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Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, Hüben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X. Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. J Med Chem 2023; 66:934-950. [PMID: 36581322 PMCID: PMC9841527 DOI: 10.1021/acs.jmedchem.2c01789] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Indexed: 12/31/2022]
Abstract
Antivirulence agents targeting endospore-transmitted Clostridioides difficile infections are urgently needed. C. difficile-specific DNA adenine methyltransferase (CamA) is required for efficient sporulation and affects persistence in the colon. The active site of CamA is conserved and closely resembles those of hundreds of related S-adenosyl-l-methionine (SAM)-dependent methyltransferases, which makes the design of selective inhibitors more challenging. We explored the solvent-exposed edge of the SAM adenosine moiety and systematically designed 42 analogs of adenosine carrying substituents at the C6-amino group (N6) of adenosine. We compare the inhibitory properties and binding affinity of these diverse compounds and present the crystal structures of CamA in complex with 14 of them in the presence of substrate DNA. The most potent of these inhibitors, compound 39 (IC50 ∼ 0.4 μM and KD ∼ 0.2 μM), is selective for CamA against closely related bacterial and mammalian DNA and RNA adenine methyltransferases, protein lysine and arginine methyltransferases, and human adenosine receptors.
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Affiliation(s)
- Jujun Zhou
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John R. Horton
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Martina Menna
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Ren Ren
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Dan Yu
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Taraneh Hajian
- Structural
Genomics Consortium, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Masoud Vedadi
- Structural
Genomics Consortium, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Toronto, ON M5S 1A8, Canada
| | - Giulia Mazzoccanti
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessia Ciogli
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Michael Hüben
- Institute
of Organic Chemistry, RWTH Aachen University, D-52056 Aachen, Germany
| | - Robert M. Blumenthal
- Department
of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life
Sciences, Toledo, Ohio 43614, United States
| | - Xing Zhang
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- Pasteur
Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Dante Rotili
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Xiaodong Cheng
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
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da Silva RMRJ, Gandi MO, Mendonça JS, Carvalho AS, Coutinho JP, Aguiar ACC, Krettli AU, Boechat N. New hybrid trifluoromethylquinolines as antiplasmodium agents. Bioorg Med Chem 2019; 27:1002-1008. [PMID: 30737133 DOI: 10.1016/j.bmc.2019.01.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/18/2022]
Abstract
Malaria remains a major public health problem worldwide, and it is responsible for high rates of morbidity and mortality. Resistance to current antimalarial drugs has been identified, and new drugs are urgently needed. In this study, we designed and synthesized seventeen novel quinolines based on the structures of mefloquine ((2,8-bis(trifluoromethyl)quinolin-4-yl)(piperidin-2-yl)methanol) and amodiaquine (4-((7-chloroquinolin-4-yl)amino)-2-((diethylamino)methyl)phenol) using ring bioisosteric replacement and molecular hybridization of the functional groups. The compounds were evaluated in vitro against Plasmodium falciparum and in vivo in mice infected with P. berghei. All derivatives presented anti-P. falciparum activity with IC50 values ranging from 0.083 to 33.0 µM. The compound with the best anti-P. falciparum activity was N-(5-methyl-4H-1,2,4-triazol-3-yl)-2,8-bis(trifluoromethyl)quinolin-4-amine (12) which showed an IC50 of 0.083 µM. The three most active compounds were selected for antimalarial activity tests against P. berghei-infected mice. Compound 12 was the most active on the 5th day after infection, reducing parasitemia by 66%, which is consistent with its in vitro activity. This is an important result as 12, a simpler molecule than mefloquine, does not contain the stereogenic center, and consequently, its synthesis in the laboratory is easier and less expensive. This system proved promising for the design of potential antimalarial compounds.
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Affiliation(s)
- Renata M R J da Silva
- Programa de Pós-Graduação Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, UFRJ, Av. Carlos Chagas, 373 - bl. K, 2° andar, sala 35 - Prédio do Centro de Ciências da Saúde, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil; Departamento de Síntese Orgânica, Instituto de Tecnologia em Fármacos - Farmanguinhos - Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Marilia O Gandi
- Programa de Pós-Graduação Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, UFRJ, Av. Carlos Chagas, 373 - bl. K, 2° andar, sala 35 - Prédio do Centro de Ciências da Saúde, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil; Departamento de Síntese Orgânica, Instituto de Tecnologia em Fármacos - Farmanguinhos - Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil; Faculdade de Farmácia Universidade Iguaçu-UNIG, Av. Abílio Augusto Távora, 2134, Nova Iguaçu, RJ 26275-580, Brazil
| | - Jorge S Mendonça
- Departamento de Síntese Orgânica, Instituto de Tecnologia em Fármacos - Farmanguinhos - Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Alcione S Carvalho
- Departamento de Síntese Orgânica, Instituto de Tecnologia em Fármacos - Farmanguinhos - Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil
| | - Julia Penna Coutinho
- Laboratório de Malária, Instituto René Rachou, Fiocruz/MG, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte, MG 30190-002, Brazil
| | - Anna C C Aguiar
- Laboratório de Malária, Instituto René Rachou, Fiocruz/MG, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte, MG 30190-002, Brazil
| | - Antoniana U Krettli
- Laboratório de Malária, Instituto René Rachou, Fiocruz/MG, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte, MG 30190-002, Brazil
| | - Nubia Boechat
- Departamento de Síntese Orgânica, Instituto de Tecnologia em Fármacos - Farmanguinhos - Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro, RJ 21041-250, Brazil.
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Hu YQ, Gao C, Zhang S, Xu L, Xu Z, Feng LS, Wu X, Zhao F. Quinoline hybrids and their antiplasmodial and antimalarial activities. Eur J Med Chem 2017; 139:22-47. [DOI: 10.1016/j.ejmech.2017.07.061] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 11/30/2022]
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Olafson KN, Nguyen TQ, Vekilov PG, Rimer JD. Deconstructing Quinoline-Class Antimalarials to Identify Fundamental Physicochemical Properties of Beta-Hematin Crystal Growth Inhibitors. Chemistry 2017; 23:13638-13647. [PMID: 28833627 DOI: 10.1002/chem.201702251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Indexed: 11/12/2022]
Abstract
A versatile approach to control crystallization involves the use of modifiers, which are additives that interact with crystal surfaces and alter their growth rates. Elucidating a modifier's binding specificity to anisotropic crystal surfaces is a ubiquitous challenge that is critical to their design. In this study, we select hematin, a byproduct of malaria parasites, as a model system to examine the complementarity of modifiers (i.e., antimalarial drugs) to β-hematin crystal surfaces. We divide two antimalarials, chloroquine and amodiaquine, into segments consisting of a quinoline base, common to both drugs, and side chains that differentiate their modes of action. Using a combination of scanning probe microscopy, bulk crystallization, and analytical techniques, we show that the base and side chain work synergistically to reduce the rate of hematin crystallization. In contrast to general observations that modifiers retain their function upon segmentation, we show that the constituents do not act as modifiers. A systematic study of quinoline isomers and analogues shows how subtle rearrangement and removal of functional moieties can create effective constituents from previously ineffective modifiers, along with tuning their inhibitory modes of action. These findings highlight the importance of specific functional moieties in drug compounds, leading to an improved understanding of modifier-crystal interactions that could prove to be applicable to the design of new antimalarials.
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Affiliation(s)
- Katy N Olafson
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Tam Q Nguyen
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA.,Department of Chemistry, University of Houston, 3585 Cullen Boulevard, Houston, TX 77204, USA
| | - Jeffrey D Rimer
- Department of Chemical and Biomolecular Engineering, University of Houston, 4726 Calhoun Road, Houston, TX 77204, USA.,Department of Chemistry, University of Houston, 3585 Cullen Boulevard, Houston, TX 77204, USA
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Oh KH, Kim JG, Park JK. A Modular Synthesis of 4-Aminoquinolines and [1,3] N-to-C Rearrangement to Quinolin-4-ylmethanesulfonamides. Org Lett 2017; 19:3994-3997. [DOI: 10.1021/acs.orglett.7b01701] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kyung Hwan Oh
- Department of Chemistry and
Chemistry Institute of Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Jin Gyeong Kim
- Department of Chemistry and
Chemistry Institute of Functional Materials, Pusan National University, Busan 609-735, Korea
| | - Jin Kyoon Park
- Department of Chemistry and
Chemistry Institute of Functional Materials, Pusan National University, Busan 609-735, Korea
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Lu D, Shen A, Liu Y, Peng X, Xing W, Ai J, Geng M, Hu Y. Design and synthesis of novel benzo[d]oxazol-2(3H)-one derivatives bearing 7-substituted-4-enthoxyquinoline moieties as c-Met kinase inhibitors. Eur J Med Chem 2016; 115:191-200. [DOI: 10.1016/j.ejmech.2016.03.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 01/22/2023]
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Kuter D, Streltsov V, Davydova N, Venter GA, Naidoo KJ, Egan TJ. Solution structures of chloroquine-ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy. J Inorg Biochem 2015; 154:114-25. [PMID: 26088729 DOI: 10.1016/j.jinorgbio.2015.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/07/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe-O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe-O-Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm(-1) with the aid of the O(18) isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure-activity relationships for quinoline-ferriheme association.
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Affiliation(s)
- David Kuter
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Victor Streltsov
- Manufacturing Flagship, CSIRO, Parkville, Victoria 3050, Australia
| | - Natalia Davydova
- Manufacturing Flagship, CSIRO, Parkville, Victoria 3050, Australia
| | - Gerhard A Venter
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J Naidoo
- Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
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Reemergence of chloroquine (CQ) analogs as multi-targeting antimalarial agents: a review. Eur J Med Chem 2014; 90:280-95. [PMID: 25461328 DOI: 10.1016/j.ejmech.2014.11.022] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 11/22/2022]
Abstract
Amongst several communicable diseases (CDs), malaria is one of the deadliest parasitic disease all over the world, particularly in African and Asian countries. To curb this menace, numbers of antimalarial agents are being sold as over the counter (OTC) drugs. Chloroquine (CQ) is one of them and is one of the oldest, cheapest, and easily available synthetic agents used to curb malaria. Unfortunately, after the reports of CQ-resistance against different strains of malarial parasite strains worldwide, scientist are continuously modifying the core structure of CQ to get an efficient drug. Interestingly, several new drugs have been emerged in due course having unique and enhanced properties (like dual stage inhibitors, resistance reversing ability etc.) and are ready to enter into the clinical trial. In this course, some new agents have also been discovered which are; though inactive against CQS strain, highly active against CQR strains. The present article describes the role of modification of the core structure of CQ and its effects on the biological activities. Moreover, the attempt has also been made to predict the future prospects of such drugs to reemerge as antimalarial agents.
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Teixeira C, Vale N, Pérez B, Gomes A, Gomes JRB, Gomes P. "Recycling" classical drugs for malaria. Chem Rev 2014; 114:11164-220. [PMID: 25329927 DOI: 10.1021/cr500123g] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Cátia Teixeira
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal.,CICECO, Departamento de Química, Universidade de Aveiro , P-3810-193 Aveiro, Portugal
| | - Nuno Vale
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Bianca Pérez
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - Ana Gomes
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
| | - José R B Gomes
- CICECO, Departamento de Química, Universidade de Aveiro , P-3810-193 Aveiro, Portugal
| | - Paula Gomes
- Centro de Investigação em Química da Universidade do Porto, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto , P-4169-007 Porto, Portugal
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In vitro antimalarial activity, β-haematin inhibition and structure–activity relationships in a series of quinoline triazoles. Eur J Med Chem 2013; 69:338-47. [DOI: 10.1016/j.ejmech.2013.08.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 08/19/2013] [Accepted: 08/25/2013] [Indexed: 11/23/2022]
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