1
|
Francesconi V, Rizzo M, Schenone S, Carbone A, Tonelli M. State-of-the-art Review on the Antiparasitic Activity of Benzimidazolebased Derivatives: Facing Malaria, Leishmaniasis, and Trypanosomiasis. Curr Med Chem 2024; 31:1955-1982. [PMID: 37718524 PMCID: PMC11071657 DOI: 10.2174/0929867331666230915093928] [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: 05/09/2023] [Revised: 06/19/2023] [Accepted: 08/27/2023] [Indexed: 09/19/2023]
Abstract
Protozoan parasites represent a significant risk for public health worldwide, afflicting particularly people in more vulnerable categories and cause large morbidity and heavy economic impact. Traditional drugs are limited by their toxicity, low efficacy, route of administration, and cost, reflecting their low priority in global health management. Moreover, the drug resistance phenomenon threatens the positive therapy outcome. This scenario claims the need of addressing more adequate therapies. Among the diverse strategies implemented, the medicinal chemistry efforts have also focused their attention on the benzimidazole nucleus as a promising pharmacophore for the generation of new drug candidates. Hence, the present review provides a global insight into recent progress in benzimidazole-based derivatives drug discovery against important protozoan diseases, such as malaria, leishmaniasis and trypanosomiasis. The more relevant chemical features and structure-activity relationship studies of these molecules are discussed for the purpose of paving the way towards the development of more viable drugs for the treatment of these parasitic infections.
Collapse
Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Marco Rizzo
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, Genoa, 16132, Italy
| |
Collapse
|
2
|
Siutkina A, Kalinina S, Liu R, Heitman LH, Junker A, Daniliuc CG, Kalinin DV. Microwave-Assisted Synthesis, Structure, and Preliminary Biological Evaluation of Novel 6-Methoxy-5,6-dihydro-5-azapurines. ACS OMEGA 2023; 8:14097-14112. [PMID: 37091407 PMCID: PMC10116508 DOI: 10.1021/acsomega.3c00765] [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: 02/06/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
We herein disclose the microwave-assisted synthesis of previously unreported 6-methoxy-5,6-dihydro-5-azapurines, whose purine-like scaffold is promising for drug discovery. The method is simple, fast, and relies on easily accessible reagents such as trimethyl orthoformate, acetic acid, and aminotriazole-derived N,N'-disubstituted formamidines. The preliminary biological evaluation revealed that selected representatives of synthesized 6-methoxy-5,6-dihydro-5-azapurines dose-dependently reduce the viability of HepG2 and A549 cancer cells having little to no influence on five tested purinergic receptors.
Collapse
Affiliation(s)
- Alena
I. Siutkina
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Svetlana Kalinina
- Institute
of Food Chemistry, University of Münster, 48149 Münster, Germany
| | - Rongfang Liu
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 CC Leiden, The Netherlands
| | - Laura H. Heitman
- Leiden
Academic Centre for Drug Research (LACDR), Division of Drug Discovery
and Safety, Leiden University, 2333 CC Leiden, The Netherlands
| | - Anna Junker
- European
Institute for Molecular Imaging (EIMI), University of Münster, 48149 Münster, Germany
| | | | - Dmitrii V. Kalinin
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
- . Tel.: +49-2-51-83-33372
| |
Collapse
|
3
|
Guerra F, Winzeler EA. New targets for antimalarial drug discovery. Curr Opin Microbiol 2022; 70:102220. [PMID: 36228458 PMCID: PMC9934905 DOI: 10.1016/j.mib.2022.102220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023]
Abstract
Phenotypic screening methods have placed numerous preclinical candidates into the antimalarial drug-discovery pipeline. As more chemically validated targets become available, efforts are shifting to target-based drug discovery. Here, we briefly review some of the most attractive targets that have been identified in recent years.
Collapse
Affiliation(s)
- Francisco Guerra
- Department of Pediatrics MC 0760, School of Medicine, University of California, La Jolla, San Diego, CA 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics MC 0760, School of Medicine, University of California, La Jolla, San Diego, CA 92093, USA.
| |
Collapse
|
4
|
Babai R, Izrael R, Vértessy BG. Characterization of the dynamics of Plasmodium falciparum deoxynucleotide-triphosphate pool in a stage-specific manner. Sci Rep 2022; 12:19926. [PMID: 36402851 PMCID: PMC9675800 DOI: 10.1038/s41598-022-23807-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/06/2022] [Indexed: 11/21/2022] Open
Abstract
Understanding and characterizing the molecular background of the maintenance of genomic integrity might be a major factor in comprehending the exceptional ability of the malaria parasite, Plasmodium falciparum to adapt at a fast pace to antimalarials. A balanced nucleotide pool is an essential factor for high-fidelity replication. The lack of detailed studies on deoxynucleotide-triphosphate (dNTP) pools in various intraerythrocytic stages of Plasmodium falciparum motivated our present study. Here, we focused on the building blocks of DNA and utilized an EvaGreen-based dNTP incorporation assay to successfully measure the temporal dynamics of dNTPs in every intraerythrocytic stage and in drug-treated trophozoites. Our findings show that the ratio of dNTPs in the ring-stage parasites significantly differs from the more mature trophozoite and schizont stages. We were also able to detect dGTP levels that have never been shown before and found it to be the least abundant dNTP in all stages. Treatment with WR99210, a TS-DHFR inhibitor drug, affected not only dTTP, but also dGTP levels, despite its presumed selective action on pyrimidine biosynthesis. Results from our studies might assist in a better understanding of genome integrity mechanisms and may potentially lead to novel drug related aspects involving purine and pyrimidine metabolic targets.
Collapse
Affiliation(s)
- Réka Babai
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451George A. Olah Doctoral School of Chemistry and Chemical Technology, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
| | - Richard Izrael
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, 6720 Hungary
| | - Beáta G. Vértessy
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
| |
Collapse
|
5
|
Somandi K, Seanego TD, Dlamini (née Molatsane) T, Maree M, de Koning CB, Vanichtanankul J, Rattanajak R, Saeyang T, Yuthavong Y, Kamchonwongpaisan S, Rousseau AL. Molecular Docking Studies, Synthesis and Biological Evaluation of Substituted Pyrimidine-2,4-diamines as Inhibitors of Plasmodium falciparum Dihydrofolate Reductase. ChemMedChem 2022; 17:e202200418. [PMID: 36193872 PMCID: PMC9827987 DOI: 10.1002/cmdc.202200418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/03/2022] [Indexed: 01/14/2023]
Abstract
A series of 5-[(phenethylamino)methyl]pyrimidine-2,4-diamines were assessed in silico as potential inhibitors of Plasmodium falciparum dihydrofolate reductase (PfDHFR), synthesised and tested for inhibitory activity against PfDHFR in vitro. The compounds displayed promising inhibitory activity against both wild-type (Ki 1.3-243 nM) and quadruple mutant (Ki 13-208 nM) PfDHFR in the biochemical enzyme assay, but were less potent in the whole-cell P. falciparum assay (IC50 (TM4/8.2) 0.4-28 μM; IC50 (V1S) 3.7-54 μM). Further investigation into the pharmacokinetic properties of these compounds may guide the development of more potent analogues.
Collapse
Affiliation(s)
- Khonzisizwe Somandi
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Tswene D. Seanego
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Tebogo Dlamini (née Molatsane)
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Matthew Maree
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Charles B. de Koning
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Roonglawan Rattanajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Thanaya Saeyang
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Amanda L. Rousseau
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| |
Collapse
|
6
|
Recent metabolomic developments for antimalarial drug discovery. Parasitol Res 2022; 121:3351-3380. [PMID: 36194273 DOI: 10.1007/s00436-022-07673-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/14/2022] [Indexed: 10/10/2022]
Abstract
Malaria is a parasitic disease that remains a global health issue, responsible for a significant death and morbidity toll. Various factors have impacted the use and delayed the development of antimalarial therapies, such as the associated financial cost and parasitic resistance. In order to discover new drugs and validate parasitic targets, a powerful omics tool, metabolomics, emerged as a reliable approach. However, as a fairly recent method in malaria, new findings are timely and original practices emerge frequently. This review aims to discuss recent research towards the development of new metabolomic methods in the context of uncovering antiplasmodial mechanisms of action in vitro and to point out innovative metabolic pathways that can revitalize the antimalarial pipeline.
Collapse
|
7
|
Seetin S, Saparpakorn P, Vanichtanankul J, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S, Hannongbua S. Key interactions of pyrimethamine derivatives specific to wild-type and mutant P. falciparum dihydrofolate reductase based on 3D-QSAR, MD simulations and quantum chemical calculations. J Biomol Struct Dyn 2022:1-16. [DOI: 10.1080/07391102.2022.2096114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Sasipha Seetin
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, PathumThani, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, Kasetsart University, Chatuchak, Bangkok, Thailand
| |
Collapse
|
8
|
Shamshad H, Bakri R, Mirza AZ. Dihydrofolate reductase, thymidylate synthase, and serine hydroxy methyltransferase: successful targets against some infectious diseases. Mol Biol Rep 2022; 49:6659-6691. [PMID: 35253073 PMCID: PMC8898753 DOI: 10.1007/s11033-022-07266-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Parasitic diseases have a serious impact on the world in terms of health and economics and are responsible for worldwide mortality and morbidity. The present review features the hybrid targeting involving three main enzymes for the treatment of different parasitic diseases. The enzymes Dihydrofolate reductase, thymidylate synthase, and Serine hydroxy methyltransferase play an essential role in the folate pathway. The present review focuses on these enzymes, which can be targeted against several diseases. It shed light on the past, present, and future of these targets, and it can be assessed that these targets can play a significant role against several infectious diseases. For combating viral and protozoal infectious diseases, these targets in combination should be addressed.
Collapse
Affiliation(s)
- Hina Shamshad
- Faculty of Pharmacy, Jinnah University for Women, Karachi, Pakistan
| | - Rowaida Bakri
- College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | | |
Collapse
|
9
|
Hoarau M, Suwanakitti N, Varatthan T, Thiabma R, Rattanajak R, Charoensetakul N, Redman EK, Khotavivattana T, Vilaivan T, Yuthavong Y, Kamchonwongpaisan S. Assay Development and Identification of the First Plasmodium falciparum 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113515. [PMID: 35684452 PMCID: PMC9182141 DOI: 10.3390/molecules27113515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022]
Abstract
In the fight towards eradication of malaria, identifying compounds active against new drug targets constitutes a key approach. Plasmodium falciparum 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (PfHPPK) has been advanced as a promising target, as being part of the parasite essential folate biosynthesis pathway while having no orthologue in the human genome. However, no drug discovery efforts have been reported on this enzyme. In this study, we conducted a three-step screening of our in-house antifolate library against PfHPPK using a newly designed PfHPPK-GFP protein construct. Combining virtual screening, differential scanning fluorimetry and enzymatic assay, we identified 14 compounds active against PfHPPK. Compounds’ binding modes were investigated by molecular docking, suggesting competitive binding with the HMDP substrate. Cytotoxicity and in vitro ADME properties of hit compounds were also assessed, showing good metabolic stability and low toxicity. The most active compounds displayed low micromolar IC50 against drug-resistant parasites. The reported hit compounds constitute a good starting point for inhibitor development against PfHPPK, as an alternative approach to tackle the malaria parasite.
Collapse
Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
- Correspondence:
| | - Nattida Suwanakitti
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Thaveechai Varatthan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Ratthiya Thiabma
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Roonglawan Rattanajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Netnapa Charoensetakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Emily K. Redman
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (E.K.R.); (T.V.)
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (E.K.R.); (T.V.)
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (N.S.); (T.V.); (R.T.); (R.R.); (N.C.); (Y.Y.); (S.K.)
| |
Collapse
|
10
|
Tanramluk D, Pakotiprapha D, Phoochaijaroen S, Chantravisut P, Thampradid S, Vanichtanankul J, Narupiyakul L, Akavipat R, Yuvaniyama J. MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure 2021; 30:181-189.e5. [PMID: 34614393 DOI: 10.1016/j.str.2021.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/25/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances, and active-site boundaries are used for the analysis of active sites. The algorithms derived provide model equations that can predict whether changes in distances, such as contraction or expansion, will result in improved binding affinity. The algorithm is confirmed using kinetic studies of dihydrofolate reductase (DHFR), together with two DHFR-TS crystal structures. Empirical analyses of 881 crystal structures involving 180 ligands are used to interpret protein-ligand binding affinities. MANORAA links to major biological databases for web-based analysis of drug design. The frequency of atoms inside the main protease structures, including those from SARS-CoV-2, shows how the rigid part of the ligand can be used as a probe for molecular design (http://manoraa.org).
Collapse
Affiliation(s)
- Duangrudee Tanramluk
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand.
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok 10400, Thailand
| | - Sakao Phoochaijaroen
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Pattra Chantravisut
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Sirikanya Thampradid
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok 10400, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Lalita Narupiyakul
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand; Department of Computer Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Ruj Akavipat
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Jirundon Yuvaniyama
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok 10400, Thailand
| |
Collapse
|
11
|
Hoarau M, Vanichtanankul J, Srimongkolpithak N, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S. Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem 2021; 36:198-206. [PMID: 33530764 PMCID: PMC8759724 DOI: 10.1080/14756366.2020.1854244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC50 in the 28-695 μM range and selectivity for PfDHFR. In addition to the known pyrimidine, three new anti-PfDHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with PfDHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.
Collapse
Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| |
Collapse
|
12
|
Remcho TP, Guggilapu SD, Cruz P, Nardone GA, Heffernan G, O'Connor RD, Bewley CA, Wellems TE, Lane KD. Regioisomerization of Antimalarial Drug WR99210 Explains the Inactivity of a Commercial Stock. Antimicrob Agents Chemother 2020; 65:e01385-20. [PMID: 33077647 PMCID: PMC7927815 DOI: 10.1128/aac.01385-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/09/2020] [Indexed: 11/20/2022] Open
Abstract
WR99210, a former antimalarial drug candidate now widely used for the selection of Plasmodium transfectants, selectively targets the parasite's dihydrofolate reductase thymidine synthase bifunctional enzyme (DHFR-TS) but not human DHFR, which is not fused with TS. Accordingly, WR99210 and plasmids expressing the human dhfr gene have become valued tools for the genetic modification of parasites in the laboratory. Concerns over the ineffectiveness of WR99210 from some sources encouraged us to investigate the biological and chemical differences of supplies from two different companies (compounds 1 and 2). Compound 1 proved effective at low nanomolar concentrations against Plasmodium falciparum parasites, whereas compound 2 was ineffective, even at micromolar concentrations. Intact and fragmented mass spectra indicated identical molecular formulae of the unprotonated (free base) structures of compounds 1 and 2; however, the compounds displayed differences by thin-layer chromatography, reverse-phase high-performance liquid chromatography, and UV-visible spectroscopy, indicating important isomeric differences. Structural evaluations by 1H, 13C, and 15N nuclear magnetic resonance spectroscopy confirmed compound 1 as WR99210 and compound 2 as a dihydrotriazine regioisomer. Induced fit computational docking models showed that compound 1 binds tightly and specifically in the P. falciparum DHFR active site, whereas compound 2 fits poorly to the active site in loose and varied orientations. Stocks and concentrates of WR99210 should be monitored for the presence of regioisomer 2, particularly when they are not supplied as the hydrochloride salt or are exposed to basic conditions that may promote rearrangement. Absorption spectroscopy can serve for assays of the unrearranged and rearranged triazines.
Collapse
Affiliation(s)
- T Parks Remcho
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Sravanthi D Guggilapu
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Phillip Cruz
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Glenn A Nardone
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Gavin Heffernan
- Jacobus Pharmaceutical Company, Inc., Princeton, New Jersey, USA
| | - Robert D O'Connor
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Kristin D Lane
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| |
Collapse
|