1
|
Suwanakitti N, Talawanich Y, Vanichtanankul J, Taweechai S, Yuthavong Y, Kamchonwongpaisan S, Kongkasuriyachai D. folA thyA knockout E. coli as a suitable surrogate model for evaluation of antifolate sensitivity against PfDHFR-TS. Acta Trop 2024; 258:107360. [PMID: 39142549 DOI: 10.1016/j.actatropica.2024.107360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024]
Abstract
A new superior bacteria complementation model was achieved for testing antifolate compounds and investigating antifolate resistance in the dihydrofolate reductase (DHFR) enzyme of the malaria parasite. Earlier models depended on the addition of trimethoprim (TMP) to chemically suppress the host Escherichia coli (Ec) DHFR function. However, incomplete suppression of EcDHFR and potential interference of antibiotics needed to maintain plasmids for complementary gene expression can complicate the interpretations. To overcome such limitations, the folA (F) and thyA (T) genes were genetically knocked out (Δ) in E. coli BL21(DE3). The resulting EcΔFΔT cells were thymidine auxotroph where thymidine supplementation or functional complementation with heterologous DHFR-thymidylate synthase (TS) is needed to restore the loss of gene functions. When tested against pyrimethamine (PYR) and its analogs designed to target Plasmodium falciparum (Pf) DHFR-TS, the 50 % inhibitory concentration values obtained from EcΔFΔT surrogates expressing wildtype (PfTM4) or double mutant (PfK1) DHFR-TS showed strong correlations to the results obtained from the standard in vitro P. falciparum growth inhibition assay. Interestingly, while TMP had little effect on the susceptibility to PYR and analogs in EcΔFΔT expressing PfDHFR-TS, it hypersensitized the chemically knockdown E. coli BL21(DE3) expressing PfTM4 DHFR-TS but desensitized the one carrying PfK1 DHFR-TS. The low intrinsic expression level of PfTM4 in E. coli BL21(DE3) by western blot analysis may explain the hypersensitive to antifolates of chemical knockdown bacteria surrogate. These results demonstrated the usefulness of EcΔFΔT surrogate as a new tool for antifolate antimalarial screening with potential application for investigation of antifolate resistance mechanism.
Collapse
Affiliation(s)
- Nattida Suwanakitti
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Yuwadee Talawanich
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Supannee Taweechai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand
| | - Darin Kongkasuriyachai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Thailand Science Park, Pathumthani, Thailand.
| |
Collapse
|
2
|
Akinnusi PA, Olubode SO, Adebesin AO, Osadipe TJ, Nwankwo DO, Adebisi AD, Titilayo I BA, Alo YM, Owoloye A, Oyebola KM. Structure-based scoring of anthocyanins and molecular modeling of PfLDH, PfDHODH, and PfDHFR reveal novel potential P. falciparum inhibitors. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
|
3
|
An In Silico Study of the Interactions of Alkaloids from Cryptolepis sanguinolenta with Plasmodium falciparum Dihydrofolate Reductase and Dihydroorotate Dehydrogenase. J CHEM-NY 2022. [DOI: 10.1155/2022/5314179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Plasmodium falciparum dihydrofolate reductase (PfDHFR) and dihydroorotate dehydrogenase (PfDHODH) are essential for Plasmodium falciparum growth and development, and have been validated as targets for the development of new antimalarial agents. Several alkaloids isolated from Cryptolepis sanguinolenta have been reported to have antiplasmodial activity, but their protein targets are unknown. Therefore, molecular docking and molecular dynamics simulations were used to investigate the interactions and stability of the alkaloids with PfDHFR and PfDHODH. Based on physicochemical characteristics, alkaloids were grouped as sterically bulky (sb) or planar (pg). Docking results revealed strong binding affinities (−6.0 to −13.4 kcal/mol) of the alkaloids against PfDHODH and various strains of PfDHFR while interacting with key residues such as Asp54 and Phe58 in PfDHFR. The pg alkaloids had high binding affinity and preference for the inhibitor binding domain over the flavin mononucleotide (FMN) binding domain in PfDHODH due to size considerations. From the molecular dynamics trajectories, protein-alkaloid complexes were stable throughout the simulation, with supporting evidence from root mean square deviations, root mean square fluctuations, radius of gyration, free binding energies, and other parameters. We report herein that biscryptolepine and cryptomisrine (sb class), as well as cryptolepinone, cryptoheptine, cryptolepine, and neocryptolepine (pg class), are capable of inhibiting PfDHFR effectively in pyrimethamine sensitive and resistant cells. Also, our results show that alkaloids of the pg class can inhibit PfDHODH as FMN decoys, as well as direct enzyme inhibitors, thereby halting crucial protein function.
Collapse
|
4
|
Sakpal S, Kothari SL, Bastikar V. Characterization of Human-malarial Parasite Species based on DHFR and GST Targets Resulting in Changes in Anti-malarial Drug Binding Conformations. DRUG METABOLISM AND BIOANALYSIS LETTERS 2022; 15:22-37. [PMID: 35232369 DOI: 10.2174/1872312815666220225155728] [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: 10/03/2021] [Revised: 12/19/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In this study, we focused primarily on three anti-malarial drugs, namely chloroquine, mefloquine, and proguanil, and these were tested against two malarial targets DHFR and GST. The species Plasmodium falciparum, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax were used for the study. OBJECTIVE The purpose of this study was to determine the sequence and structural similarity of the proteins DHFR and GST among four Plasmodium species as well as to discover the in silico interactions with the aforementioned drug candidates. METHODS Bioinformatics databases, such as PDB, UniProt, DrugBank, PubChem, and tools, and software like Phyre 2.0, Clustal O (1.2.4), AutoDock 4, AutoDock Vina, and Discovery Studio Visualizer were used to determine the evolutionary significance of the Plasmodium species. RESULT The variations showed a difference in the binding patterns of drugs with our target proteins. Our finding reveals the Plasmodium spp divergence or convergence as well as the structural and sequential similarity or dissimilarity features. CONCLUSION Our result suggests that due to the deviation in the sequences and structures, variations in protein-drug binding patterns have emerged.
Collapse
Affiliation(s)
- Shrutika Sakpal
- Amity Institute of Biotechnology, Amity University Rajasthan 303002, Jaipur, Rajasthan, India
- Department of Biotechnology, Dr. Homi Bhabha State University, The Institute of Science, Fort 400032, Mumbai, India
| | - Shanker Lal Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan 303002, Jaipur, Rajasthan, India
| | - Virupaksha Bastikar
- Amity Institute of Biotechnology, Amity University, Panvel 410206, Maharashtra, India
| |
Collapse
|
5
|
Iwaloye O, Elekofehinti OO, Kikiowo B, Fadipe TM, Akinjiyan MO, Ariyo EO, Aiyeku OO, Adewumi NA. Discovery of Traditional Chinese Medicine Derived Compounds as Wild Type and Mutant Plasmodium falciparum Dihydrofolate Reductase Inhibitors: Induced Fit Docking and ADME Studies. Curr Drug Discov Technol 2021; 18:554-569. [PMID: 32729419 DOI: 10.2174/1570163817999200729122753] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND In a bid to come up with effective compounds as inhibitors for antimalarial treatment, we built a library of 2,000 traditional Chinese medicine(TCM)-derived compounds retrieved from TCM Database@Taiwan. METHODS The active sites of both the wild type and mutant Plasmodium falciparum dihydrofolatereductase (pfDHFR) were explored using computational tools. pfDHFR, one of the prime drug targets in the prevention of malaria infection induced by the female anopheles mosquito has continued to offer resistance to drugs (antifolates) due to mutation in some of the key amino acid residues crucial for its inhibition. RESULTS We utilized virtual throughput screening and glide XP docking to screen the compounds, and 8 compounds were found to have promising docking scores with both the wild type and mutant pfDHFR. They were further subjected to Induce Fit Docking (IFD) to affirm their inhibitory potency. The ADME properties and biological activity spectrum of the compounds were also considered. The inhibition profile of the compounds revealed that a number of compounds formed intermolecular interactions with ASP54, ILE14, LEU164, SER108/ASN108, ARG122 and ASP58. Most of the compounds can be considered as drug candidates due to their antiprotozoal activities and accordance with the Lipinski's Rule of Five (ROF). CONCLUSION The outcome of the present study should further be investigated to attest the efficacy of these compounds as better drug candidates than the antifolates.
Collapse
Affiliation(s)
- Opeyemi Iwaloye
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olusola Olalekan Elekofehinti
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Toyin Mary Fadipe
- Department of Bioscience, International Institute of Agriculture, Ibadan, Oyo State, Nigeria
| | - Moses Orimoloye Akinjiyan
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Esther Opeyemi Ariyo
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olabisi Olapade Aiyeku
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Nicholas Adeyemi Adewumi
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| |
Collapse
|
6
|
In silico studies of semi-synthetic benzo[a]phenazines as inhibitors of dihydrofolate reductase from Plasmodium falciparum. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
7
|
Flexible diaminodihydrotriazine inhibitors of Plasmodium falciparum dihydrofolate reductase: Binding strengths, modes of binding and their antimalarial activities. Eur J Med Chem 2020; 195:112263. [DOI: 10.1016/j.ejmech.2020.112263] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 01/12/2023]
|
8
|
Jyoti, Gaur R, Kumar Y, Cheema HS, Kapkoti DS, Darokar MP, Khan F, Bhakuni RS. Synthesis, molecular modelling studies of indolyl chalcone derivatives and their antimalarial activity evaluation. Nat Prod Res 2019; 35:3261-3268. [DOI: 10.1080/14786419.2019.1696788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jyoti
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Rashmi Gaur
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Yogesh Kumar
- Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Harveer Singh Cheema
- Molecular Bio-Prospection Department Metabolic, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Deepak Singh Kapkoti
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Mahendra P. Darokar
- Molecular Bio-Prospection Department Metabolic, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Feroz Khan
- Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Rajendra Singh Bhakuni
- Medicinal Chemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| |
Collapse
|
9
|
Valente M, Vidal AE, González-Pacanowska D. Targeting Kinetoplastid and Apicomplexan Thymidylate Biosynthesis as an Antiprotozoal Strategy. Curr Med Chem 2019; 26:4262-4279. [PMID: 30259810 DOI: 10.2174/0929867325666180926154329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/23/2018] [Accepted: 09/14/2018] [Indexed: 02/04/2023]
Abstract
Kinetoplastid and apicomplexan parasites comprise a group of protozoans responsible for human diseases, with a serious impact on human health and the socioeconomic growth of developing countries. Chemotherapy is the main option to control these pathogenic organisms and nucleotide metabolism is considered a promising area for the provision of antimicrobial therapeutic targets. Impairment of thymidylate (dTMP) biosynthesis severely diminishes the viability of parasitic protozoa and the absence of enzymatic activities specifically involved in the formation of dTMP (e.g. dUTPase, thymidylate synthase, dihydrofolate reductase or thymidine kinase) results in decreased deoxythymidine triphosphate (dTTP) levels and the so-called thymineless death. In this process, the ratio of deoxyuridine triphosphate (dUTP) versus dTTP in the cellular nucleotide pool has a crucial role. A high dUTP/dTTP ratio leads to uracil misincorporation into DNA, the activation of DNA repair pathways, DNA fragmentation and eventually cell death. The essential character of dTMP synthesis has stimulated interest in the identification and development of drugs that specifically block the biochemical steps involved in thymine nucleotide formation. Here, we review the available literature in relation to drug discovery studies targeting thymidylate biosynthesis in kinetoplastid (genera Trypanosoma and Leishmania) and apicomplexan (Plasmodium spp and Toxoplasma gondii) protozoans. The most relevant findings concerning novel inhibitory molecules with antiparasitic activity against these human pathogens are presented herein.
Collapse
Affiliation(s)
- María Valente
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| |
Collapse
|
10
|
Bhagat S, Arfeen M, Das G, Ramkumar M, Khan SI, Tekwani BL, Bharatam PV. Design, synthesis and biological evaluation of 4-aminoquinoline-guanylthiourea derivatives as antimalarial agents. Bioorg Chem 2019; 91:103094. [PMID: 31376783 DOI: 10.1016/j.bioorg.2019.103094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/10/2019] [Accepted: 06/26/2019] [Indexed: 11/15/2022]
Abstract
Guanylthiourea (GTU) has been identified as an important antifolate antimalarial pharmacophore unit, whereas, 4-amino quinolones are already known for antimalarial activity. In the present work molecules carrying 4-aminoquinoline and GTU moiety have been designed using molecular docking analysis with PfDHFR enzyme and heme unit. The docking results indicated that the necessary interactions (Asp54 and Ile14) and docking score (-9.63 to -7.36 kcal/mmol) were comparable to WR99210 (-9.89 kcal/mol). From these results nine molecules were selected for synthesis. In vitro analysis of these synthesized compounds reveal that out of the nine molecules, eight show antimalarial activity in the range of 0.61-7.55 μM for PfD6 strain and 0.43-8.04 μM for PfW2 strain. Further, molecular dynamics simulations were performed on the most active molecule to establish comparative binding interactions of these compounds and reference ligand with Plasmodium falciparum dihydrofolate reductase (PfDHFR).
Collapse
Affiliation(s)
- Shweta Bhagat
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - Minhajul Arfeen
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - Gourav Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - Mridula Ramkumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India
| | - Shabana I Khan
- National Center for Natural Products Research, University of Mississippi, MS 38677, USA
| | - Babu L Tekwani
- National Center for Natural Products Research, University of Mississippi, MS 38677, USA
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector-67, S.A.S. Nagar 160062, Punjab, India.
| |
Collapse
|
11
|
Manhas A, Lone MY, Jha PC. Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors. J Biomol Struct Dyn 2019; 37:4181-4199. [DOI: 10.1080/07391102.2018.1540362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
| |
Collapse
|
12
|
Corral MG, Haywood J, Stehl LH, Stubbs KA, Murcha MW, Mylne JS. Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:727-742. [PMID: 29876984 DOI: 10.1111/tpj.13983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/16/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.
Collapse
Affiliation(s)
- Maxime G Corral
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Luca H Stehl
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- Faculty of Biology, The University of Freiburg, Schaenzlestrasse 1, Freiburg, 79104, Germany
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| |
Collapse
|
13
|
Das D, Khan HPA, Shivahare R, Gupta S, Sarkar J, Siddiqui MI, Ampapathi RS, Chakraborty TK. Synthesis, SAR and biological studies of sugar amino acid-based almiramide analogues: N-methylation leads the way. Org Biomol Chem 2018; 15:3337-3352. [PMID: 28368065 DOI: 10.1039/c6ob02610a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Leishmaniasis, caused by the protozoan parasites of the genus Leishmania, is one of the most neglected diseases endemic in many continents posing enormous global health threats and therefore the discovery of new antileishmanial compounds is of utmost urgency. The antileishmanial activities of a library of sugar amino acid-based linear lipopeptide analogues were examined with the aim to identify potential drug candidates to treat visceral leishmaniasis. It was found that among the synthesized analogues, most of the permethylated compounds exhibited more activity in in vitro studies against intra-macrophagic amastigotes than the non-methylated analogues. SAR and NMR studies revealed that introduction of the N-methyl groups inhibited the formation of any turn structure in these molecules, which led to their improved activities.
Collapse
Affiliation(s)
- Dipendu Das
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Pathak M, Ojha H, Tiwari AK, Sharma D, Saini M, Kakkar R. Design, synthesis and biological evaluation of antimalarial activity of new derivatives of 2,4,6-s-triazine. Chem Cent J 2017; 11:132. [PMID: 29256159 PMCID: PMC5735044 DOI: 10.1186/s13065-017-0362-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Dihydrofolate reductase (DHFR) is an important enzyme for de novo synthesis of nucleotides in Plasmodium falciparum and it is essential for cell proliferation. DHFR is a well known antimalarial target for drugs like cycloguanil and pyrimethamine which target its inhibition for their pharmacological actions. However, the clinical efficacies of these antimalarial drugs have been compromising due to multiple mutations occurring in DHFR that lead to drug resistance. In this background, we have designed 22 s -triazine compounds using the best five parameters based 3D-QSAR model built by using genetic function approximation. In-silico designed compounds were further filtered to 6 compounds based upon their ADME properties, docking studies and predicted minimum inhibitory concentrations (MIC). Out of 6 compounds, 3 compounds were synthesized in good yield over 95% and characterized using IR, 1HNMR, 13CNMR and mass spectroscopic techniques. Parasitemia inhibition assay was used to evaluate the antimalarial activity of s -triazine compounds against 3D7 strain of P. falciparum. All the three compounds (7, 13 and 18) showed 30 times higher potency than cycloguanil (standard drug). It was observed that compound 18 was the most active while the compound 13 was the least active. On the closer inspection of physicochemical properties and SAR, it was observed that the presence of electron donating groups, number of hydrogen bond formation, lipophilicity of ligands and coulson charge of nitrogen atom present in the triazine ring enhances the DHFR inhibition significantly. This study will contribute to further endeavours of more potent DHFR inhibitors.
Collapse
Affiliation(s)
- Mallika Pathak
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India.,Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Himanshu Ojha
- Department of Chemistry, University of Delhi, Delhi, 110007, India. .,Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, DRDO, Timarpur, Delhi, 110054, India.
| | - Anjani K Tiwari
- Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Deepti Sharma
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, DRDO, Timarpur, Delhi, 110054, India
| | - Manisha Saini
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India
| | - Rita Kakkar
- Department of Chemistry, University of Delhi, Delhi, 110007, India
| |
Collapse
|
15
|
Theoretical Investigation of the Enantioselective Complexations between pfDHFR and Cycloguanil Derivatives. Sci Pharm 2017; 85:scipharm85040037. [PMID: 29160825 PMCID: PMC5748534 DOI: 10.3390/scipharm85040037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/10/2017] [Accepted: 11/14/2017] [Indexed: 11/30/2022] Open
Abstract
Point mutations in Plasmodium falciparum dihydrofolate reductase (pfDHFR), especially the double mutant variant (A16V + S108T), led to ineffective inhibiting by cycloguanil (Cyc). Cycloguanil derivatives showed good inhibiting properties against wild-type and mutant pfDHFR with an inhibition constant as low as the nanomolar level. However, there have been no reports on the stereochemistry of the compounds, and this is important because the pure enantiomeric form of a chiral drug can exert desirable, as well as non-desirable responses on the body or both. In this work, three-dimensional structures of Cyc derivatives in R and S configuration were constructed and optimized using Hartree-Fock/6-31G (d,p). Their structures were docked into the binding pocket of wild-type and double mutant (A16V + S108T) pfDHFR, complexed with nicotinamide adenine dinucleotide phosphate (NADPH). Results indicate that both wild-type and mutant pfDHFR are enantioselective towards enantiomeric Cyc derivatives (R and S configuration).
Collapse
|
16
|
Bhatt JD, Chudasama CJ, Patel KD. Diarylpyrazole Ligated Dihydropyrimidine Hybrids as Potent Non-Classical Antifolates and Their Efficacy Against Plasmodium falciparum. Arch Pharm (Weinheim) 2017; 350. [PMID: 28796406 DOI: 10.1002/ardp.201700088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/07/2017] [Accepted: 07/18/2017] [Indexed: 11/09/2022]
Abstract
A series of diarylpyrazole clubbed dihydropyrimidine derivatives (J1-J30) was synthesized under microwave-assisted heating conditions by employing Biginelli reaction methodology and utilizing triethylammonium acetate both as a catalyst and as reaction medium, leading towards a greener reaction pathway. The synthesized entities were screened for their antimalarial efficacy against a Plasmodium falciparum strain in vitro. The active entities (J9, J15, J21, J25, and J27) obtained out of the in vitro screening were further evaluated for their enzyme inhibitory potency against the Pf-DHFR enzyme in vitro as well as in silico using Glide. Furthermore, the active scaffolds were tested for their cytotoxicity against Vero cells, proving their nontoxic behavior and selectivity. The ADME parameters were also evaluated and predicted in silico, indicating good oral bioavailability of the compounds.
Collapse
Affiliation(s)
- Jaimin D Bhatt
- Chemistry Department, V. P. & R. P. T. P. Science College, Affiliated To Sardar Patel University, Vallabh Vidyanagar, Gujarat, India.,Sophisticated Instrumentation Center for Applied Research and Testing (SICART), Affiliated To Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Chaitanya J Chudasama
- Department of Biochemistry, Shree Alpesh N. Patel P. G. Institute, Sardar Patel University, Anand, Gujarat, India
| | - Kanuprasad D Patel
- Chemistry Department, V. P. & R. P. T. P. Science College, Affiliated To Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| |
Collapse
|
17
|
Guanylthiourea derivatives as potential antimalarial agents: Synthesis, in vivo and molecular modelling studies. Eur J Med Chem 2017; 135:339-348. [DOI: 10.1016/j.ejmech.2017.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 04/03/2017] [Accepted: 04/10/2017] [Indexed: 11/21/2022]
|
18
|
Balabadra S, Kotni M, Manga V, Allanki AD, Prasad R, Sijwali PS. Synthesis and evaluation of naphthyl bearing 1,2,3-triazole analogs as antiplasmodial agents, cytotoxicity and docking studies. Bioorg Med Chem 2016; 25:221-232. [PMID: 27816268 DOI: 10.1016/j.bmc.2016.10.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/22/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
Novel series of naphthyl bearing 1,2,3-triazoles (4a-t) were synthesized and evaluated for their in vitro antiplasmodial activity against pyrimethamine (Pyr)-sensitive and resistant strains of Plasmodium falciparum. The synthesized compounds were assessed for their cytotoxicity employing human embryonic kidney cell line (HEK-293), and none of them was found to be toxic. Among them 4j, 4k, 4l, 4m, 4n, 4t exhibited significant antiplasmodial activity in both strains, of which compounds 4m, 4n and 4t (∼3.0-fold) displayed superior activity to Pyr against resistant strain. Pyr and selected compounds (4n, 4p and 4t) that repressed parasite development also inhibited PfDHFR activity of the soluble parasite extract, suggesting that anti-parasitic activity of these compounds is a result of inhibition of the parasite DHFR. In silico studies suggest that activity of these compounds might be enhanced due to π-π stacking.
Collapse
Affiliation(s)
- Saikrishna Balabadra
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, Osmania University, Hyderabad 500007, Telangana, India
| | - MeenaKumari Kotni
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, Osmania University, Hyderabad 500007, Telangana, India
| | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, Osmania University, Hyderabad 500007, Telangana, India.
| | - Aparna Devi Allanki
- Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Rajesh Prasad
- Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| | - Puran Singh Sijwali
- Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, Telangana, India
| |
Collapse
|
19
|
Sahu S, Ghosh SK, Ghoshal A, Kalita J, Gahtori P, Bhattacharyya DR. Microwave assisted synthesis, antimalarial screening and structure–activity-relationship exploration of some phenylthiazolyl-triazine derivatives against dihydrofolate reductase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1714-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Bhatt JD, Chudasama CJ, Patel KD. Microwave Assisted Synthesis of Pyrimidines in Ionic Liquid and Their Potency as Non-Classical Malarial Antifolates. Arch Pharm (Weinheim) 2016; 349:791-800. [PMID: 27528517 DOI: 10.1002/ardp.201600148] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/21/2016] [Accepted: 07/29/2016] [Indexed: 11/07/2022]
Abstract
Synthesis of pyrazole-linked triazolo-pyrimidine hybrids was achieved by employing Biginelli-type reaction methodology in an ionic liquid (triethylammonium acetate) under microwave irradiation. This method proved to be highly efficient and the ionic liquid employed was found recyclable for up to five consecutive cycles. The synthesized molecules were further screened for their antimalarial efficacy screening out the active scaffolds J15, J18, J21, J24, J27, and J30. The active molecules were evaluated in an enzyme inhibition study against the active Plasmodium falciparum dihydrofolate reductase (Pf-DHFR), computationally as well as in vitro, demonstrating their potency as DHFR inhibitors. The active entities were also investigated for their oral bioavailability by predicting ADME properties in silico, indicating good bioavailability.
Collapse
Affiliation(s)
- Jaimin D Bhatt
- Chemistry Department, V. P. & R. P. T. P. Science College, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India
| | - Chaitanya J Chudasama
- Department of Biochemistry, Shree Alpesh N. Patel P. G. Institute, Sardar Patel University, Anand, Gujarat, India
| | - Kanuprasad D Patel
- Chemistry Department, V. P. & R. P. T. P. Science College, Sardar Patel University, Vallabh Vidyanagar, Gujarat, India.
| |
Collapse
|
21
|
Bagchi S, Kumar M, Sharma A. A multilayer screening approach toward the discovery of novel Pf-DHFR inhibitors. Comput Biol Chem 2016; 62:36-46. [PMID: 27061145 DOI: 10.1016/j.compbiolchem.2016.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/26/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
Abstract
A small yet diverse xanthone library was build and computationally docked against wild type Pf-DHFR by Molegro Virtual Docker (MolDock). For analysis of results an integrated approach based on re-ranking, scaling (based on heavy atom counts), pose clustering and visual inspection was implemented. Standard methods such as self-docking (for docking), EF analysis, average rank determinations (for size normalization), and cluster quality indices (for pose clustering) were used for validation of results. Three compounds X5, X113A and X164B displayed contact footprints similar to the known inhibitors with good scores. Finally, 16 compounds were extracted from ZINC data base by similarity based screening, docking score and drug/lead likeness. Out of these 16 compounds, 11 displayed very close contact footprints to experimentally known inhibitors, indicating there potential utility in further drug discovery efforts.
Collapse
Affiliation(s)
- Sourav Bagchi
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Manoj Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Anuj Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247667, India.
| |
Collapse
|
22
|
Lourens ACU, Gravestock D, van Zyl RL, Hoppe HC, Kolesnikova N, Taweechai S, Yuthavong Y, Kamchonwongpaisan S, Rousseau AL. Design, synthesis and biological evaluation of 6-aryl-1,6-dihydro-1,3,5-triazine-2,4-diamines as antiplasmodial antifolates. Org Biomol Chem 2016; 14:7899-911. [DOI: 10.1039/c6ob01350c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One-pot multistep synthesis of 1,6-dihydro-1,3,5-triazines displaying potent antiplasmodial activity in vitro.
Collapse
Affiliation(s)
- Anna C. U. Lourens
- CSIR Biosciences
- 0001 Gauteng
- South Africa
- Pharmaceutical Chemistry
- School of Pharmacy
| | - David Gravestock
- CSIR Biosciences
- 0001 Gauteng
- South Africa
- Syngenta
- Jealott's Hill International Research Centre
| | - Robyn L. van Zyl
- Pharmacology Division
- Department of Pharmacy and Pharmacology
- WITS Research Institute for Malaria (WRIM)
- Faculty of Health Sciences
- University of the Witwatersrand
| | - Heinrich C. Hoppe
- CSIR Biosciences
- 0001 Gauteng
- South Africa
- Department of Biochemistry and Microbiology
- Rhodes University
| | | | - Supannee Taweechai
- BIOTEC
- National Science and Technology Development Agency
- Pathumthani 12120
- Thailand
| | - Yongyuth Yuthavong
- BIOTEC
- National Science and Technology Development Agency
- Pathumthani 12120
- Thailand
| | | | - Amanda L. Rousseau
- CSIR Biosciences
- 0001 Gauteng
- South Africa
- Molecular Sciences Institute
- School of Chemistry
| |
Collapse
|
23
|
Bhat HR, Singh UP, Gahtori P, Ghosh SK, Gogoi K, Prakash A, Singh RK. Synthesis, Docking,In VitroandIn VivoAntimalarial Activity of Hybrid 4-aminoquinoline-1,3,5-triazine Derivatives Against Wild and Mutant Malaria Parasites. Chem Biol Drug Des 2015; 86:265-71. [DOI: 10.1111/cbdd.12490] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Hans Raj Bhat
- Drug Design and Discovery Laboratory; Department of Pharmaceutical Sciences; Sam Higginbottom Institute of Agriculture Technology and Science; Deemed University; Allahabad 211007 India
| | - Udaya Pratap Singh
- Drug Design and Discovery Laboratory; Department of Pharmaceutical Sciences; Sam Higginbottom Institute of Agriculture Technology and Science; Deemed University; Allahabad 211007 India
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
| | - Prashant Gahtori
- Faculty of Pharmacy; Uttarakhand Technical University; Dehradun 248007 India
| | - Surajit Kumar Ghosh
- Department of Pharmaceutical Sciences; Dibrugarh University; Dibrugarh 786004 India
| | - Kabita Gogoi
- Regional Medical Research Centre; ICMR; Dibrugarh 786005 India
| | - Anil Prakash
- Regional Medical Research Centre; ICMR; Dibrugarh 786005 India
| | - Ramendra K. Singh
- Nucleic Acids and Antiviral Research Laboratory; Department of Chemistry; University of Allahabad; Allahabad 211002 India
| |
Collapse
|
24
|
Abbat S, Jain V, Bharatam PV. Origins of the specificity of inhibitor P218 toward wild-type and mutantPfDHFR: a molecular dynamics analysis. J Biomol Struct Dyn 2014; 33:1913-28. [DOI: 10.1080/07391102.2014.979231] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
25
|
Sharma MC, Sharma S, Bhadoriya KS. Molecular modeling studies on substituted aminopyrimidines derivatives as potential antimalarial compounds. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1199-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
26
|
Mokmak W, Chunsrivirot S, Hannongbua S, Yuthavong Y, Tongsima S, Kamchonwongpaisan S. Molecular dynamics of interactions between rigid and flexible antifolates and dihydrofolate reductase from pyrimethamine-sensitive and pyrimethamine-resistant Plasmodium falciparum. Chem Biol Drug Des 2014; 84:450-61. [PMID: 24716467 DOI: 10.1111/cbdd.12334] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/04/2014] [Accepted: 04/03/2014] [Indexed: 01/16/2023]
Abstract
Currently, the usefulness of antimalarials such as pyrimethamine (PYR) is drastically reduced due to the emergence of resistant Plasmodium falciparum (Pf) caused by its dihydrofolate reductase (PfDHFR) mutations, especially the quadruple N51I/C59R/S108N/I164L mutations. The resistance was due to the steric conflict of PYR with S108N. WR99210 (WR), a dihydrotriazine antifolate with a flexible side chain that can avoid such conflict, can overcome this resistance through tight binding with the mutant. To understand factors contributing to different binding affinities of PYR/WR to the wild type (WT) and quadruple mutant (QM), we performed simulations on WR-WT, WR-QM, PYR-WT, and PYR-QM complexes and found that Ile14 and Asp54 were crucial for PYR/WR binding to PfDHFR due to strong hydrogen bonds. The quadruple mutations cause PYR to form, on average, fewer hydrogen bonds with Ile14 and Leu164, and to be displaced from its optimal orientation for Asp54 interaction. The predicted binding affinity ranking (WR-QM ≈ WR-WT ≈ PYR-WT >> PYR-QM) reasonably agrees with the inhibition constant (K(i)) ranking. Our results reveal important residues for tight binding of PYR/WR to WT/QM, which may be used to evaluate the inhibition effectiveness of antimalarials and to provide fundamental information for designing new drugs effective against drug-resistant P. falciparum.
Collapse
Affiliation(s)
- Wanwimon Mokmak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Klong Luang, Pathum Thani, 12120, Thailand
| | | | | | | | | | | |
Collapse
|
27
|
Dube PN, Mokale S, Datar P. CoMFA and docking study of 2,N6-disubstituted 1,2-dihydro-1,3,5-triazine-4,6-diamines as novel PfDHFR enzyme inhibitors for antimalarial activity. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.bfopcu.2014.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
28
|
Design and synthesis of guanylthiourea derivatives as potential inhibitors of Plasmodium falciparum dihydrofolate reductase enzyme. Bioorg Med Chem Lett 2014; 24:613-7. [DOI: 10.1016/j.bmcl.2013.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/22/2013] [Accepted: 12/02/2013] [Indexed: 11/18/2022]
|
29
|
Jiang PP, Corbett-Detig RB, Hartl DL, Lozovsky ER. Accessible mutational trajectories for the evolution of pyrimethamine resistance in the malaria parasite Plasmodium vivax. J Mol Evol 2013; 77:81-91. [PMID: 24071997 DOI: 10.1007/s00239-013-9582-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/31/2013] [Indexed: 10/26/2022]
Abstract
Antifolate antimalarials, such as pyrimethamine, have experienced a dramatic reduction in therapeutic efficacy as resistance has evolved in multiple malaria species. We present evidence from one such species, Plasmodium vivax, which has experienced sustained selection for pyrimethamine resistance at the dihydrofolate reductase (DHFR) locus since the 1970s. Using a transgenic Saccharomyces cerevisiae model expressing the P. vivax DHFR enzyme, we assayed growth rate and resistance of all 16 combinations of four DHFR amino acid substitutions. These substitutions were selected based on their known association with drug resistance, both in natural isolates and in laboratory settings, in the related malaria species P. falciparum. We observed a strong correlation between the resistance phenotypes for these 16 P. vivax alleles and previously observed resistance data for P. falciparum, which was surprising since nucleotide diversity levels and common polymorphic variants of DHFR differ between the two species. Similar results were observed when we expressed the P. vivax alleles in a transgenic bacterial system. This suggests common constraints on enzyme evolution in the orthologous DHFR proteins. The interplay of negative trade-offs between the evolution of novel resistance and compromised endogenous function varies at different drug dosages, and so too do the major trajectories for DHFR evolution. In simulations, it is only at very high drug dosages that the most resistant quadruple mutant DHFR allele is favored by selection. This is in agreement with common polymorphic DHFR data in P. vivax, from which this quadruple mutant is missing. We propose that clinical dosages of pyrimethamine may have historically been too low to select for the most resistant allele, or that the fitness cost of the most resistant allele was untenable without a compensatory mutation elsewhere in the genome.
Collapse
Affiliation(s)
- Pan-Pan Jiang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA,
| | | | | | | |
Collapse
|
30
|
In silico docking studies of bioactive natural plant products as putative DHFR antagonists. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0654-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
31
|
Sharma M, Chauhan K, Shivahare R, Vishwakarma P, Suthar MK, Sharma A, Gupta S, Saxena JK, Lal J, Chandra P, Kumar B, Chauhan PMS. Discovery of a new class of natural product-inspired quinazolinone hybrid as potent antileishmanial agents. J Med Chem 2013; 56:4374-92. [PMID: 23611626 DOI: 10.1021/jm400053v] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The high potential of quinazolinone containing natural products and their derivatives in medicinal chemistry led us to discover four novel series of 53 compounds of quinazolinone based on the concept of molecular hybridization. Most of the synthesized analogues exhibited potent leishmanicidal activity against intracellular amastigotes (IC50 from 0.65 ± 0.2 to 7.76 ± 2.1 μM) as compared to miltefosine (IC50 = 8.4 ± 2.1 μM) and nontoxic toward the J-774A.1 cell line and Vero cells. Moreover, activation of Th1 type and suppression of Th2 type immune responses and induction in nitric oxide generation proved that 8a and 8g induce murine macrophages to prevent survival of parasites. Compounds 8a and 8g exhibited significant in vivo inhibition of parasite 73.15 ± 12.69% and 80.93 ± 10.50% against Leishmania donovani /hamster model. Our results indicate that compounds 8a, 8g, and 9f represent a new structural lead for this serious and neglected disease.
Collapse
Affiliation(s)
- Moni Sharma
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow-226 001, U.P., India
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
McKeever C, Kaiser M, Rozas I. Aminoalkyl derivatives of guanidine diaromatic minor groove binders with antiprotozoal activity. J Med Chem 2013; 56:700-11. [PMID: 23301592 DOI: 10.1021/jm301614w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Considering the strong DNA minor groove binding observed for our previous series of diaromatic symmetric and asymmetric guanidinium and 2-aminoimidazolinium derivatives, we report now the synthesis of new aminoalkyl derivatives of diaromatic guanidines with potential as DNA minor groove binders and antiprotozoal activity. The preparation of these aminoalkyl derivatives (12a-e, 13a-e, 14a-c,e, 15a-e, 16a-e) is presented as well as their affinity for DNA which was evaluated by means of DNA thermal denaturation experiments. Finally, the antiprotozoal activity of most of these aminoalkyl minor groove binders was evaluated in vitro against Trypanosoma brucei rhodesiense (8 compounds) and Plasmodium falciparum (18 compounds). The O-linked derivatives 13c and 14c showed 100 nM activities against P. falciparum, whereas for T. b. rhodesiense all compounds tested showed micromolar activity. Some of the derivatives prepared seem to exert the antimalarial activity by binding to the DNA minor groove whereas other sets of compounds could exert this antimalarial activity by inhibiting the parasite dihydrofolate reductase, for example.
Collapse
Affiliation(s)
- Caitriona McKeever
- School of Chemistry, Trinity Biomedical Sciences Institute, University of Dublin, Trinity College, 152-160 Pearse St., Dublin 2, Ireland
| | | | | |
Collapse
|
33
|
|
34
|
Dihydrofolate reductase as a therapeutic target for infectious diseases: opportunities and challenges. Future Med Chem 2012; 4:1335-65. [DOI: 10.4155/fmc.12.68] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Infectious diseases caused by parasites continue to take a massive toll on human health in the poor regions of the world. Filling the anti-infective drug-discovery pipeline has never been as challenging as it is now. The organisms responsible for these diseases have interesting biology with many potential biochemical targets. Inhibition of metabolic enzymes has been established as an attractive strategy for anti-infectious drug development. In this field, dihydrofolate reductase (DHFR) is an important enzyme in nucleic and amino acid synthesis and an extensively studied drug target over the past 50 years. The challenges for novel DHFR inhibition-based chemotherapeutics for the treatment of infectious diseases are now focused on overcoming the resistance problem as well as cost–effectiveness. Each year, the large number of literature citations attest the continued popularity of DHFR. It becomes truly the ‘enzyme of choice for all seasons and almost all reasons’. Herein, we summarize the opportunities and challenges in developing novel lead based on this target.
Collapse
|
35
|
Combined spatial limitation around residues 16 and 108 of Plasmodium falciparum dihydrofolate reductase explains resistance to cycloguanil. Antimicrob Agents Chemother 2012; 56:3928-35. [PMID: 22526319 DOI: 10.1128/aac.00301-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Natural mutations of Plasmodium falciparum dihydrofolate reductase (PfDHFR) at A16V and S108T specifically confer resistance to cycloguanil (CYC) but not to pyrimethamine (PYR). In order to understand the nature of CYC resistance, the effects of various mutations at A16 on substrate and inhibitor binding were examined. Three series of mutations at A16 with or without the S108T/N mutation were generated. Only three mutants with small side chains at residue 16 (G, C, and S) were viable from bacterial complementation assay in the S108 series, whereas these three and an additional four mutants (T, V, M, and I) with slightly larger side chains were viable with simultaneous S108T mutation. Among these combinations, the A16V+S108T mutant was the most CYC resistant, and all of the S108T series ranged from being highly to moderately sensitive to PYR. In the S108N series, a strict requirement for alanine was observed at position 16. Crystal structure analyses reveal that in PfDHFR-TS variant T9/94 (A16V+S108T) complexed with CYC, the ligand has substantial steric conflicts with the side chains of both A16V and S108T, whereas in the complex with PYR, the ligand only showed mild conflict with S108T. CYC analogs designed to avoid such conflicts improved the binding affinity of the mutant enzymes. These results show that there is greater spatial limitation around the S108T/N residue when combined with the limitation imposed by A16V. The limitation of mutation of this series provides opportunities for drug design and development against antifolate-resistant malaria.
Collapse
|
36
|
2-Aminopyrimidine based 4-aminoquinoline anti-plasmodial agents. Synthesis, biological activity, structure-activity relationship and mode of action studies. Eur J Med Chem 2012; 52:82-97. [PMID: 22459876 PMCID: PMC7115513 DOI: 10.1016/j.ejmech.2012.03.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/02/2012] [Accepted: 03/02/2012] [Indexed: 11/22/2022]
Abstract
2-Aminopyrimidine based 4-aminoquinolines were synthesized using an efficacious protocol. Some of the compounds showed in vitro anti-plasmodial activity against drug-sensitive CQ(S) (3D7) and drug-resistant CQ(R) (K1) strains of Plasmodium falciparum in the nM range. In particular, 5-isopropyloxycarbonyl-6-methyl-4-(2-nitrophenyl)-2-[(7-chloroquinolin-4-ylamino)butylamino] pyrimidine depicted the lowest IC(50) (3.6 nM) value (56-fold less than CQ) against CQ(R) strain. Structure-activity profile and binding with heme, μ-oxo-heme have been studied. Binding assays with DNA revealed better binding with target parasite type AT rich pUC18 DNA. Most compounds were somewhat cytotoxic, but especially cytostatic. Molecular docking analysis with Pf DHFR allowed identification of stabilizing interactions.
Collapse
|
37
|
Costanzo MS, Hartl DL. The evolutionary landscape of antifolate resistance in Plasmodium falciparum. J Genet 2012; 90:187-90. [PMID: 21869466 DOI: 10.1007/s12041-011-0072-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resistance to antifolates in Plasmodium falciparum is well described and has been observed in clinical settings for decades. At the molecular level, point mutations in the dhfr gene that lead to resistance have been identified, and the crystal structure of the wildtype and mutant dihydrofolate reductase enzymes have been solved in complex with native substrate and drugs. However, we are only beginning to understand the complexities of the evolutionary pressures that lead to the evolution of drug resistance in this system. Microbial systems that allow heterologous expression of malarial proteins provide a tractable way to investigate patterns of evolution that can inform our eventual understanding of the more complex factors that influence the evolution of drug resistance in clinical settings. In this paper we will review work in Escherichia coli and Saccharomyces cerevisiae expression systems that explore the fitness landscape of mutations implicated in drug resistance and show that (i) a limited number of evolutionary pathways to resistance are followed with high probability; (ii) fitness costs associated with the maintenance of high levels of resistance are modest; and (iii) different antifolates may exert opposing selective forces.
Collapse
Affiliation(s)
- Marna S Costanzo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | |
Collapse
|
38
|
Saesaengseerung N, Vilaivan T, Thebtaranonth Y. AN EFFICIENT SYNTHESIS OF 1-ARYL-4,6-DIAMINO-1,2-DIHYDRO- 1,3,5-TRIAZINES. SYNTHETIC COMMUN 2011. [DOI: 10.1081/scc-120005415] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Neungruthai Saesaengseerung
- a Organic Synthesis Research Unit , Department of Chemistry , Faculty of Science , Chulalongkorn University , Phayathai Road, Bangkok , 10330 , Thailand
| | - Tirayut Vilaivan
- a Organic Synthesis Research Unit , Department of Chemistry , Faculty of Science , Chulalongkorn University , Phayathai Road, Bangkok , 10330 , Thailand
| | - Yodhathai Thebtaranonth
- a Organic Synthesis Research Unit , Department of Chemistry , Faculty of Science , Chulalongkorn University , Phayathai Road, Bangkok , 10330 , Thailand
| |
Collapse
|
39
|
Adane L, Bharatam PV. Binding modes of 2,4-diaminoquinazoline and 2,4-diaminopteridine analogs to P. falciparum dihydrofolate reductase enzyme: Molecular docking studies. Indian J Pharm Sci 2011; 72:324-33. [PMID: 21188041 PMCID: PMC3003165 DOI: 10.4103/0250-474x.70478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 02/03/2010] [Accepted: 04/20/2010] [Indexed: 11/30/2022] Open
Abstract
A molecular docking study was carried out on 28 compounds belonging to 2,4-diaminoquinazoline and 2,4-diaminopteridine analogs using Glide, FlexX and GOLD programs and the X-ray crystallographic structures of the quadruple mutant (1J3K:pdb) and wild type (1J3I:pdb) Plasmodium falciparum dihydrofolate reductase enzyme. The experimental conformation the bound ligand WR99210 was precisely reproduced by the docking procedures as demonstrated by low (<2.00 Å) root-mean-square deviations. The results indicated that most of the compounds dock into the active sites of both the wild type and quadruple mutant P. falciparum dihydrofolate reductase enzymes. Visual inspection of the binding modes also demonstrated that most of the compounds could form H-bond interactions with the key amino acid residues (Asp54, Ile14 and Leu/Ile164) and with better docking scores than the bound compound (5). Their long side chains orient in the hydrophobic portion of the active site which is occupied by trichloro aryloxy side chain of WR99210 (5). Thus, avoid potential steric clashes with Asn108 (mutated from Ser108). Such a clash is known to be responsible for the resistance of the P. falciparum to pyrimethamine and cycloguanil.
Collapse
Affiliation(s)
- L Adane
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar-160 062, India
| | | |
Collapse
|
40
|
Patel DS, Bharatam PV. Divalent N(I) compounds with two lone pairs on nitrogen. J Phys Chem A 2011; 115:7645-55. [PMID: 21650162 DOI: 10.1021/jp111017u] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon with the C(0) state has been reported recently, examples of which were known for the past decades. Silicon in the Si(0) state and phosphorus in the P(I) state are also known experimentally. This prompted us to search for divalent N(I) compounds, which resulted in the identification of ::N(←L)(2)(⊕) systems with bicoordinated nitrogen in the N(I) formal oxidation state. It was found that several biguanide derivatives (especially in their protonated state) belong to this class. Quantum chemical analysis provided the structural details, molecular orbitals, charge localization (vs delocalization) trends, etc. This class of compounds has been found to be characterized by two lone pairs on the central nitrogen, very similar to the central carbon in divalent C(0) compounds (::C(←L)(2)). The new bonding environment for nitrogen reported in this article, divalent nitrogen N(I), is clearly different from the nitrenium ions NR(2)(⊕). The electronic structure and reactivity of representative examples of this novel class of divalent nitrogen N(I) systems (::N(←L)(2)(⊕)) have been analyzed in detail, in terms of molecular orbitals, atomic charges, protonation energies, complexation energies with Lewis acids like BH(3), AlCl(3), and AuCl and compared with those of divalent C(0) systems.
Collapse
Affiliation(s)
- Dhilon S Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S. A. S. Nagar (Mohali), Punjab 160 062, India
| | | |
Collapse
|
41
|
Gravestock D, Rousseau AL, Lourens AC, Moleele SS, van Zyl RL, Steenkamp PA. Expeditious synthesis and biological evaluation of novel 2,N6-disubstituted 1,2-dihydro-1,3,5-triazine-4,6-diamines as potential antimalarials. Eur J Med Chem 2011; 46:2022-30. [DOI: 10.1016/j.ejmech.2011.02.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/10/2011] [Accepted: 02/22/2011] [Indexed: 11/25/2022]
|
42
|
Costanzo MS, Brown KM, Hartl DL. Fitness trade-offs in the evolution of dihydrofolate reductase and drug resistance in Plasmodium falciparum. PLoS One 2011; 6:e19636. [PMID: 21625425 PMCID: PMC3100297 DOI: 10.1371/journal.pone.0019636] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 04/10/2011] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Patterns of emerging drug resistance reflect the underlying adaptive landscapes for specific drugs. In Plasmodium falciparum, the parasite that causes the most serious form of malaria, antifolate drugs inhibit the function of essential enzymes in the folate pathway. However, a handful of mutations in the gene coding for one such enzyme, dihydrofolate reductase, confer drug resistance. Understanding how evolution proceeds from drug susceptibility to drug resistance is critical if new antifolate treatments are to have sustained usefulness. METHODOLOGY/PRINCIPAL FINDINGS We use a transgenic yeast expression system to build on previous studies that described the adaptive landscape for the antifolate drug pyrimethamine, and we describe the most likely evolutionary trajectories for the evolution of drug resistance to the antifolate chlorcycloguanil. We find that the adaptive landscape for chlorcycloguanil is multi-peaked, not all highly resistant alleles are equally accessible by evolution, and there are both commonalities and differences in adaptive landscapes for chlorcycloguanil and pyrimethamine. CONCLUSIONS/SIGNIFICANCE Our findings suggest that cross-resistance between drugs targeting the same enzyme reflect the fitness landscapes associated with each particular drug and the position of the genotype on both landscapes. The possible public health implications of these findings are discussed.
Collapse
Affiliation(s)
- Marna S Costanzo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
| | | | | |
Collapse
|
43
|
Basak SC, Mills D, Hawkins DM. Characterization of Dihydrofolate Reductases from Multiple Strains of Plasmodium falciparum Using Mathematical Descriptors of Their Inhibitors. Chem Biodivers 2011; 8:440-53. [DOI: 10.1002/cbdv.201000111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
44
|
Adane L, Bharatam PV, Sharma V. A common feature-based 3D-pharmacophore model generation and virtual screening: identification of potential PfDHFR inhibitors. J Enzyme Inhib Med Chem 2011; 25:635-45. [PMID: 19995305 DOI: 10.3109/14756360903393817] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A four-feature 3D-pharmacophore model was built from a set of 24 compounds whose activities were reported against the V1/S strain of the Plasmodium falciparum dihydrofolate reductase (PfDHFR) enzyme. This is an enzyme harboring Asn51Ile + Cys59Arg + Ser108Asn + Ile164Leu mutations. The HipHop module of the Catalyst program was used to generate the model. Selection of the best model among the 10 hypotheses generated by HipHop was carried out based on rank and best-fit values or alignments of the training set compounds onto a particular hypothesis. The best model (hypo1) consisted of two H-bond donors, one hydrophobic aromatic, and one hydrophobic aliphatic features. Hypo1 was used as a query to virtually screen Maybridge2004 and NCI2000 databases. The hits obtained from the search were subsequently subjected to FlexX and Glide docking studies. Based on the binding scores and interactions in the active site of quadruple-mutant PfDHFR, a set of nine hits were identified as potential inhibitors.
Collapse
Affiliation(s)
- Legesse Adane
- National Institute of Pharmacuetical Education and Research, S.A.S. Nagar, Mohali, India
| | | | | |
Collapse
|
45
|
Adane L, Bharatam PV. Computer-aided molecular design of 1H-imidazole-2,4-diamine derivatives as potential inhibitors of Plasmodium falciparum DHFR enzyme. J Mol Model 2010; 17:657-67. [DOI: 10.1007/s00894-010-0756-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 05/12/2010] [Indexed: 11/30/2022]
|
46
|
Adane L, Patel DS, Bharatam PV. Shape- and Chemical Feature-Based 3D-Pharmacophore Model Generation and Virtual Screening: Identification of Potential Leads forP. falciparumDHFR Enzyme Inhibition. Chem Biol Drug Des 2010; 75:115-26. [DOI: 10.1111/j.1747-0285.2009.00908.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
47
|
Adane L, Bharatam PV. 3D-QSAR analysis of cycloguanil derivatives as inhibitors of A16V+S108T mutant Plasmodium falciparum dihydrofolate reductase enzyme. J Mol Graph Model 2009; 28:357-67. [DOI: 10.1016/j.jmgm.2009.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 08/27/2009] [Accepted: 09/01/2009] [Indexed: 12/17/2022]
|
48
|
Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A 2009; 106:12025-30. [PMID: 19587242 PMCID: PMC2715478 DOI: 10.1073/pnas.0905922106] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Indexed: 11/18/2022] Open
Abstract
The spread of high-level pyrimethamine resistance in Africa threatens to curtail the therapeutic lifetime of antifolate antimalarials. We studied the possible evolutionary pathways in the evolution of pyrimethamine resistance using an approach in which all possible mutational intermediates were created by site-directed mutagenesis and assayed for their level of drug resistance. The coding sequence for dihydrofolate reductase (DHFR) from the malaria parasite Plasmodium falciparum was mutagenized, and tests were carried out in Escherichia coli under conditions in which the endogenous bacterial enzyme was selectively inhibited. We studied 4 key amino acid replacements implicated in pyrimethamine resistance: N51I, C59R, S108N, and I164L. Using empirical estimates of the mutational spectrum in P. falciparum and probabilities of fixation based on the relative levels of resistance, we found that the predicted favored pathways of drug resistance are consistent with those reported in previous kinetic studies, as well as DHFR polymorphisms observed in natural populations. We found that 3 pathways account for nearly 90% of the simulated realizations of the evolution of pyrimethamine resistance. The most frequent pathway (S108N and then C59R, N51I, and I164L) accounts for more than half of the simulated realizations. Our results also suggest an explanation for why I164L is detected in Southeast Asia and South America, but not at significant frequencies in Africa.
Collapse
Affiliation(s)
- Elena R. Lozovsky
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kyle M. Brown
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Mallika Imwong
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani 12120, Thailand
| | | | | | | | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| |
Collapse
|
49
|
Kasam V, Salzemann J, Botha M, Dacosta A, Degliesposti G, Isea R, Kim D, Maass A, Kenyon C, Rastelli G, Hofmann-Apitius M, Breton V. WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures. Malar J 2009; 8:88. [PMID: 19409081 PMCID: PMC2691744 DOI: 10.1186/1475-2875-8-88] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 05/01/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. MOTIVATION Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase. METHODS In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures. RESULTS On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed. CONCLUSION The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.
Collapse
Affiliation(s)
- Vinod Kasam
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Jean Salzemann
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Marli Botha
- CSIR Biosciences, Modderfontein, Johannesburg, 1645, South Africa
| | - Ana Dacosta
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Gianluca Degliesposti
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia. Via Campi 183, 41100 Modena Italy
| | - Raul Isea
- Fundacion IDEA, Centro de Biociencias, Hoyo de la Puerta, Baruta 1080, Venezuela
| | - Doman Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwang-Ju, South Korea
| | - Astrid Maass
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
| | - Colin Kenyon
- CSIR Biosciences, Modderfontein, Johannesburg, 1645, South Africa
| | - Giulio Rastelli
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia. Via Campi 183, 41100 Modena Italy
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
| | - Vincent Breton
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| |
Collapse
|
50
|
Maitarad P, Kamchonwongpaisan S, Vanichtanankul J, Vilaivan T, Yuthavong Y, Hannongbua S. Interactions between cycloguanil derivatives and wild type and resistance-associated mutant Plasmodium falciparum dihydrofolate reductases. J Comput Aided Mol Des 2009; 23:241-52. [PMID: 19156529 DOI: 10.1007/s10822-008-9254-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 11/20/2008] [Indexed: 11/29/2022]
Abstract
Comparative molecular field analysis (CoMFA) and quantum chemical calculations were performed on cycloguanil (Cyc) derivatives of the wild type and the quadruple mutant (Asn51Ile, Cys59Arg, Ser108Asn, Ile164Leu) of Plasmodium falciparum dihydrofolate reductase (PfDHFR). The represented CoMFA models of wild type (r(2) = 0.727 and r(2) = 0.985) and mutant type (r(2) = 0.786 and r(2) = 0.979) can describe the differences of the Cyc structural requirements for the two types of PfDHFR enzymes and can be useful to guide the design of new inhibitors. Moreover, the obtained particular interaction energies between the Cyc and the surrounding residues in the binding pocket indicated that Asn108 of mutant enzyme was the cause of Cyc resistance by producing steric clash with p-Cl of Cyc. Consequently, comparing the energy contributions with the potent flexible WR99210 inhibitor, it was found that the key mutant residue, Asn108, demonstrates attractive interaction with this inhibitor and some residues, Leu46, Ile112, Pro113, Phe116, and Leu119, seem to perform as second binding site with WR99210. Therefore, quantum chemical calculations can be useful for investigating residue interactions to clarify the cause of drug resistance.
Collapse
Affiliation(s)
- Phornphimon Maitarad
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | | | | | | | | | | |
Collapse
|