, Building 1/3, GSP-1, Moscow, 119991, Russian Federation
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9
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2-Pyrazol-1-yl-thiazole derivatives as novel highly potent antibacterials. J Antibiot (Tokyo) 2019; 72:827-833. [DOI: 10.1038/s41429-019-0211-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/23/2019] [Accepted: 06/16/2019] [Indexed: 02/06/2023]
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