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Marín M, López M, Gallego-Yerga L, Álvarez R, Peláez R. Experimental structure based drug design (SBDD) applications for anti-leishmanial drugs: A paradigm shift? Med Res Rev 2024; 44:1055-1120. [PMID: 38142308 DOI: 10.1002/med.22005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
Leishmaniasis is a group of neglected tropical diseases caused by at least 20 species of Leishmania protozoa, which are spread by the bite of infected sandflies. There are three main forms of the disease: cutaneous leishmaniasis (CL, the most common), visceral leishmaniasis (VL, also known as kala-azar, the most serious), and mucocutaneous leishmaniasis. One billion people live in areas endemic to leishmaniasis, with an annual estimation of 30,000 new cases of VL and more than 1 million of CL. New treatments for leishmaniasis are an urgent need, as the existing ones are inefficient, toxic, and/or expensive. We have revised the experimental structure-based drug design (SBDD) efforts applied to the discovery of new drugs against leishmaniasis. We have grouped the explored targets according to the metabolic pathways they belong to, and the key achieved advances are highlighted and evaluated. In most cases, SBDD studies follow high-throughput screening campaigns and are secondary to pharmacokinetic optimization, due to the majoritarian belief that there are few validated targets for SBDD in leishmaniasis. However, some SBDD strategies have significantly contributed to new drug candidates against leishmaniasis and a bigger number holds promise for future development.
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Affiliation(s)
- Miguel Marín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Marta López
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
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Linciano P, Pozzi C, Tassone G, Landi G, Mangani S, Santucci M, Luciani R, Ferrari S, Santarem N, Tagliazucchi L, Cordeiro-da-Silva A, Tonelli M, Tondi D, Bertarini L, Gul S, Witt G, Moraes CB, Costantino L, Costi MP. The discovery of aryl-2-nitroethyl triamino pyrimidines as anti-Trypanosoma brucei agents. Eur J Med Chem 2024; 264:115946. [PMID: 38043491 DOI: 10.1016/j.ejmech.2023.115946] [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: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/05/2023]
Abstract
Pteridine reductase 1 (PTR1) is a catalytic protein belonging to the folate metabolic pathway in Trypanosmatidic parasites. PTR1 is a known target for the medicinal chemistry development of antiparasitic agents against Trypanosomiasis and Leishmaniasis. In previous studies, new nitro derivatives were elaborated as PTR1 inhibitors. The compounds showing a diamino-pyrimidine core structure were previously developed but they showed limited efficacy. Therefore, a new class of phenyl-, heteroaryl- and benzyloxy-nitro derivatives based on the 2-nitroethyl-2,4,6-triaminopyrimidine scaffold were designed and tested. The compounds were assayed for their ability to inhibit T. brucei and L. major PTR1 enzymes and for their antiparasitic activity towards T. brucei and L. infantum parasites. To understand the structure-activity relationships of the compounds against TbPTR1, the X-ray crystallographic structure of the 2,4,6-triaminopyrimidine (TAP) was obtained and molecular modelling studies were performed. As a next step, only the most effective compounds against T. brucei were then tested against the amastigote cellular stage of T. cruzi, searching for a broad-spectrum antiprotozoal agent. An early ADME-Tox profile evaluation was performed. The early toxicity profile of this class of compounds was investigated by measuring their inhibition of hERG and five cytochrome P450 isoforms (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4), cytotoxicity towards A549 cells and mitochondrial toxicity. Pharmacokinetic studies (SNAP-PK) were performed on selected compounds using hydroxypropyl-β-cyclodextrins (50 % w/v) to preliminarily study their plasma concentration when administered per os at a dose of 20 mg/kg. Compound 1p, showed the best pharmacodynamic and pharmacokinetic properties, can be considered a good candidate for further bioavailability and efficacy studies.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Nuno Santarem
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual; Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge ViterboFerreira 228, 4050-313 Porto, Portugal
| | - Lorenzo Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy; Clinical and Experimental Medicine (CEM) PhD Program, University of Modena and Reggio Emilia, Via Campi 278, 41125, Modena, Italy
| | - Anabela Cordeiro-da-Silva
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual; Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge ViterboFerreira 228, 4050-313 Porto, Portugal
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132, Genoa, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Laura Bertarini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Hamburg, Germany
| | - Gesa Witt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Hamburg, Germany
| | - Carolina B Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), 13083-100, Campinas, SP, Brazil
| | - Luca Costantino
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy.
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3
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Mohamed MAA, Kadry AM, Bekhit SA, Abourehab MAS, Amagase K, Ibrahim TM, El-Saghier AMM, Bekhit AA. Spiro heterocycles bearing piperidine moiety as potential scaffold for antileishmanial activity: synthesis, biological evaluation, and in silico studies. J Enzyme Inhib Med Chem 2023; 38:330-342. [PMID: 36444862 PMCID: PMC11003478 DOI: 10.1080/14756366.2022.2150763] [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: 10/11/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022] Open
Abstract
New spiro-piperidine derivatives were synthesised via the eco-friendly ionic liquids in a one-pot fashion. The in vitro antileishmanial activity against Leishmania major promastigote and amastigote forms highlighted promising antileishmanial activity for most of the derivatives, with superior activity compared to miltefosine. The most active compounds 8a and 9a exhibited sub-micromolar range of activity, with IC50 values of 0.89 µM and 0.50 µM, respectively, compared to 8.08 µM of miltefosine. Furthermore, the antileishmanial activity reversal of these compounds via folic and folinic acids displayed comparable results to the positive control trimethoprim. This emphasises that their antileishmanial activity is through the antifolate mechanism via targeting DHFR and PTR1. The most active compounds showed superior selectivity and safety profile compared to miltefosine against VERO cells. Moreover, the docking experiments of 8a and 9a against Lm-PTR1 rationalised the observed in vitro activities. Molecular dynamics simulations confirmed a stable and high potential binding to Lm-PTR1.
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Affiliation(s)
| | - Asmaa M. Kadry
- Chemistry Department, Faculty of Science, Sohag University, Sohag, Egypt
| | - Salma A. Bekhit
- High Institute of Public Health, Alexandria University, Alexandria, Egypt
| | | | - Kikuko Amagase
- Laboratory of Pharmacology & Pharmacotherapeutics, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | | | - Adnan A. Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Cancer Nanotechnology Research Laboratory (CNRL), Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Allied Health Department, College of Health and Sport Sciences, University of Bahrain, Sakhir, Kingdom of Bahrain
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4
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Possart K, Herrmann FC, Jose J, Schmidt TJ. In Silico and In Vitro Search for Dual Inhibitors of the Trypanosoma brucei and Leishmania major Pteridine Reductase 1 and Dihydrofolate Reductase. Molecules 2023; 28:7526. [PMID: 38005256 PMCID: PMC10673058 DOI: 10.3390/molecules28227526] [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: 09/27/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The parasites Trypanosoma brucei (Tb) and Leishmania major (Lm) cause the tropical diseases sleeping sickness, nagana, and cutaneous leishmaniasis. Every year, millions of humans, as well as animals, living in tropical to subtropical climates fall victim to these illnesses' health threats. The parasites' frequent drug resistance and widely spread natural reservoirs heavily impede disease prevention and treatment. Due to pteridine auxotrophy, trypanosomatid parasites have developed a peculiar enzyme system consisting of dihydrofolate reductase-thymidylate synthase (DHFR-TS) and pteridine reductase 1 (PTR1) to support cell survival. Extending our previous studies, we conducted a comparative study of the T. brucei (TbDHFR, TbPTR1) and L. major (LmDHFR, LmPTR1) enzymes to identify lead structures with a dual inhibitory effect. A pharmacophore-based in silico screening of three natural product databases (approximately 4880 compounds) was performed to preselect possible inhibitors. Building on the in silico results, the inhibitory potential of promising compounds was verified in vitro against the recombinant DHFR and PTR1 of both parasites using spectrophotometric enzyme assays. Twelve compounds were identified as dual inhibitors against the Tb enzymes (0.2 μM < IC50 < 85.1 μM) and ten against the respective Lm enzymes (0.6 μM < IC50 < 84.5 μM). These highly promising results may represent the starting point for the future development of new leads and drugs utilizing the trypanosomatid pteridine metabolism as a target.
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Affiliation(s)
- Katharina Possart
- University of Muenster, Institute for Pharmaceutical Biology and Phytochemistry (IPBP), PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany; (K.P.); (F.C.H.)
| | - Fabian C. Herrmann
- University of Muenster, Institute for Pharmaceutical Biology and Phytochemistry (IPBP), PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany; (K.P.); (F.C.H.)
| | - Joachim Jose
- University of Muenster, Institute of Pharmaceutical and Medicinal Chemistry, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany;
| | - Thomas J. Schmidt
- University of Muenster, Institute for Pharmaceutical Biology and Phytochemistry (IPBP), PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany; (K.P.); (F.C.H.)
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5
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Panecka-Hofman J, Poehner I. Structure and dynamics of pteridine reductase 1: the key phenomena relevant to enzyme function and drug design. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:521-532. [PMID: 37608196 PMCID: PMC10618315 DOI: 10.1007/s00249-023-01677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/08/2023] [Accepted: 07/24/2023] [Indexed: 08/24/2023]
Abstract
Pteridine reductase 1 (PTR1) is a folate and pterin pathway enzyme unique for pathogenic trypanosomatids. As a validated drug target, PTR1 has been the focus of recent research efforts aimed at finding more effective treatments against human parasitic diseases such as leishmaniasis or sleeping sickness. Previous PTR1-centered structural studies highlighted the enzyme characteristics, such as flexible regions around the active site, highly conserved structural waters, and species-specific differences in pocket properties and dynamics, which likely impacts the binding of natural substrates and inhibitors. Furthermore, several aspects of the PTR1 function, such as the substrate inhibition phenomenon and the level of ligand binding cooperativity in the enzyme homotetramer, likely related to the global enzyme dynamics, are poorly known at the molecular level. We postulate that future drug design efforts could greatly benefit from a better understanding of these phenomena through studying both the local and global PTR1 dynamics. This review highlights the key aspects of the PTR1 structure and dynamics relevant to structure-based drug design that could be effectively investigated by modeling approaches. Particular emphasis is given to the perspective of molecular dynamics, what has been accomplished in this area to date, and how modeling could impact the PTR1-targeted drug design in the future.
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Affiliation(s)
- Joanna Panecka-Hofman
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Ina Poehner
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211, Kuopio, Finland
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Silva JV, Sueyoshi S, Snape TJ, Lal S, Giarolla J. Pteridine reductase (PTR1): initial structure-activity relationships studies of potential leishmanicidal arylindole derivatives compounds. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:661-687. [PMID: 37606690 DOI: 10.1080/1062936x.2023.2247331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/08/2023] [Indexed: 08/23/2023]
Abstract
Leishmaniasis is a public health concern, especially in Brazil and India. The drugs available for therapy are old, cause toxicity and have reports of resistance. Therefore, this paper aimed to carry out initial structure-activity relationships (applying molecular docking and dynamic simulations) of arylindole scaffolds against the pteridine reductase (PTR1), which is essential target for the survival of the parasite. Thus, we used a series of 43 arylindole derivatives as a privileged skeleton, which have been evaluated previously for different biological actions. Compound 7 stood out among its analogues presenting the best results of average number of interactions with binding site (2.00) and catalytic triad (1.00). Additionally, the same compound presented the best binding free energy (-32.33 kcal/mol) in dynamic simulations. Furthermore, with computational studies, it was possible to comprehend and discuss the influences of the substituent sizes, positions of substitutions in the aromatic ring and electronic influences. Therefore, this study can be a starting point for the structural improvements needed to obtain a good leishmanicidal drug.
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Affiliation(s)
- J V Silva
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - S Sueyoshi
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - T J Snape
- Leicester School of Pharmacy, De Montfort University, Leicester, UK
| | - S Lal
- Amity Institute of Pharmacy, Amity University, Gurugram, India
| | - J Giarolla
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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7
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Sabt A, Eldehna WM, Ibrahim TM, Bekhit AA, Batran RZ. New antileishmanial quinoline linked isatin derivatives targeting DHFR-TS and PTR1: Design, synthesis, and molecular modeling studies. Eur J Med Chem 2023; 246:114959. [PMID: 36493614 DOI: 10.1016/j.ejmech.2022.114959] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/13/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
In a search for new drug candidates for one of the neglected tropical diseases, leishmaniasis, twenty quinoline-isatin hybrids were synthesized and tested for their in vitro antileishmanial activity against Leishmaniamajor strain. All the synthesized compounds showed promising in vitro activity against the promastigote form in a low micromolar range (IC50 = 0.5084-5.9486 μM) superior to the reference miltefosine (IC50 = 7.8976 μM). All the target compounds were then tested against the intracellular amastigote form and showed promising inhibition effects (IC50 = 0.60442-8.2948 μM versus 8.08 μM for miltefosine). Compounds 4e, 4b and 4f were shown to possess the highest antileishmanial activity against both promastigote and amastigote forms. The most active compounds were proven to exhibit their significant antileishmanial effects through antifolate mechanism, targeting DHFR-TS and PTR1. To evaluate the safety profile of the most active derivatives 4e, 4b and 4f, the in vitro cytotoxicity test was carried out and displayed higher selectivity indices than the reference miltefosine. Molecular docking within putative target protein PTR1 confirmed the high potentiality of the most active compounds 4e, 4b and 4f to block the catalytic activity of Lm-PTR1.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt; School of Biotechnology, Badr University in Cairo, Badr City, 11829, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt; Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
| | - Adnan A Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Pharmacy Program, Allied Health Department, College of Health Sciences, University of Bahrain, P.O. Box 32038, Bahrain
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, 12622, Egypt.
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8
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In vitro antileishmanial activity and molecular docking studies of lupeol and monostearin, isolated from Parkia biglobosa. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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9
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Dello Iacono L, Di Pisa F, Mangani S. Crystal structure of the ternary complex of Leishmania major pteridine reductase 1 with the cofactor NADP +/NADPH and the substrate folic acid. Acta Crystallogr F Struct Biol Commun 2022; 78:170-176. [PMID: 35400669 PMCID: PMC8996148 DOI: 10.1107/s2053230x22002795] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Pteridine reductase 1 (PTR1) is a key enzyme of the folate pathway in protozoan parasites of the genera Leishmania and Trypanosoma and is a valuable drug target for tropical diseases. This enzyme is able to catalyze the NADPH-dependent reduction of both conjugated (folate) and unconjugated (biopterin) pterins to their tetrahydro forms, starting from oxidized- or dihydro-state substrates. The currently available X-ray structures of Leishmania major PTR1 (LmPTR1) show the enzyme in its unbound, unconjugated substrate-bound (with biopterin derivatives) and inhibitor-bound forms. However, no structure has yet been determined of LmPTR1 bound to a conjugated substrate. Here, the high-resolution crystal structure of LmPTR1 in complex with folic acid is presented and the intermolecular forces that drive the binding of the substrate in the catalytic pocket are described. By expanding the collection of LmPTR1 structures in complex with process intermediates, additional insights into the active-site rearrangements that occur during the catalytic process are provided. In contrast to previous structures with biopterin derivatives, a small but significant difference in the orientation of Asp181 and Tyr194 of the catalytic triad is found. This feature is shared by PTR1 from T. brucei (TbPTR1) in complex with the same substrate molecule and may be informative in deciphering the importance of such residues at the beginning of the catalytic process.
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Affiliation(s)
- Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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10
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Synthesis, Antileishmanial Activity and Molecular Docking Study of New 3,4-Dihydropyrimidinones/Thiones. Pharm Chem J 2022. [DOI: 10.1007/s11094-021-02536-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Ramesh D, Sarkar D, Joji A, Singh M, Mohanty AK, G Vijayakumar B, Chatterjee M, Sriram D, Muthuvel SK, Kannan T. First-in-class pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones against leishmaniasis and tuberculosis: Rationale, in vitro, ex vivo studies and mechanistic insights. Arch Pharm (Weinheim) 2022; 355:e2100440. [PMID: 35106845 DOI: 10.1002/ardp.202100440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 11/06/2022]
Abstract
Pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones were synthesized, for the first time, from indole chalcones and 6-aminouracil, and their ability to inhibit leishmaniasis and tuberculosis (Tb) infections was evaluated. The in vitro antileishmanial activity against promastigotes of Leishmania donovani revealed exceptional activities of compounds 3, 12 and 13, with IC50 values ranging from 10.23 ± 1.50 to 15.58 ± 1.67 µg/ml, which is better than the IC50 value of the standard drug pentostam of 500 μg/ml. The selectivity of the compounds towards Leishmania parasites was evaluated via ex vivo studies in Swiss albino mice. The efficiency of these compounds against Tb infection was then evaluated using the in vitro anti-Tb microplate Alamar Blue assay. Five compounds, 3, 7, 8, 9 and 12, showed MIC100 values against the Mycobacterium tuberculosis H37 Rv strain at 25 µg/ml, and compound 20 yielded an MIC100 value of 50 µg/ml. Molecular modelling of these compounds highlighted interactions with binding sites of dihydrofolate reductase, pteridine reductase and thymidylate kinase, thus establishing the rationale of their pharmacological activity against both pathogens, which is consistent with the in vitro results. From the above results, it is clear that compounds 3 and 12 are promising lead candidates for Leishmania and Mycobacterium infections and may be promising for coinfections.
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Deblina Sarkar
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Annu Joji
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Monica Singh
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Amaresh K Mohanty
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
| | | | - Mitali Chatterjee
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Suresh K Muthuvel
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
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12
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Osman MS, Shantier SW, Awad TA, Garelnabi EA. In vitro evaluation, in silico studies and toxicological assay of some xanthones as potential Leishmania donovani inhibitors. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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13
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Porter I, Neal T, Walker Z, Hayes D, Fowler K, Billups N, Rhoades A, Smith C, Smith K, Staker BL, Dranow DM, Mayclin SJ, Subramanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis. Acta Crystallogr F Struct Biol Commun 2022; 78:31-38. [PMID: 34981773 PMCID: PMC8725004 DOI: 10.1107/s2053230x21013078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2023] Open
Abstract
Members of the bacterial genus Brucella cause brucellosis, a zoonotic disease that affects both livestock and wildlife. Brucella are category B infectious agents that can be aerosolized for biological warfare. As part of the structural genomics studies at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were produced and their structures are reported. The enzymes share ∼95% sequence identity but have less than 33% sequence identity to other homologues with known structure. The structures are prototypical NADPH-dependent short-chain reductases that share their highest tertiary-structural similarity with protozoan pteridine reductases, which are being investigated for rational therapeutic development.
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Affiliation(s)
- Imani Porter
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Trinity Neal
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Zion Walker
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Dylan Hayes
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Fowler
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Nyah Billups
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Anais Rhoades
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Christian Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kaelyn Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Oluwatoyin A Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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Santucci M, Luciani R, Gianquinto E, Pozzi C, Pisa FD, dello Iacono L, Landi G, Tagliazucchi L, Mangani S, Spyrakis F, Costi MP. Repurposing the Trypanosomatidic GSK Kinetobox for the Inhibition of Parasitic Pteridine and Dihydrofolate Reductases. Pharmaceuticals (Basel) 2021; 14:ph14121246. [PMID: 34959646 PMCID: PMC8704748 DOI: 10.3390/ph14121246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Three open-source anti-kinetoplastid chemical boxes derived from a whole-cell phenotypic screening by GlaxoSmithKline (Tres Cantos Anti-Kinetoplastid Screening, TCAKS) were exploited for the discovery of a novel core structure inspiring new treatments of parasitic diseases targeting the trypansosmatidic pteridine reductase 1 (PTR1) and dihydrofolate reductase (DHFR) enzymes. In total, 592 compounds were tested through medium-throughput screening assays. A subset of 14 compounds successfully inhibited the enzyme activity in the low micromolar range of at least one of the enzymes from both Trypanosoma brucei and Lesihmania major parasites (pan-inhibitors), or from both PTR1 and DHFR-TS of the same parasite (dual inhibitors). Molecular docking studies of the protein–ligand interaction focused on new scaffolds not reproducing the well-known antifolate core clearly explaining the experimental data. TCMDC-143249, classified as a benzenesulfonamide derivative by the QikProp descriptor tool, showed selective inhibition of PTR1 and growth inhibition of the kinetoplastid parasites in the 5 μM range. In our work, we enlarged the biological profile of the GSK Kinetobox and identified new core structures inhibiting selectively PTR1, effective against the kinetoplastid infectious protozoans. In perspective, we foresee the development of selective PTR1 and DHFR inhibitors for studies of drug combinations.
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Affiliation(s)
- Matteo Santucci
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.S.); (R.L.); (L.T.)
| | - Rosaria Luciani
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.S.); (R.L.); (L.T.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125 Turin, Italy; (E.G.); (F.S.)
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018–2020, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (C.P.); (F.d.P.); (L.d.I.); (G.L.); (S.M.)
| | - Flavio di Pisa
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018–2020, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (C.P.); (F.d.P.); (L.d.I.); (G.L.); (S.M.)
| | - Lucia dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018–2020, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (C.P.); (F.d.P.); (L.d.I.); (G.L.); (S.M.)
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018–2020, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (C.P.); (F.d.P.); (L.d.I.); (G.L.); (S.M.)
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.S.); (R.L.); (L.T.)
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy—Department of Excellence 2018–2020, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy; (C.P.); (F.d.P.); (L.d.I.); (G.L.); (S.M.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Giuria 9, 10125 Turin, Italy; (E.G.); (F.S.)
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy; (M.S.); (R.L.); (L.T.)
- Correspondence:
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15
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Boniface PK, Sano CM, Elizabeth FI. Unveiling the Targets Involved in the Quest of Antileishmanial Leads Using In silico Methods. Curr Drug Targets 2021; 21:681-712. [PMID: 32003668 DOI: 10.2174/1389450121666200128112948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/01/2023]
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease associated with several clinical manifestations, including cutaneous, mucocutaneous, and visceral forms. As currently available drugs have some limitations (toxicity, resistance, among others), the target-based identification has been an important approach to develop new leads against leishmaniasis. The present study aims to identify targets involved in the pharmacological action of potent antileishmanial compounds. METHODS The literature information regarding molecular interactions of antileishmanial compounds studied over the past half-decade is discussed. The information was obtained from databases such as Wiley, SciFinder, Science Direct, National Library of Medicine, American Chemical Society, Scientific Electronic Library Online, Scopus, Springer, Google Scholar, Web of Science, etc. Results: Numerous in vitro antileishmanial compounds showed affinity and selective interactions with enzymes such as arginase, pteridine reductase 1, trypanothione reductase, pyruvate kinase, among others, which are crucial for the survival and virulence of the Leishmania parasite. CONCLUSION The in-silico activity of small molecules (enzymes, proteins, among others) might be used as pharmacological tools to develop candidate compounds for the treatment of leishmaniasis. As some pharmacologically active compounds may act on more than one target, additional studies of the mechanism (s) of action of potent antileishmanial compounds might help to better understand their pharmacological action. Also, the optimization of promising antileishmanial compounds might improve their biological activity.
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Affiliation(s)
- Pone K Boniface
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Cinthya M Sano
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Ferreira I Elizabeth
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
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Herrera-Acevedo C, Perdomo-Madrigal C, Muratov EN, Scotti L, Scotti MT. Discovery of Alternative Chemotherapy Options for Leishmaniasis through Computational Studies of Asteraceae. ChemMedChem 2021; 16:1234-1245. [PMID: 33336460 DOI: 10.1002/cmdc.202000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a complex disease caused by over 20 Leishmania species that primarily affects populations with poor socioeconomic conditions. Currently available drugs for treating leishmaniasis include amphotericin B, paromomycin, and pentavalent antimonials, which have been associated with several limitations, such as low efficacy, the development of drug resistance, and high toxicity. Natural products are an interesting source of new drug candidates. The Asteraceae family includes more than 23 000 species worldwide. Secondary metabolites that can be found in species from this family have been widely explored as potential new treatments for leishmaniasis. Recently, computational tools have become more popular in medicinal chemistry to establish experimental designs, identify new drugs, and compare the molecular structures and activities of novel compounds. Herein, we review various studies that have used computational tools to examine various compounds identified in the Asteraceae family in the search for potential drug candidates against Leishmania.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Camilo Perdomo-Madrigal
- School of Science, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 n° 55-37, Bogotá D.C., Colombia
| | - Eugene N Muratov
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
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Shamshad H, Hafiz A, Althagafi II, Saeed M, Mirza AZ. Characterization of the Trypanosoma brucei Pteridine Reductase Active- Site using Computational Docking and Virtual Screening Techniques. Curr Comput Aided Drug Des 2020; 16:583-598. [DOI: 10.2174/1573409915666190827163327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/21/2019] [Accepted: 08/01/2019] [Indexed: 01/19/2023]
Abstract
Background:
Human African trypanosomiasis is a fatal disease prevalent in approximately
36 sub-Saharan countries. Emerging reports of drug resistance in Trypanosoma brucei are a serious
cause of concern as only limited drugs are available for the treatment of the disease. Pteridine reductase
is an enzyme of Trypanosoma brucei.
Methods:
It plays a critical role in the pterin metabolic pathway that is absolutely essential for its survival
in the human host. The success of finding a potent inhibitor in structure-based drug design lies
within the ability of computational tools to efficiently and accurately dock a ligand into the binding
cavity of the target protein. Here we report the computational characterization of Trypanosoma brucei
pteridine reductase (Tb-PR) active-site using twenty-four high-resolution co-crystal structures with various
drugs. Structurally, the Tb-PR active site can be grouped in two clusters; one with high Root Mean
Square Deviation (RMSD) of atomic positions and another with low RMSD of atomic positions. These
clusters provide fresh insight for rational drug design against Tb-PR. Henceforth, the effect of several
factors on docking accuracy, including ligand and protein flexibility were analyzed using Fred.
Results:
The online server was used to analyze the side chain flexibility and four proteins were selected
on the basis of results. The proteins were subjected to small-scale virtual screening using 85 compounds,
and statistics were calculated using Bedroc and roc curves. The enrichment factor was also calculated
for the proteins and scoring functions. The best scoring function was used to understand the ligand
protein interactions with top common compounds of four proteins. In addition, we made a 3D
structural comparison between the active site of Tb-PR and Leishmania major pteridine reductase (Lm-
PR). We described key structural differences between Tb-PR and Lm-PR that can be exploited for rational
drug design against these two human parasites.
Conclusion:
The results indicated that relying just on re-docking and cross-docking experiments for
virtual screening of libraries isn’t enough and results might be misleading. Hence it has been suggested
that small scale virtual screening should be performed prior to large scale screening.
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Affiliation(s)
- Hina Shamshad
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, University of Karachi, Karachi-75270, Pakistan
| | - Abdul Hafiz
- Department of Medical Parasitology, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ismail I. Althagafi
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Maria Saeed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi- 75270, Pakistan
| | - Agha Zeeshan Mirza
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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Kronenberger T, Ferreira GM, de Souza ADF, da Silva Santos S, Poso A, Ribeiro JA, Tavares MT, Pavan FR, Trossini GHG, Dias MVB, Parise-Filho R. Design, synthesis and biological activity of novel substituted 3-benzoic acid derivatives as MtDHFR inhibitors. Bioorg Med Chem 2020; 28:115600. [DOI: 10.1016/j.bmc.2020.115600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/02/2020] [Accepted: 06/16/2020] [Indexed: 10/24/2022]
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19
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Landi G, Linciano P, Tassone G, Costi MP, Mangani S, Pozzi C. High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor. Acta Crystallogr D Struct Biol 2020; 76:558-564. [PMID: 32496217 DOI: 10.1107/s2059798320004891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/06/2020] [Indexed: 11/10/2022] Open
Abstract
The protozoan parasite Trypanosoma brucei is the etiological agent of human African trypanosomiasis (HAT). HAT, together with other neglected tropical diseases, causes serious health and economic issues, especially in tropical and subtropical areas. The classical antifolates targeting dihydrofolate reductase (DHFR) are ineffective towards trypanosomatid parasites owing to a metabolic bypass by the expression of pteridine reductase 1 (PTR1). The combined inhibition of PTR1 and DHFR activities in Trypanosoma parasites represents a promising strategy for the development of new effective treatments for HAT. To date, only monocyclic and bicyclic aromatic systems have been proposed as inhibitors of T. brucei PTR1 (TbPTR1); nevertheless, the size of the catalytic cavity allows the accommodation of expanded molecular cores. Here, an innovative tricyclic-based compound has been explored as a TbPTR1-targeting molecule and its potential application for the development of a new class of PTR1 inhibitors has been evaluated. 2,4-Diaminopyrimido[4,5-b]indol-6-ol (1) was designed and synthesized, and was found to be effective in blocking TbPTR1 activity, with a Ki in the low-micromolar range. The binding mode of 1 was clarified through the structural characterization of its ternary complex with TbPTR1 and the cofactor NADP(H), which was determined to 1.30 Å resolution. The compound adopts a substrate-like orientation inside the cavity that maximizes the binding contributions of hydrophobic and hydrogen-bond interactions. The binding mode of 1 was compared with those of previously reported bicyclic inhibitors, providing new insights for the design of innovative tricyclic-based molecules targeting TbPTR1.
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Affiliation(s)
- Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy - Department of Excellence 2018-2022, 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
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy - Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy - Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy - Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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Crentsil JA, Yamthe LRT, Anibea BZ, Broni E, Kwofie SK, Tetteh JKA, Osei-Safo D. Leishmanicidal Potential of Hardwickiic Acid Isolated From Croton sylvaticus. Front Pharmacol 2020; 11:753. [PMID: 32523532 PMCID: PMC7261830 DOI: 10.3389/fphar.2020.00753] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/06/2020] [Indexed: 01/31/2023] Open
Abstract
Leishmania is a parasitic protozoon responsible for the neglected tropical disease Leishmaniasis. Approximately, 350 million people are susceptible and close to 70,000 death cases globally are reported annually. The lack of effective leishmanicides, the emergence of drug resistance and toxicity concerns necessitate the pursuit for effective antileishmanial drugs. Natural compounds serve as reservoirs for discovering new drugs due to their chemical diversity. Hardwickiic acid (HA) isolated from the stembark of Croton sylvaticus was evaluated for its leishmanicidal potential against Leishmania donovani and L. major promastigotes. The susceptibility of the promastigotes to HA was determined using the 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide/phenazine methosulfate colorimetric assay with Amphotericin B serving as positive control. HA showed a significant antileishmanial activity on L. donovani promastigotes with an IC50 value of 31.57± 0.06 µM with respect to the control drug, amphotericin B with IC50 of 3.35 ± 0.14 µM). The cytotoxic activity was observed to be CC50 = 247.83 ± 6.32 µM against 29.99 ± 2.82 µM for curcumin, the control, resulting in a selectivity index of SI = 7.85. Molecular modeling, docking and dynamics simulations of selected drug targets corroborated the observed antileishmanial activity of HA. Novel insights into the mechanisms of binding were obtained for trypanothione reductase (TR), pteridine reductase 1 (PTR1), and glutamate cysteine ligase (GCL). The binding affinity of HA to the drug targets LmGCL, LmPTR1, LdTR, LmTR, LdGCL, and LdPTR1 were obtained as -8.0, -7.8, -7.6, -7.5, -7.4 and -7.1 kcal/mol, respectively. The role of Lys16, Ser111, and Arg17 as critical residues required for binding to LdPTR1 was reinforced. HA was predicted as a Caspase-3 stimulant and Caspase-8 stimulant, implying a possible role in apoptosis, which was shown experimentally that HA induced parasite death by loss of membrane integrity. HA was also predicted as antileishmanial molecule corroborating the experimental activity. Therefore, HA is a promising antileishmanial molecule worthy of further development as a biotherapeutic agent.
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Affiliation(s)
- Justice Afrifa Crentsil
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences (CBAS), University of Ghana, Accra, Ghana
| | - Lauve Rachel Tchokouaha Yamthe
- Institute for Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon.,Department of Parasitology, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.,Antimicrobial and Biocontrol Agents Unit, Laboratory for Phytobiochemistry and Medicinal Plants Studies, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Barbara Zenabu Anibea
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences (CBAS), University of Ghana, Accra, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, CBAS, University of Ghana, Accra, Ghana
| | - Samuel Kojo Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, CBAS, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, CBAS, University of Ghana, Accra, Ghana.,Department of Medicine, Loyola University Medical Center, Maywood, IL, United States.,Department of Physics and Engineering Science, Coastal Carolina University, Conway, SC, United States
| | - John Kweku Amissah Tetteh
- Department of Immunology, College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorcas Osei-Safo
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences (CBAS), University of Ghana, Accra, Ghana
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Targeting pteridine reductase 1 and dihydrofolate reductase: the old is a new trend for leishmaniasis drug discovery. Future Med Chem 2019; 11:2107-2130. [DOI: 10.4155/fmc-2018-0512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases in the world and it is considered endemic in 88 countries. This disease is transmitted by a Leishmania spp. infected sandfly and it may lead to cutaneous or systemic manifestations. The preconized treatment has low efficacy and there are cases of resistance to some drugs. Therefore, the search for new efficient molecular targets that can lead to the preparation of new drugs must be pursued. This review aims to evaluate both Leishmania enzymes PTR1 and DHFR-TS as potential drug targets, highlight their inhibitors and to discuss critically the use of chemoinformatics to elucidate interactions and propose new molecules against these enzymes.
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Eldehna WM, Almahli H, Ibrahim TM, Fares M, Al-Warhi T, Boeckler FM, Bekhit AA, Abdel-Aziz HA. Synthesis, in vitro biological evaluation and in silico studies of certain arylnicotinic acids conjugated with aryl (thio)semicarbazides as a novel class of anti-leishmanial agents. Eur J Med Chem 2019; 179:335-346. [PMID: 31260888 DOI: 10.1016/j.ejmech.2019.06.051] [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] [Received: 03/07/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 11/29/2022]
Abstract
Herein we introduce new compounds as conjugates of arylnicotinic acids with aryl (thio)semicarbazide derivatives. Based on a structure-guided approach, they were designed to possess anti-leishmanial activity through anti-folate mechanism, via targeting Leishmania major pteridine reductase 1 (Lm-PTR1). The in vitro anti-promastigote and anti-amastigote activity were promising for many thiosemicarbazide derivatives and superior to the reference miltefosine. The most active compounds 8i and 8j exhibited their anti-amastigote activity with IC50 values of 4.2 and 3.3 μM, respectively, compared to reference miltefosine (IC50 value of 7.3). Their anti-folate mechanism was confirmed via the ability of folic and folinic acids to reverse the anti-leishmanial activity of these compounds, comparably to Lm-PTR1 inhibitor trimethoprim. Interestingly, the in vitro cytotoxicity test of the most active compounds displayed higher selectivity indices than that of miltefosine emphasizing their safety on mammalian cells. Furthermore, the docking experiments on Lm-PTR1 as a putative target rationalized the in vitro anti-leishmanial activity. The in silico predictions exhibited promising pharmacokinetics and drug-likeness profiles of the most active compounds. Generally, this work introduces a fruitful matrix for new anti-leishmanial chemotype which would extend the chemical space for the anti-leishmanial activity.
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Affiliation(s)
- Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
| | - Hadia Almahli
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt; Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany.
| | - Mohamed Fares
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, 11829, Egypt; School of Chemistry, University of Wollongong, Wollongong, 2522, New South Wales, Australia
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Frank M Boeckler
- Molecular Design and Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Adnan A Bekhit
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Pharmacy Program, Allied Health Department, College of Health Sciences, University of Bahrain, P.O. Box 32038, Kingdom of Bahrain
| | - Hatem A Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Cairo, 12622, Egypt
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Determination of Urinary Pterins by Capillary Electrophoresis Coupled with LED-Induced Fluorescence Detector. Molecules 2019; 24:molecules24061166. [PMID: 30909656 PMCID: PMC6470587 DOI: 10.3390/molecules24061166] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 11/18/2022] Open
Abstract
Urinary pterins have been found as potential biomarkers in many pathophysiological conditions including inflammation, viral infections, and cancer. However, pterins determination in biological samples is difficult due to their degradation under exposure to air, light, and heat. Besides, they occur at shallow concentration levels, and thus, standard UV detectors cannot be used without additional sample preconcentration. On the other hand, ultra-sensitive laser-induced fluorescence (LIF) detection can be used since pterins exhibit native fluorescence. The main factor that limits an everyday use of LIF detectors is its high price. Here, an alternative detector, i.e., light-emitted diode induced fluorescence (LEDIF) detector, was evaluated for the determination of pterins in urine samples after capillary electrophoresis (CE) separation. An optimized method was validated in terms of linearity range, limit of detection (LOD), limit of quantification (LOQ), intra- and interday precision and accuracy, sample stability in the autosampler, and sample stability during the freezing/thawing cycle. The obtained LOD (0.1 µM) and LOQ (0.3 µM) values were three-order of magnitude lower compared to UV detector, and two orders of magnitude higher compared to previously reported house-built LIF detector. The applicability of the validated method was demonstrated in the analysis of urine samples from healthy individuals and cancer patients.
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Kimuda MP, Laming D, Hoppe HC, Tastan Bishop Ö. Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays. Molecules 2019; 24:molecules24010142. [PMID: 30609681 PMCID: PMC6337619 DOI: 10.3390/molecules24010142] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 11/16/2022] Open
Abstract
Pteridine reductase 1 (PTR1) is a trypanosomatid multifunctional enzyme that provides a mechanism for escape of dihydrofolate reductase (DHFR) inhibition. This is because PTR1 can reduce pterins and folates. Trypanosomes require folates and pterins for survival and are unable to synthesize them de novo. Currently there are no anti-folate based Human African Trypanosomiasis (HAT) chemotherapeutics in use. Thus, successful dual inhibition of Trypanosoma brucei dihydrofolate reductase (TbDHFR) and Trypanosoma brucei pteridine reductase 1 (TbPTR1) has implications in the exploitation of anti-folates. We carried out molecular docking of a ligand library of 5742 compounds against TbPTR1 and identified 18 compounds showing promising binding modes. The protein-ligand complexes were subjected to molecular dynamics to characterize their molecular interactions and energetics, followed by in vitro testing. In this study, we identified five compounds which showed low micromolar Trypanosome growth inhibition in in vitro experiments that might be acting by inhibition of TbPTR1. Compounds RUBi004, RUBi007, RUBi014, and RUBi018 displayed moderate to strong antagonism (mutual reduction in potency) when used in combination with the known TbDHFR inhibitor, WR99210. This gave an indication that the compounds might inhibit both TbPTR1 and TbDHFR. RUBi016 showed an additive effect in the isobologram assay. Overall, our results provide a basis for scaffold optimization for further studies in the development of HAT anti-folates.
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Affiliation(s)
- Magambo Phillip Kimuda
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa.
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala 00256, Uganda.
| | - Dustin Laming
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa.
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Yao P, Xu Z, Yu S, Wu Q, Zhu D. Imine Reductase‐Catalyzed Enantioselective Reduction of Bulky α,β‐Unsaturated Imines en Route to a Pharmaceutically Important Morphinan Skeleton. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Peiyuan Yao
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme EngineeringSouth China University of Technology Guangzhou 510006 People's Republic of China
| | - Zefei Xu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Shanshan Yu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Qiaqing Wu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Dunming Zhu
- University of Chinese Academy of Sciences 19(A) Yuquan Road, Shijingshan District Beijing 100049 People's Republic of China
- National Engineering Laboratory for Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
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26
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Ghoneim AA, Ahmed Elkanzi NA, Bakr RB. Synthesis and studies molecular docking of some new thioxobenzo[g]pteridine derivatives and 1,4-dihydroquinoxaline derivatives with glycosidic moiety. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2018. [DOI: 10.1080/16583655.2018.1510163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Amira A. Ghoneim
- Chemistry Department, College of Science, Jouf University, Sakaka, Aljouf, Kingdom of Saudi Arabia
- Chemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Nadia Ali Ahmed Elkanzi
- Chemistry Department, College of Science, Jouf University, Sakaka, Aljouf, Kingdom of Saudi Arabia
- Chemistry Department, Faculty of Science, Aswan University, Aswan, Egypt
| | - Rania B. Bakr
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, Kingdom of Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
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Estébanez S, Lorente C, Kaufman TS, Larghi EL, Thomas AH, Serrano MP. Photophysical and Photochemical Properties of 3-methylpterin as a New and More Stable Pterin-type Photosensitizer. Photochem Photobiol 2018; 94:881-889. [PMID: 29729023 DOI: 10.1111/php.12931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/12/2018] [Indexed: 11/27/2022]
Abstract
Pterin derivatives are heterocyclic compounds which are present in different biological systems. Neutral aqueous solutions of pterins present acid-base and keto-enol equilibria. These compounds, under UV-A radiation fluoresce, undergo photooxidation, generate reactive oxygen species and photoinduce the oxidation of biological substrates. As photosensitizers, they may act through different mechanisms, mainly through an electron transfer-initiated process (type-I mechanism), but they also produce singlet molecular oxygen (1 O2 ) upon irradiation (type-II mechanism). In general, upon UV-A excitation two triplet states, corresponding to the lactim and lactam tautomers, are formed, but only the last one is the responsible for the photosensitized reactions of biomolecules. We present a study of the photochemical properties of 3-methylpterin (3-Mep) which, in contrast to most pterin derivatives, exists only in the lactam form. Also an improvement in the synthesis of 3-Mep is reported. The spectroscopic properties 3-Mep in aqueous solution were similar to those of the unsubstituted pterin derivative (Ptr) in its acid form, such as absorption, fluorescent and phosphorescent emission spectra. Experiments using 2'-deoxyguanosine 5'-monophosphate (dGMP) as oxidizable target demonstrated that methylation at C-3 position of the pterin moiety does not affect significantly the efficiency of photosensitization, but results in a more photostable sensitizer.
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Affiliation(s)
- Sandra Estébanez
- Departamento de Química, Facultad de Ciencias Exactas, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Carolina Lorente
- Departamento de Química, Facultad de Ciencias Exactas, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Teodoro S Kaufman
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Enrique L Larghi
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Andrés H Thomas
- Departamento de Química, Facultad de Ciencias Exactas, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Mariana P Serrano
- Departamento de Química, Facultad de Ciencias Exactas, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata (UNLP), La Plata, Argentina
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28
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Xiong X, Zhang Y, Zhang W. Simultaneous determination of twelve polar pteridines including dihydro- and tetrahydropteridine in human urine by hydrophilic interaction liquid chromatography with tandem mass spectrometry. Biomed Chromatogr 2018; 32:e4244. [PMID: 29575016 DOI: 10.1002/bmc.4244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 11/07/2022]
Abstract
Pteridines and their derivatives are important cofactors in the process of cell metabolism, and the level of urinary excretion of these compounds is considered as an important clinical criterion. In this work, a new separation method involving hydrophilic interaction chromatography (HILIC) with tandem mass spectrometric detection has been developed for the simultaneous analysis of 12 pteridines including oxidized, di- and tetrahydroforms, namely neopterin, 7,8-dihydroneopterin, biopterin, 7,8-dihydrobiopterin, 5,6,7,8-tetrahydrobiopterin, dimethylpterin, dimethyltetrahydropterin, pterin, isoxanthopterin, xanthopterin, sepiapterin and pterin-6-carboxylic acid, in human urine without oxidative pretreatments. The stabilizing agent (dithiothreitol) at various concentrations and the stability of oxidized, di- and tetrahydroforms during the sample's short-term storage and processing and of the extracts were tested. In the developed method, 12 pteridines were chromatographically separated on an ZIC-HILIC column by gradient elution, and the run time was 20 min. Matrix effect was evaluated and several dilutions of urine were tested in order to study the evolution of signal suppression. Spiked recovery studies demonstrated that the technique was both accurate (83.1-116.7%) and precise (RSD 1.4-15.6%). Finally, several clinical urine specimens without oxidative pretreatments were examined with the new technique and compared with previous reports.
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Affiliation(s)
- Xin Xiong
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
| | - Yuanyuan Zhang
- Department of Pharmacy, Peking University Third Hospital, Beijing, China
| | - Wenjing Zhang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
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29
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Herrmann FC, Sivakumar N, Jose J, Costi MP, Pozzi C, Schmidt TJ. In Silico Identification and In Vitro Evaluation of Natural Inhibitors of Leishmania major Pteridine Reductase I. Molecules 2017; 22:molecules22122166. [PMID: 29211037 PMCID: PMC6149668 DOI: 10.3390/molecules22122166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 12/29/2022] Open
Abstract
In a continuation of our computational efforts to find new natural inhibitors of a variety of target enzymes from parasites causing neglected tropical diseases (NTDs), we now report on 15 natural products (NPs) that we have identified as inhibitors of Leishmania major pteridine reductase I (LmPTR1) through a combination of in silico and in vitro investigations. Pteridine reductase (PTR1) is an enzyme of the trypanosomatid parasites’ peculiar folate metabolism, and has previously been validated as a drug target. Initially, pharmacophore queries were created based on four 3D structures of LmPTR1 using co-crystallized known inhibitors as templates. Each of the pharmacophore queries was used to virtually screen a database of 1100 commercially available natural products. The resulting hits were submitted to molecular docking analyses in the substrate binding site of the respective protein structures used for the pharmacophore design. This approach led to the in silico identification of a total of 18 NPs with predicted binding affinity to LmPTR1. These compounds were subsequently tested in vitro for inhibitory activity towards recombinant LmPTR1 in a spectrophotometric inhibition assay. Fifteen out of the 18 tested compounds (hit rate = 83%) showed significant inhibitory activity against LmPTR1 when tested at a concentration of 50 µM. The IC50 values were determined for the six NPs that inhibited the target enzyme by more than 50% at 50 µM, with sophoraflavanone G being the most active compound tested (IC50 = 19.2 µM). The NPs identified and evaluated in the present study may represent promising lead structures for the further rational drug design of more potent inhibitors against LmPTR1.
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Affiliation(s)
- Fabian C Herrmann
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
| | - Nirina Sivakumar
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, Correnstrasse 48, D-48149 Muenster, Germany.
| | - Maria P Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy.
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Thomas J Schmidt
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Muenster, PharmaCampus, Corrensstrasse 48, D-48149 Muenster, Germany.
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30
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Synthesis, modeling and biological evaluation of hybrids from pyrazolo[1,5c]pyrimidine as antileishmanial agents. Future Med Chem 2017; 9:1913-1929. [DOI: 10.4155/fmc-2017-0120] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: A new series of pyrazolo[1,5-c]pyrimidines were synthesized by different hybridization strategies. Methodology: All structures were confirmed by IR, 1H, 13C, 1H-13C heteronuclear multiple-quantum correlation (HMQC) spectra and microanalysis. They were evaluated for their in vitro antileishmanial activity against miltefosine and amphotericin B deoxycholate as reference drugs. Results: The most active compounds 2a and 9a demonstrated superior potencies to miltefosine by ten- and six-fold, respectively, for the promastigote form, and by 5.5-fold for the amastigote form. Their binding scenario to Leishmania major pteridine reductase was rationalized by docking experiments. In addition, all compounds were safe for the experimental animals orally up to 150 mg/kg and parenterally up to 75 mg/kg. Conclusion: This study provides novel chemotype class for antileishmanial activity. [Formula: see text]
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31
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Wachsmuth LM, Johnson MG, Gavenonis J. Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions. PLoS Negl Trop Dis 2017; 11:e0005720. [PMID: 28662026 PMCID: PMC5507555 DOI: 10.1371/journal.pntd.0005720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 07/12/2017] [Accepted: 06/16/2017] [Indexed: 12/18/2022] Open
Abstract
Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide synthesis. Computational alanine scanning of these protein-protein interfaces has revealed a host of potentially ligandable sites on several established and emerging anti-parasitic drug targets. Analysis of interfaces with multiple clustered hotspots has suggested several potentially inhibitable protein-protein interactions that may have been overlooked by previous large-scale analyses focusing solely on secondary structure. These protein-protein interactions provide a promising lead for the development of new peptide and macrocycle inhibitors of these enzymes.
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Affiliation(s)
- Leah M. Wachsmuth
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
| | - Meredith G. Johnson
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
| | - Jason Gavenonis
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
- * E-mail:
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32
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Di Pisa F, Landi G, Dello Iacono L, Pozzi C, Borsari C, Ferrari S, Santucci M, Santarem N, Cordeiro-da-Silva A, Moraes CB, Alcantara LM, Fontana V, Freitas-Junior LH, Gul S, Kuzikov M, Behrens B, Pöhner I, Wade RC, Costi MP, Mangani S. Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules 2017; 22:molecules22030426. [PMID: 28282886 PMCID: PMC6155272 DOI: 10.3390/molecules22030426] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 01/28/2023] Open
Abstract
Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues (1–3) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes (Trypanosoma brucei PTR1–TbPTR1 and Leishmania major–LmPTR1) and parasites (Trypanosoma brucei and Leishmania infantum). A crystal structure of TbPTR1 in complex with compound 1 and the first crystal structures of LmPTR1-flavanone complexes (compounds 1 and 3) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.
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Affiliation(s)
- Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Chiara Borsari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Nuno Santarem
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Anabela Cordeiro-da-Silva
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Carolina B Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Laura M Alcantara
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Vanessa Fontana
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Lucio H Freitas-Junior
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
- GARDE, Instituto Butantan, São Paulo SP05503-900, Brazil.
| | - Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Birte Behrens
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino (FI), Italy.
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Sebestyén M, Kóczán G, Hudecz F. Pitfalls in the synthesis of fluorescent methotrexate oligopeptide conjugates. Amino Acids 2016; 48:2599-2604. [PMID: 27357306 DOI: 10.1007/s00726-016-2285-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/20/2016] [Indexed: 11/28/2022]
Abstract
Methotrexate (MTX) conjugates with poly[Lys(DL-Alam)] based polymeric polypeptides are efficient against Leishmania donovani parasite infection, but the mechanism of the effect is not known yet. We prepared therefore the 5(6)-carboxyfluorescein (Cf) labeled oligopeptide [Cf-K(AaAa)] (a: D-alanine, A: L-alanine) and the corresponding MTX conjugates [Cf-K(MTX-AaAa)] as model compounds for structure-activity experiments. The conjugate aimed to be synthesized with solid phase methodology on MBHA resin with Boc strategy, using Fmoc-Lys(Boc)-OH. However, various side reactions were identified. Here we report three problems observed during the synthesis as well as solutions developed by us: (1) unexpected cyclopeptide-formation with the lactone-carboxylic group of the Cf was detected, when Cf was attached to the α-amino group of the Lys residue on solid phase. This was avoided by changing the order of Cf incorporation with using Fmoc/Dde strategy. Alternatively, we have built the peptide with Fmoc strategy on solid phase first and performed the labeling with Cf-OSu subsequently in solution. (2) During HF cleavage of the protected conjugates, MTX was demonstrated to form adducts with anisole and p-cresol scavengers, and the TMSOTf cleavage methodology was also found to be inadequate due to the large number of side products formed. We report here that using Fmoc/Dde strategy is an appropriate method to circumvent the cleavage with HF or TMSOTf. (3) During the coupling of MTX with oligopeptide, structural and stereo isomers are formed. We have described here the suitable conditions of HPLC separation of these products.
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Affiliation(s)
- Mónika Sebestyén
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest 112, POB. 32, 1518, Hungary
| | - György Kóczán
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest 112, POB. 32, 1518, Hungary
| | - Ferenc Hudecz
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest 112, POB. 32, 1518, Hungary. .,Department of Organic Chemistry, Eötvös Loránd University, Budapest 112, POB. 32, 1518, Hungary.
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34
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Bekhit AA, Hassan AM, Abd El Razik HA, El-Miligy MM, El-Agroudy EJ, Bekhit AEDA. New heterocyclic hybrids of pyrazole and its bioisosteres: Design, synthesis and biological evaluation as dual acting antimalarial-antileishmanial agents. Eur J Med Chem 2015; 94:30-44. [DOI: 10.1016/j.ejmech.2015.02.038] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/01/2014] [Accepted: 02/19/2015] [Indexed: 10/24/2022]
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Thermodynamics and solvent linkage of macromolecule-ligand interactions. Methods 2014; 76:51-60. [PMID: 25462561 DOI: 10.1016/j.ymeth.2014.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 02/06/2023] Open
Abstract
Binding involves two steps, desolvation and association. While water is ubiquitous and occurs at high concentration, it is typically ignored. In vitro experiments typically use infinite dilution conditions, while in vivo, the concentration of water is decreased due to the presence of high concentrations of molecules in the cellular milieu. This review discusses isothermal titration calorimetry approaches that address the role of water in binding. For example, use of D2O allows the contribution of solvent reorganization to the enthalpy component to be assessed. Further, the addition of osmolytes will decrease the water activity of a solution and allow effects on Ka to be determined. In most cases, binding becomes tighter in the presence of osmolytes as the desolvation penalty associated with binding is minimized. In other cases, the osmolytes prefer to interact with the ligand or protein, and if their removal is more difficult than shedding water, then binding can be weakened. These complicating layers can be discerned by different slopes in ln(Ka) vs osmolality plots and by differential scanning calorimetry in the presence of the osmolyte.
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Waugh B, Ghosh A, Bhattacharyya D, Ghoshal N, Banerjee R. In silico work flow for scaffold hopping in Leishmania. BMC Res Notes 2014; 7:802. [PMID: 25399834 PMCID: PMC4247209 DOI: 10.1186/1756-0500-7-802] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/29/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Leishmaniasis,a broad spectrum of diseases caused by several sister species of protozoa belonging to family trypanosomatidae and genus leishmania , generally affects poorer sections of the populace in third world countries. With the emergence of strains resistant to traditional therapies and the high cost of second line drugs which generally have severe side effects, it becomes imperative to continue the search for alternative drugs to combat the disease. In this work, the leishmanial genomes and the human genome have been compared to identify proteins unique to the parasite and whose structures (or those of close homologues) are available in the Protein Data Bank. Subsequent to the prioritization of these proteins (based on their essentiality, virulence factor etc.), inhibitors have been identified for a subset of these prospective drug targets by means of an exhaustive literature survey. A set of three dimensional protein-ligand complexes have been assembled from the list of leishmanial drug targets by culling structures from the Protein Data Bank or by means of template based homology modeling followed by ligand docking with the GOLD software. Based on these complexes several structure based pharmacophores have been designed and used to search for alternative inhibitors in the ZINC database. RESULT This process led to a list of prospective compounds which could serve as potential antileishmanials. These small molecules were also used to search the Drug Bank to identify prospective lead compounds already in use as approved drugs. Interestingly, paromomycin which is currently being used as an antileishmanial drug spontaneously appeared in the list, probably giving added confidence to the 'scaffold hopping' computational procedures adopted in this work. CONCLUSIONS The report thus provides the basis to experimentally verify several lead compounds for their predicted antileishmanial activity and includes several useful data bases of prospective drug targets in leishmania, their inhibitors and protein--inhibitor three dimensional complexes.
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Affiliation(s)
- Barnali Waugh
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
| | - Ambarnil Ghosh
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
| | - Dhananjay Bhattacharyya
- />Computer Science Division, Saha Institute of Nuclear Physics, Sector-1, Block AF, Biddhannagar, Kolkata, 700064 India
| | - Nanda Ghoshal
- />Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Rahul Banerjee
- />Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Sector - 1, Block – AF, Bidhannagar, Kolkata, 700064 India
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Krajíček J, Kozlík P, Exnerová A, Štys P, Bursová M, Čabala R, Bosáková Z. Capillary electrophoresis of pterin derivatives responsible for the warning coloration of Heteroptera. J Chromatogr A 2014; 1336:94-100. [DOI: 10.1016/j.chroma.2014.02.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Bhojane PP, Duff MR, Patel HC, Vogt ME, Howell EE. Investigation of osmolyte effects on FolM: comparison with other dihydrofolate reductases. Biochemistry 2014; 53:1330-41. [PMID: 24517487 DOI: 10.1021/bi4014165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A weak association between osmolytes and dihydrofolate (DHF) decreases the affinity of the substrate for the Escherichia coli chromosomal and R67 plasmid dihydrofolate reductase (DHFR) enzymes. To test whether the osmolyte-DHF association also interferes with binding of DHF to FolM, an E. coli enzyme that possesses weak DHFR activity, ligand binding was monitored in the presence of osmolytes. The affinity of FolM for DHF, measured by kcat/Km(DHF), was decreased by the addition of an osmolyte. Additionally, binding of the antifolate drug, methotrexate, to FolM was weakened by the addition of an osmolyte. The changes in ligand binding with water activity were unique for each osmolyte, indicating preferential interaction between the osmolyte and folate and its derivatives; however, additional evidence provided support for further interactions between FolM and osmolytes. Binding of the reduced nicotinamide adenine dinucleotide phosphate (NADPH) cofactor to FolM was monitored by isothermal titration calorimetry as a control for protein-osmolyte association. In the presence of betaine (proposed to be the osmolyte most excluded from protein surfaces), the NADPH Kd decreased, consistent with dehydration effects. However, other osmolytes did not tighten binding to the cofactor. Rather, dimethyl sulfoxide (DMSO) had no effect on the NADPH Kd, while ethylene glycol and polyethylene glycol 400 weakened cofactor binding. Differential scanning calorimetry of FolM in the presence of osmolytes showed that both DMSO and ethylene glycol decreased the stability of FolM, while betaine increased the stability of the protein. These results suggest that some osmolytes can destabilize FolM by preferentially interacting with the protein. Further, these weak attractions can impede ligand binding. These various contributions have to be considered when interpreting osmotic pressure results.
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Affiliation(s)
- Purva P Bhojane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996-0840, United States
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Dube D, Sharma S, Singh TP, Kaur P. Pharmacophore Mapping, In Silico Screening and Molecular Docking to Identify SelectiveTrypanosoma bruceiPteridine Reductase Inhibitors. Mol Inform 2014; 33:124-34. [DOI: 10.1002/minf.201300023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 11/05/2013] [Indexed: 12/17/2022]
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Ogungbe IV, Erwin WR, Setzer WN. Antileishmanial phytochemical phenolics: molecular docking to potential protein targets. J Mol Graph Model 2014; 48:105-17. [PMID: 24463105 DOI: 10.1016/j.jmgm.2013.12.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 12/21/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022]
Abstract
A molecular docking analysis has been carried out to examine potential Leishmania protein targets of antiprotozoal plant-derived polyphenolic compounds. A total of 352 phenolic phytochemicals, including 10 aurones, six cannabinoids, 34 chalcones, 20 chromenes, 52 coumarins, 92 flavonoids, 41 isoflavonoids, 52 lignans, 25 quinones, eight stilbenoids, nine xanthones, and three miscellaneous phenolic compounds, were used in the virtual screening study using 24 Leishmania enzymes (52 different protein structures from the Protein Data Bank). Noteworthy protein targets were Leishmania dihydroorotate dehydrogenase, N-myristoyl transferase, phosphodiesterase B1, pteridine reductase, methionyl-tRNA synthetase, tyrosyl-tRNA synthetase, uridine diphosphate-glucose pyrophosphorylase, nicotinamidase, and glycerol-3-phosphate dehydrogenase. Based on in-silico analysis of antiparasitic polyphenolics in this study, two aurones, one chalcone, five coumarins, six flavonoids, one isoflavonoid, three lignans, and one stilbenoid, can be considered to be promising drug leads worthy of further investigation.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry & Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William R Erwin
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Interactions of antiparasitic alkaloids with Leishmania protein targets: a molecular docking analysis. Future Med Chem 2013; 5:1777-99. [DOI: 10.4155/fmc.13.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Background: Leishmaniasis is a collection of chronic diseases caused by protozoa of the genus Leishmania. Current antileishmanial chemotherapeutics have demonstrated adverse side effects and therefore R&D into new safer alternative treatments are needed. Methods: A molecular docking analysis has been carried out to assess possible Leishmania biochemical targets of antiparasitic alkaloids. A total of 209 antiparasitic alkaloids were docked with 24 Leishmania protein targets. Results: The strongest docking alkaloid ligands were flinderoles A and B and juliflorine with Leishmania major methionyl-tRNA synthetase; juliflorine, juliprosine, prosopilosidine and prosopilosine with Leishmania mexicana glycerol-3-phosphate dehydrogenase; and ancistrogriffithine A with L. major N-myristoyl transferase. Conclusion: This molecular docking study has provided evidence for what classes and structural types of alkaloids may be targeting specific Leishmania protein targets.
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In-silico Leishmania target selectivity of antiparasitic terpenoids. Molecules 2013; 18:7761-847. [PMID: 23823876 PMCID: PMC6270436 DOI: 10.3390/molecules18077761] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 01/21/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), like leishmaniasis, are major causes of mortality in resource-limited countries. The mortality associated with these diseases is largely due to fragile healthcare systems, lack of access to medicines, and resistance by the parasites to the few available drugs. Many antiparasitic plant-derived isoprenoids have been reported, and many of them have good in vitro activity against various forms of Leishmania spp. In this work, potential Leishmania biochemical targets of antiparasitic isoprenoids were studied in silico. Antiparasitic monoterpenoids selectively docked to L. infantum nicotinamidase, L. major uridine diphosphate-glucose pyrophosphorylase and methionyl t-RNA synthetase. The two protein targets selectively targeted by germacranolide sesquiterpenoids were L. major methionyl t-RNA synthetase and dihydroorotate dehydrogenase. Diterpenoids generally favored docking to L. mexicana glycerol-3-phosphate dehydrogenase. Limonoids also showed some selectivity for L. mexicana glycerol-3-phosphate dehydrogenase and L. major dihydroorotate dehydrogenase while withanolides docked more selectively with L. major uridine diphosphate-glucose pyrophosphorylase. The selectivity of the different classes of antiparasitic compounds for the protein targets considered in this work can be explored in fragment- and/or structure-based drug design towards the development of leads for new antileishmanial drugs.
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Sturm N, Desaphy J, Quinn RJ, Rognan D, Kellenberger E. Structural insights into the molecular basis of the ligand promiscuity. J Chem Inf Model 2012; 52:2410-21. [PMID: 22920885 DOI: 10.1021/ci300196g] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Selectivity is a key factor in drug development. In this paper, we questioned the Protein Data Bank to better understand the reasons for the promiscuity of bioactive compounds. We assembled a data set of >1000 pairs of three-dimensional structures of complexes between a "drug-like" ligand (as its physicochemical properties overlap that of approved drugs) and two distinct "druggable" protein targets (as their binding sites are likely to accommodate "drug-like" ligands). Studying the similarity between the ligand-binding sites in the different targets revealed that the lack of selectivity of a ligand can be due (i) to the fact that Nature has created the same binding pocket in different proteins, which do not necessarily have otherwise sequence or fold similarity, or (ii) to specific characteristics of the ligand itself. In particular, we demonstrated that many ligands can adapt to different protein environments by changing their conformation, by using different chemical moieties to anchor to different targets, or by adopting unusual extreme binding modes (e.g., only apolar contact between the ligand and the protein, even though polar groups are present on the ligand or at the protein surface). Lastly, we provided new elements in support to the recent studies which suggest that the promiscuity of a ligand might be inferred from its molecular complexity.
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Affiliation(s)
- Noé Sturm
- UMR 7200 CNRS/Université de Strasbourg, MEDALIS Drug Discovery Center, 74 Route du Rhin, 67401 Illkirch, France
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Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases. Proc Natl Acad Sci U S A 2012; 109:5681-6. [PMID: 22451903 DOI: 10.1073/pnas.1118680109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacterial NRPSs performs two consecutive [2 + 2]e(-) reductions to release thioester-bound lipopeptides as corresponding alcohols, using a nonprocessive mechanism of catalysis. The first crystal structure of an R domain from Mycobacterium tuberculosis NRPS provides strong support to this mechanistic model and suggests that the displacement of intermediate would be required for cofactor recycling. We show that 4e(-) reductases produce alcohols through a committed aldehyde intermediate, and the reduction of this intermediate is at least 10 times more efficient than the thioester-substrate. Structural and biochemical studies also provide evidence for the conformational changes associated with the reductive cycle. Further, we show that the large substrate-binding pocket with a hydrophobic platform accounts for the remarkable substrate promiscuity of these domains. Our studies present an elegant example of the recruitment of a canonical short-chain dehydrogenase/reductase family member as an off-loading domain in the context of assembly-line enzymology.
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46
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Eadsforth TC, Cameron S, Hunter WN. The crystal structure of Leishmania major N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase and assessment of a potential drug target. Mol Biochem Parasitol 2012; 181:178-85. [PMID: 22108435 PMCID: PMC3368264 DOI: 10.1016/j.molbiopara.2011.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/03/2011] [Accepted: 11/07/2011] [Indexed: 01/24/2023]
Abstract
Three enzyme activities in the protozoan Leishmania major, namely N(5),N(10)-methylenetetrahydrofolate dehydrogenase/N(5),N(10)-methenyltetrahydrofolate cyclohydrolase (DHCH) and N(10)-formyltetrahydrofolate ligase (FTL) produce the essential intermediate N(10)-formyltetrahydrofolate. Although trypanosomatids possess at least one functional DHCH, the same is not true for FTL, which is absent in Trypanosoma brucei. Here, we present the 2.7 Å resolution crystal structure of the bifunctional apo-DHCH from L. major, which is a potential drug target. Sequence alignments show that the cytosolic enzymes found in trypanosomatids share a high level of identity of approximately 60%. Additionally, residues that interact and participate in catalysis in the human homologue are conserved amongst trypanosomatid sequences and this may complicate attempts to derive potent, parasite specific DHCH inhibitors.
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Affiliation(s)
| | | | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Dube D, Periwal V, Kumar M, Sharma S, Singh TP, Kaur P. 3D-QSAR based pharmacophore modeling and virtual screening for identification of novel pteridine reductase inhibitors. J Mol Model 2011; 18:1701-11. [PMID: 21826447 DOI: 10.1007/s00894-011-1187-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/12/2011] [Indexed: 10/17/2022]
Abstract
Pteridine reductase is a promising target for development of novel therapeutic agents against Trypanosomatid parasites. A 3D-QSAR pharmacophore hypothesis has been generated for a series of L. major pteridine reductase inhibitors using Catalyst/HypoGen algorithm for identification of the chemical features that are responsible for the inhibitory activity. Four pharmacophore features, namely: two H-bond donors (D), one Hydrophobic aromatic (H) and one Ring aromatic (R) have been identified as key features involved in inhibitor-PTR1 interaction. These features are able to predict the activity of external test set of pteridine reductase inhibitors with a correlation coefficient (r) of 0.80. Based on the analysis of the best hypotheses, some potent Pteridine reductase inhibitors were screened out and predicted with anti-PTR1 activity. It turned out that the newly identified inhibitory molecules are at least 300 fold more potent than the current crop of existing inhibitors. Overall the current SAR study is an effort for elucidating quantitative structure-activity relationship for the PTR1 inhibitors. The results from the combined 3D-QSAR modeling and molecular docking approach have led to the prediction of new potent inhibitory scaffolds.
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Affiliation(s)
- Divya Dube
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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Barrack KL, Tulloch LB, Burke LA, Fyfe PK, Hunter WN. Structure of recombinant Leishmania donovani pteridine reductase reveals a disordered active site. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:33-7. [PMID: 21206018 PMCID: PMC3079966 DOI: 10.1107/s174430911004724x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 11/15/2010] [Indexed: 02/04/2023]
Abstract
Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species, protozoa that are responsible for a range of serious diseases found in tropical and subtropical parts of the world. As part of a structure-based approach to inhibitor development, specifically targeting Leishmania species, well ordered crystals of L. donovani PTR1 were sought to support the characterization of complexes formed with inhibitors. An efficient system for recombinant protein production was prepared and the enzyme was purified and crystallized in an orthorhombic form with ammonium sulfate as the precipitant. Diffraction data were measured to 2.5 Å resolution and the structure was solved by molecular replacement. However, a sulfate occupies a phosphate-binding site used by NADPH and occludes cofactor binding. The nicotinamide moiety is a critical component of the active site and without it this part of the structure is disordered. The crystal form obtained under these conditions is therefore unsuitable for the characterization of inhibitor complexes.
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Affiliation(s)
- Keri L. Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Lindsay B. Tulloch
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Lynsey-Ann Burke
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Paul K. Fyfe
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Dawson A, Tulloch LB, Barrack KL, Hunter WN. High-resolution structures of Trypanosoma brucei pteridine reductase ligand complexes inform on the placement of new molecular entities in the active site of a potential drug target. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1334-40. [PMID: 21123874 PMCID: PMC3655514 DOI: 10.1107/s0907444910040886] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/12/2010] [Indexed: 03/07/2023]
Abstract
Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species. These protozoa cause serious diseases for which current therapies are inadequate. High-resolution structures have been determined, using data between 1.6 and 1.1 Å resolution, of T. brucei PTR1 in complex with pemetrexed, trimetrexate, cyromazine and a 2,4-diaminopyrimidine derivative. The structures provide insight into the interactions formed by new molecular entities in the enzyme active site with ligands that represent lead compounds for structure-based inhibitor development and to support early-stage drug discovery.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | | | - Keri L. Barrack
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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