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Francesconi V, Rizzo M, Pozzi C, Tagliazucchi L, Konchie Simo CU, Saporito G, Landi G, Mangani S, Carbone A, Schenone S, Santarém N, Tavares J, Cordeiro-da-Silva A, Costi MP, Tonelli M. Identification of Innovative Folate Inhibitors Leveraging the Amino Dihydrotriazine Motif from Cycloguanil for Their Potential as Anti- Trypanosoma brucei Agents. ACS Infect Dis 2024; 10:2755-2774. [PMID: 38953453 DOI: 10.1021/acsinfecdis.4c00113] [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] [Indexed: 07/04/2024]
Abstract
Folate enzymes, namely, dihydrofolate reductase (DHFR) and pteridine reductase (PTR1) are acknowledged targets for the development of antiparasitic agents against Trypanosomiasis and Leishmaniasis. Based on the amino dihydrotriazine motif of the drug Cycloguanil (Cyc), a known inhibitor of both folate enzymes, we have identified two novel series of inhibitors, the 2-amino triazino benzimidazoles (1) and 2-guanidino benzimidazoles (2), as their open ring analogues. Enzymatic screening was carried out against PTR1, DHFR, and thymidylate synthase (TS). The crystal structures of TbDHFR and TbPTR1 in complex with selected compounds experienced in both cases a substrate-like binding mode and allowed the rationalization of the main chemical features supporting the inhibitor ability to target folate enzymes. Biological evaluation of both series was performed against T. brucei and L. infantum and the toxicity against THP-1 human macrophages. Notably, the 5,6-dimethyl-2-guanidinobenzimidazole 2g resulted to be the most potent (Ki = 9 nM) and highly selective TbDHFR inhibitor, 6000-fold over TbPTR1 and 394-fold over hDHFR. The 5,6-dimethyl tricyclic analogue 1g, despite showing a lower potency and selectivity profile than 2g, shared a comparable antiparasitic activity against T. brucei in the low micromolar domain. The dichloro-substituted 2-guanidino benzimidazoles 2c and 2d revealed their potent and broad-spectrum antitrypanosomatid activity affecting the growth of T. brucei and L. infantum parasites. Therefore, both chemotypes could represent promising templates that could be valorized for further drug development.
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Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Marco Rizzo
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIMMP), Via Luigi Sacconi 6, Sesto Fiorentino (FI) 50019, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
- Doctorate School in Clinical and Experimental Medicine (CEM), University of Modena and Reggio Emilia, Via Campi 287, Modena 41125, Italy
| | - Claude U Konchie Simo
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Giulia Saporito
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Nuno Santarém
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
| | - Joana Tavares
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
| | - Anabela Cordeiro-da-Silva
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
- Department of Life Science, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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Landi G, Linciano P, Borsari C, Bertolacini CP, Moraes CB, Cordeiro-da-Silva A, Gul S, Witt G, Kuzikov M, Costi MP, Pozzi C, Mangani S. Structural Insights into the Development of Cycloguanil Derivatives as Trypanosoma brucei Pteridine-Reductase-1 Inhibitors. ACS Infect Dis 2019; 5:1105-1114. [PMID: 31012301 DOI: 10.1021/acsinfecdis.8b00358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cycloguanil is a known dihydrofolate-reductase (DHFR) inhibitor, but there is no evidence of its activity on pteridine reductase (PTR), the main metabolic bypass to DHFR inhibition in trypanosomatid parasites. Here, we provide experimental evidence of cycloguanil as an inhibitor of Trypanosoma brucei PTR1 (TbPTR1). A small library of cycloguanil derivatives was developed, resulting in 1 and 2a having IC50 values of 692 and 186 nM, respectively, toward TbPTR1. Structural analysis revealed that the increased potency of 1 and 2a is due to the combined contributions of hydrophobic interactions, H-bonds, and halogen bonds. Moreover, in vitro cell-growth-inhibition tests indicated that 2a is also effective on T. brucei. The simultaneous inhibition of DHFR and PTR1 activity in T. brucei is a promising new strategy for the treatment of human African trypanosomiasis. For this purpose, 1,6-dihydrotriazines represent new molecular tools to develop potent dual PTR and DHFR inhibitors.
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Affiliation(s)
- Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018−2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Pasquale Linciano
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Chiara Borsari
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Claudia P. Bertolacini
- National Laboratory of Biosciences, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil
| | - Carolina B. Moraes
- National Laboratory of Biosciences, National Center for Research in Energy and Materials, Campinas, São Paulo 13083-970, Brazil
| | - Anabela Cordeiro-da-Silva
- Instituto de Investigação e Inovação em Saúde and IBMC-Institute for Molecular and Cell Biology, Universidade do Porto and Departamento de Ciências Biológicas, Faculdade de Farmácia da Universidade do Porto (FFUP), 4150-180 Porto, Portugal
| | - Sheraz Gul
- Fraunhofer Institute for Molecular Biology & Applied Ecology—ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Gesa Witt
- Fraunhofer Institute for Molecular Biology & Applied Ecology—ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology & Applied Ecology—ScreeningPort, Schnackenburgallee 114, D-22525 Hamburg, Germany
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018−2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018−2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
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Jaruwat A, Riangrungroj P, Ubonprasert S, Sae-Ueng U, Kuaprasert B, Yuthavong Y, Leartsakulpanich U, Chitnumsub P. Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine. Arch Biochem Biophys 2019; 667:6-13. [PMID: 31002765 DOI: 10.1016/j.abb.2019.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/14/2019] [Accepted: 04/11/2019] [Indexed: 10/27/2022]
Abstract
Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Here we report the crystal structure of a surface engineered PfADA at a resolution of 2.48 Å, together with results on kinetic studies of PfADA wild-type and active site variants. The structure reveals a novel inosine binding pocket linked to a distinctive PfADA substructure (residues 172-179) derived from a non-conserved gating helix loop (172-188) in Plasmodium spp. and other ADA enzymes. Variants of PfADA and human (h) ADA active site amino acids were generated in order to study their role in catalysis, including PfADA- Phe136, -Thr174, -Asp176, and -Leu179, and hADA-Met155, equivalent to PfADA-Asp176. PfADA-Leu179His showed no effect on kinetic parameters. However, kinetic results of PfADA-Asp176Met/Ala mutants and hADA-Met155Asp/Ala showed that the mutation reduced adenosine and 5'-methylthioadenosine substrate affinity in PfADA and kcat in hADA, thereby reducing catalytic efficiency of the enzyme. Phe136Leu mutant showed increased Km (>10-fold) for both substrates whereas Thr174Ile/Ala only affected 5'-methylthioadenosine binding affinity. Together, the structure with the novel inosine binding pocket and the kinetic data provide insights for rational design of inhibitors against PfADA.
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Affiliation(s)
- Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Pinpunya Riangrungroj
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Sakunrat Ubonprasert
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Buabarn Kuaprasert
- Synchrotron Light Research Institute (Public Organization), 111 Suranaree University Avenue, Suranaree Sub-district, Muang, Nakhon Ratchasima, 30000, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand.
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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Vanichtanankul J, Taweechai S, Yuvaniyama J, Vilaivan T, Chitnumsub P, Kamchonwongpaisan S, Yuthavong Y. Trypanosomal dihydrofolate reductase reveals natural antifolate resistance. ACS Chem Biol 2011; 6:905-11. [PMID: 21650210 DOI: 10.1021/cb200124r] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydrofolate reductase (DHFR) is a potential drug target for Trypanosoma brucei, a human parasite, which is the causative agent for African sleeping sickness. No drug is available against this target, since none of the classical antifolates such as pyrimethamine (PYR), cycloguanil, or trimethoprim are effective as selective inhibitors of T. brucei DHFR (TbDHFR). In order to design effective drugs that target TbDHFR, co-crystal structures with bound antifolates were studied. On comparison with malarial Plasmodium falciparum DHFR (PfDHFR), the co-crystal structures of wild-type TbDHFR reveal greater structural similarities to a mutant PfDHFR causing antifolate resistance than the wild-type enzyme. TbDHFR imposes steric hindrance for rigid inhibitors like PYR around Thr86, which is equivalent to Ser108Asn of the malarial enzymes. In addition, a missing residue on TbDHFR active-site loop together with the presence of Ile51 widens its active site even further than the structural effect of Asn51Ile, which is observed in PfDHFR structures. The structural similarities are paralleled by the similarly poor affinities of the trypanosomal enzyme for rigid inhibitors. Mutations of TbDHFR at Thr86 resulted in 10-fold enhancement or 7-fold reduction in the rigid inhibitors affinities for Thr86Ser or Thr86Asn, respectively. The co-crystal structure of TbDHFR with a flexible antifolate WR99210 suggests that its greater affinity result from its ability to avoid such Thr86 clash and occupy the widened binding space similarly to what is observed in the PfDHFR structures. Natural resistance to antifolates of TbDHFR can therefore be explained, and potential antifolate chemotherapy of trypanosomiasis should be possible taking this into account.
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Affiliation(s)
- Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani 12120, Thailand
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Supannee Taweechai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani 12120, Thailand
| | - Jirundon Yuvaniyama
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani 12120, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani 12120, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani 12120, Thailand
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Abstract
INTRODUCTION For > 50 years, drugs targeting the folate pathway have significantly impacted disease treatment as anticancer, antimicrobial and immunomodulatory agents. The discovery of novel antifolate agents with improved properties and superior activities remains an attractive strategy, both in academia and the pharmaceutical industry. AREAS COVERED This review surveys the patent literature from 2006 to 2010 for small molecule inhibitors of enzymatic targets in the folate biosynthetic pathway. EXPERT OPINION The pursuit of antifolates as anticancer and antimicrobial agents continues to be an active area of research. New patent disclosures reveal novel antifolate scaffolds, antifolates with improved drug-like properties and new strategies to effectively target cancer cells. The continued use of high resolution structural information has guided the discovery of several compounds. Owing to the need for high levels of potency and selectivity, especially in targeting pathogenic species, the use of high resolution crystal structures remains an important tool to guide the design of novel antifolates. Interestingly, the patents disclosing novel compounds were ones where X-ray crystallography was an integral component of the design process. Finally, a variety of new structures have been reported that may play an important role in the future development of therapeutic antifolates.
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Affiliation(s)
- Dennis L Wright
- University of Connecticut, Department of Pharmaceutical Sciences , 69 N. Eagleville Rd. Storrs, CT, USA
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