1
|
Joste V, Coppée R, Bailly J, Rakotoarivony Y, Toko Tchokoteu FG, Achache S, Pradines B, Cottrell G, Ariey F, Khim N, Popovici J, Mita T, Groger M, Ramharter M, Egbo T, Juma DW, Akala H, Houzé S, Clain J. Plasmodium ovale spp dhfr mutations associated with reduced susceptibility to pyrimethamine in sub-Saharan Africa: a retrospective genetic epidemiology and functional study. THE LANCET. MICROBE 2024; 5:669-678. [PMID: 38761813 DOI: 10.1016/s2666-5247(24)00054-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 02/21/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Mutations in the Plasmodium falciparum dhfr gene confer resistance to pyrimethamine, which is widely used for malaria chemoprevention in Africa. We aimed to evaluate the frequency and evolution of dhfr mutations in Plasmodium ovale spp in Africa and their functional consequences, which are incompletely characterised. METHODS We analysed dhfr mutations and their frequencies in P ovale spp isolates collected between Feb 1, 2004, and Aug 31, 2023, from the French National Malaria Reference Centre collection and from field studies in Benin, Gabon, and Kenya. Genetic patterns of positive selection were investigated. Full-length recombinant wild-type and mutant DHFR enzymes from both P ovale curtisi and P ovale wallikeri were expressed in bacteria to test whether the most common mutations reduced pyrimethamine susceptibility. FINDINGS We included 518 P ovale spp samples (314 P ovale curtisi and 204 P ovale wallikeri). In P ovale curtisi, Ala15Ser-Ser58Arg was the most common dhfr mutation (39%; 124 of 314 samples). In P ovale wallikeri, dhfr mutations were less frequent, with Phe57Leu-Ser58Arg reaching 17% (34 of 204 samples). These two mutants were the most prevalent in central and east Africa and were fixed in Kenyan isolates. We detected six and four other non-synonymous mutations, representing 8% (24 isolates) and 2% (five isolates) of the P ovale curtisi and P ovale wallikeri isolates, respectively. Whole-genome sequencing and microsatellite analyses revealed reduced genetic diversity around the mutant pocdhfr and powdhfr genes. The mutant DHFR proteins showed structural changes at the pyrimethamine binding site in-silico, confirmed by a 4-times increase in pyrimethamine half-maximal inhibitory concentration in an Escherichia coli growth assay for the Phe57Leu-Ser58Arg mutant and 50-times increase for the Ala15Ser-Ser58Arg mutant, compared with the wild-type counterparts. INTERPRETATION The widespread use of sulfadoxine-pyrimethamine for malaria chemoprevention might have exerted fortuitous selection pressure for dhfr mutations in P ovale spp. This calls for closer monitoring of dhfr and dhps mutations in P ovale spp. FUNDING French Ministry of Health, Agence Nationale de la Recherche, and Global Emerging Infections Surveillance branch of the Armed Forces Health Surveillance Division.
Collapse
Affiliation(s)
- Valentin Joste
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France.
| | - Romain Coppée
- Université de Rouen Normandie, Laboratoire de Parasitologie-Mycologie, UR 7510 ESCAPE, Centre Hospitalier Universitaire de Rouen, Rouen, France
| | | | - Yann Rakotoarivony
- Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
| | | | | | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France; Université Aix-Marseille, IRD, SSA, VITROME, Marseille, France; IHU Méditerranée Infection, Marseille, France; Centre National de Référence du Paludisme, Marseille, France
| | | | - Frédéric Ariey
- INSERM U1016, Institut Cochin, Laboratoire de Parasitologie-Mycologie, Hôpital Cochin, AP-HP, Université Paris Cité, Paris, France
| | - Nimol Khim
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Mirjam Groger
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Ramharter
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Egbo
- Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Dennis W Juma
- Department of Emerging and Infectious Diseases (DEID), Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Hoseah Akala
- Department of Emerging and Infectious Diseases (DEID), Walter Reed Army Institute of Research - Africa (WRAIR-A), Kisumu, Kenya
| | - Sandrine Houzé
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
| | - Jérôme Clain
- Université Paris Cité, IRD, MERIT, Paris, France; Centre National de Référence du Paludisme, AP-HP, Hôpital Bichat - Claude-Bernard, Paris, France
| |
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
|
Somandi K, Seanego TD, Dlamini (née Molatsane) T, Maree M, de Koning CB, Vanichtanankul J, Rattanajak R, Saeyang T, Yuthavong Y, Kamchonwongpaisan S, Rousseau AL. Molecular Docking Studies, Synthesis and Biological Evaluation of Substituted Pyrimidine-2,4-diamines as Inhibitors of Plasmodium falciparum Dihydrofolate Reductase. ChemMedChem 2022; 17:e202200418. [PMID: 36193872 PMCID: PMC9827987 DOI: 10.1002/cmdc.202200418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/03/2022] [Indexed: 01/14/2023]
Abstract
A series of 5-[(phenethylamino)methyl]pyrimidine-2,4-diamines were assessed in silico as potential inhibitors of Plasmodium falciparum dihydrofolate reductase (PfDHFR), synthesised and tested for inhibitory activity against PfDHFR in vitro. The compounds displayed promising inhibitory activity against both wild-type (Ki 1.3-243 nM) and quadruple mutant (Ki 13-208 nM) PfDHFR in the biochemical enzyme assay, but were less potent in the whole-cell P. falciparum assay (IC50 (TM4/8.2) 0.4-28 μM; IC50 (V1S) 3.7-54 μM). Further investigation into the pharmacokinetic properties of these compounds may guide the development of more potent analogues.
Collapse
Affiliation(s)
- Khonzisizwe Somandi
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Tswene D. Seanego
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Tebogo Dlamini (née Molatsane)
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Matthew Maree
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| | - Charles B. de Koning
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Roonglawan Rattanajak
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Thanaya Saeyang
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyThailand Science ParkPathumthani12120Thailand
| | - Amanda L. Rousseau
- Molecular Sciences InstituteSchool of ChemistryUniversity of the WitwatersrandPrivate Bag 3, POWITS2050South Africa,WITS Research Institute for Malaria (WRIM)University of the Witwatersrand7 York RoadJohannesburg, Parktown2193South Africa
| |
Collapse
|
4
|
Cannabis sativa L. chemical compositions as potential plasmodium falciparum dihydrofolate reductase-thymidinesynthase enzyme inhibitors: An in silico study for drug development. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
This study contributes to anti-malarial research effort by conducting in silico assessment of 125 compounds originated from Cannabis sativa L. against plasmodium falciparum dihydrofolate reductase-thymidinesynthase (pfDHFR-TS) enzyme for potential inhibition activity. Drug-like and pharmacokinetic criteria were used to assess the drug-like properties of the studied compounds. AutoDock4.2.6 and AutoDock Vina software were used to calculate the possible binding pose of the studied compounds to pfDHFR-TS enzyme. The docking procedure was validated using two known inhibitors cycloguanil and WR99210. 65 out of 125 compounds violated no more than 2 of Lipinski’s rule of five and were sorted out as favorable for drug development. Amongst these 65 compounds, pharmacokinetic properties and toxicity evaluation identified 60 compounds that meet the criteria of drug-like properties and were subjected to further docking studies. Docking outcomes identified 10 compounds including compounds 4, 9, 19, 22, 23, 25, 30, 42, 43, and 59 as potential candidates for inhibiting the function of pfDHFR-TS at the active site through hydrogen bonds with Ile14, Asp54, and Ile 164 residues. Compound 9 is considered as the top “hit” with docking energy far more exceeding those of the standard compounds. High correlation coefficient between the docking energy of AutoDock4.2.6 and AutoDock Vina was recorded with the value of R
2 = 0.74.
Collapse
|
5
|
Hoarau M, Vanichtanankul J, Srimongkolpithak N, Vitsupakorn D, Yuthavong Y, Kamchonwongpaisan S. Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem 2021; 36:198-206. [PMID: 33530764 PMCID: PMC8759724 DOI: 10.1080/14756366.2020.1854244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In various malaria-endemic regions, the appearance of resistance has precluded the use of pyrimidine-based antifolate drugs. Here, a three-step fragment screening was used to identify new non-pyrimidine Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors. Starting from a 1163-fragment commercial library, a two-step differential scanning fluorimetry screen identified 75 primary fragment hits. Subsequent enzyme inhibition assay identified 11 fragments displaying IC50 in the 28-695 μM range and selectivity for PfDHFR. In addition to the known pyrimidine, three new anti-PfDHFR chemotypes were identified. Fragments from each chemotype were successfully co-crystallized with PfDHFR, revealing a binding in the active site, in the vicinity of catalytic residues, which was confirmed by molecular docking on all fragment hits. Finally, comparison with similar non-hit fragments provides preliminary input on available growth vectors for future drug development.
Collapse
Affiliation(s)
- Marie Hoarau
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitipol Srimongkolpithak
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Danoo Vitsupakorn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| |
Collapse
|
6
|
Madhav H, Hoda N. An insight into the recent development of the clinical candidates for the treatment of malaria and their target proteins. Eur J Med Chem 2020; 210:112955. [PMID: 33131885 DOI: 10.1016/j.ejmech.2020.112955] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 01/18/2023]
Abstract
Malaria is an endemic disease, prevalent in tropical and subtropical regions which cost half of million deaths annually. The eradication of malaria is one of the global health priority nevertheless, current therapeutic efforts seem to be insufficient due to the emergence of drug resistance towards most of the available drugs, even first-line treatment ACT, unavailability of the vaccine, and lack of drugs with a new mechanism of action. Intensification of antimalarial research in recent years has resulted into the development of single dose multistage therapeutic agents which has advantage of overcoming the antimalarial drug resistance. The present review explored the current progress in the development of new promising antimalarials against prominent target proteins that have the potential to be a clinical candidate. Here, we also reviewed different aspects of drug resistance and highlighted new drug candidates that are currently in a clinical trial or clinical development, along with a few other molecules with excellent antimalarial activity overs ACTs. The summarized scientific value of previous approaches and structural features of antimalarials related to the activity are highlighted that will be helpful for the development of next-generation antimalarials.
Collapse
Affiliation(s)
- Hari Madhav
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University), New Delhi, 110025, India.
| | - Nasimul Hoda
- Drug Design and Synthesis Laboratory, Department of Chemistry, Jamia Millia Islamia (A Central University), New Delhi, 110025, India.
| |
Collapse
|
7
|
Tiwari MK, Coghi P, Agrawal P, Shyamlal BRK, Jun Yang L, Yadav L, Peng Y, Sharma R, Yadav DK, Sahal D, Kam Wai Wong V, Chaudhary S. Design, Synthesis, Structure‐Activity Relationship and Docking Studies of Novel Functionalized Arylvinyl‐1,2,4‐Trioxanes as Potent Antiplasmodial as well as Anticancer Agents. ChemMedChem 2020; 15:1216-1228. [DOI: 10.1002/cmdc.202000045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/21/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Mohit K. Tiwari
- Laboratory of Organic and Medicinal ChemistryDepartment of ChemistryMalaviya National Institute of Technology Jawaharlal Nehru Marg Jaipur 302017 India
| | - Paolo Coghi
- School of PharmacyMacau University of Science and Technology Avenida wai long Taipa Macau China
| | - Prakhar Agrawal
- Malaria Drug Discovery LaboratoryInternational Centre for Genetic Engineering and Biotechnology Aruna Asaf Ali Marg 110 067 New Delhi India
| | - Bharti Rajesh K. Shyamlal
- Laboratory of Organic and Medicinal ChemistryDepartment of ChemistryMalaviya National Institute of Technology Jawaharlal Nehru Marg Jaipur 302017 India
| | - Li Jun Yang
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology Avenida Wai Long Taipa Macau China
| | - Lalit Yadav
- Laboratory of Organic and Medicinal ChemistryDepartment of ChemistryMalaviya National Institute of Technology Jawaharlal Nehru Marg Jaipur 302017 India
| | - Yuzhong Peng
- School of PharmacyMacau University of Science and Technology Avenida wai long Taipa Macau China
| | - Richa Sharma
- Laboratory of Organic and Medicinal ChemistryDepartment of ChemistryMalaviya National Institute of Technology Jawaharlal Nehru Marg Jaipur 302017 India
| | - Dharmendra K. Yadav
- College of PharmacyGachon University of Medicine and Science Hambakmoeiro 191, Yeonsu-gu Incheon city 406-799 South Korea
| | - Dinkar Sahal
- Malaria Drug Discovery LaboratoryInternational Centre for Genetic Engineering and Biotechnology Aruna Asaf Ali Marg 110 067 New Delhi India
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and Technology Avenida Wai Long Taipa Macau China
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal ChemistryDepartment of ChemistryMalaviya National Institute of Technology Jawaharlal Nehru Marg Jaipur 302017 India
| |
Collapse
|
8
|
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]
|
9
|
Sharma M, Prasher P. An epigrammatic status of the ' azole'-based antimalarial drugs. RSC Med Chem 2020; 11:184-211. [PMID: 33479627 PMCID: PMC7536834 DOI: 10.1039/c9md00479c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/26/2019] [Indexed: 11/21/2022] Open
Abstract
The development of multidrug resistance in the malarial parasite has sabotaged majority of the eradication efforts by restraining the inhibition profile of first line as well as second line antimalarial drugs, thus necessitating the development of novel pharmaceutics constructed on appropriate scaffolds with superior potency against the drug-resistant and drug-susceptible Plasmodium parasite. Over the past decades, the infectious malarial parasite has developed resistance against most of the contemporary therapeutics, thus necessitating the rational development of novel approaches principally focused on MDR malaria. This review presents an epigrammatic collation of the epidemiology and the contemporary antimalarial therapeutics based on the 'azole' motif.
Collapse
Affiliation(s)
- Mousmee Sharma
- Department of Chemistry , Uttaranchal University , Dehradun 248007 , India
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
| | - Parteek Prasher
- Department of Chemistry , University of Petroleum & Energy Studies , Dehradun 248007 , India . ;
- UGC Sponsored Centre for Advanced Studies , Department of Chemistry , Guru Nanak Dev University , Amritsar 143005 , India
| |
Collapse
|
10
|
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
|
11
|
David T, Adelakun N, Omotuyi O, Metibemu D, Ekun O, eniafe G, Inyang O, Adewumi B, Enejoh O, Owolabi R, Oribamise EI. Molecular docking analysis of phyto-constituents from Cannabis sativa with pfDHFR. Bioinformation 2018; 14:574-579. [PMID: 31223216 PMCID: PMC6563669 DOI: 10.6026/97320630014574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/23/2022] Open
Abstract
Available antimalarial drugs have been associated with numerous side effects, which include skin rashes and myelo-suppression. Therefore, it is of interest to explore compounds from natural source having drug-like properties without side effect. This study focuses on the screening of compounds from Cannabis sativa against malaria Plasmodium falciparum dihydrofolate reductase for antimalarial properties using Glide (Schrodinger maestro 2018-1). The result showed that phytochemicals from Cannabis sativa binds with a higher affinity and lower free energy than the standard ligand with isovitexin and vitexin having a glide score of -11.485 and -10.601 respectively, sophoroside has a glide score of -9.711 which is lower than the cycloguanil (co-crystallized ligand) having a glide score of -6.908. This result gives new perception to the use of Cannabis sativa as antimicrobial agent.
Collapse
Affiliation(s)
- Temitope.I David
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Niyi.S Adelakun
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Olaposi.I Omotuyi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Damilohun.S Metibemu
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Oluwafemi.E Ekun
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Gabriel.O eniafe
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Olumide.K Inyang
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Bamidele Adewumi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Ojochenemi.A Enejoh
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Raymond.T Owolabi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Eunice. I Oribamise
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| |
Collapse
|
12
|
Inthajak K, Toochinda P, Lawtrakul L. Application of molecular docking and PSO-SVR intelligent approaches in antimalarial activity prediction of enantiomeric cycloguanil analogues. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:957-974. [PMID: 30381963 DOI: 10.1080/1062936x.2018.1536678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/12/2018] [Indexed: 06/08/2023]
Abstract
A series of antifolate compounds, i.e. 1-(4-chlorophenyl)-6,6-dimethyl-1,3,5-triazine-2,4-diamine, or cycloguanil analogues, have shown effective inhibiting properties against Plasmodium falciparum dihydrofolate reductase (PfDHFR). In this work, the stereoselectivity of PfDHFR to the R and S enantiomer of cycloguanil analogues was obtained from molecular docking calculations and integrated into QSAR study to obtain a more accurate prediction model. Results indicate that PfDHFR can bind to cycloguanil analogues in the R and S enantiomers. Cycloguanil analogues with alkyl chain substituent prefer the R enantiomer over S because they do not experience steric hindrance with the Phe58 side chain, while cycloguanil analogues with phenol chain substituent prefer the S enantiomer over R because they do not experience steric hindrance with Leu46 and Met55 side chains. Particle swarm optimization and support vector regression were used to select relevant descriptors and generate the effective prediction model, with a high statistical significance level (r2training = 0.941; r2test = 0.884).
Collapse
Affiliation(s)
- K Inthajak
- a School of Bio-Chemical Engineering and Technology , Sirindhorn International Institute of Technology, Thammasat University , Pathum Thani , Thailand
| | - P Toochinda
- a School of Bio-Chemical Engineering and Technology , Sirindhorn International Institute of Technology, Thammasat University , Pathum Thani , Thailand
| | - L Lawtrakul
- a School of Bio-Chemical Engineering and Technology , Sirindhorn International Institute of Technology, Thammasat University , Pathum Thani , Thailand
| |
Collapse
|
13
|
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
|
14
|
|
15
|
Wadood A, Ghufran M, Hassan SF, Khan H, Azam SS, Rashid U. In silico identification of promiscuous scaffolds as potential inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase for treatment of Falciparum malaria. PHARMACEUTICAL BIOLOGY 2017; 55:19-32. [PMID: 27650666 PMCID: PMC7011789 DOI: 10.1080/13880209.2016.1225778] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
CONTEXT Malaria remains one of the prevalent infectious diseases worldwide. Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (PfDXR) plays a role in isoprenoid biosynthesis in the malaria parasite, making this parasite enzyme an attractive target for antimalarial drug design. Fosmidomycin is a promising DXR inhibitor, which showed safety as well as efficacy against Plasmodium falciparum malaria in clinical trials. However, due to its poor oral bioavailability and non-drug-like properties, the focus of medicinal chemists is to develop inhibitors with improved pharmacological properties. OBJECTIVE This study described the computational design of new and potent inhibitors for deoxyxylulose 5-phosphate reductoisomerase and the prediction of their pharmacokinetic and pharmacodynamic properties. MATERIAL AND METHODS A complex-based pharmacophore model was generated from the complex X-ray crystallographic structure of PfDXR using MOE (Molecular Operating Environment). Furthermore, MOE-Dock was used as docking software to predict the binding modes of hits and target enzyme. RESULTS Finally, 14 compounds were selected as new and potent inhibitors of PfDXR on the basis of pharmacophore mapping, docking score, binding energy and binding interactions with the active site residues of the target protein. The predicted pharmacokinetic properties showed improved permeability by efficiently crossing blood-brain barrier. While, in silico promiscuity binding data revealed that these hits also have the ability to bind with other P. falciparum drug targets. DISCUSSION AND CONCLUSION In conclusion, innovative scaffolds with novel modes of action, improved efficacy and acceptable physiochemical/pharmacokinetic properties were computationally identified.
Collapse
Affiliation(s)
- Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- CONTACT Abdul WadoodDepartment of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; Umer Rashid Department of Chemistry, COMSAT, Abbatabad, Pakistan
| | - Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | | | - Huma Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Syed Sikandar Azam
- Department of Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Umer Rashid
- Department of Chemistry, COMSAT, Abbatabad, Pakistan
- CONTACT Abdul WadoodDepartment of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan; Umer Rashid Department of Chemistry, COMSAT, Abbatabad, Pakistan
| |
Collapse
|
16
|
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
|
17
|
Gabel SA, Duff MR, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. A Structural Basis for Biguanide Activity. Biochemistry 2017; 56:4786-4798. [PMID: 28766937 PMCID: PMC5740485 DOI: 10.1021/acs.biochem.7b00619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metformin is the most commonly prescribed treatment for type II diabetes and related disorders; however, molecular insights into its mode(s) of action have been limited by an absence of structural data. Structural considerations along with a growing body of literature demonstrating its effects on one-carbon metabolism suggest the possibility of folate mimicry and anti-folate activity. Motivated by the growing recognition that anti-diabetic biguanides may act directly upon the gut microbiome, we have determined structures of the complexes formed between the anti-diabetic biguanides (phenformin, buformin, and metformin) and Escherichia coli dihydrofolate reductase (ecDHFR) based on nuclear magnetic resonance, crystallographic, and molecular modeling studies. Interligand Overhauser effects indicate that metformin can form ternary complexes with p-aminobenzoyl-l-glutamate (pABG) as well as other ligands that occupy the region of the folate-binding site that interacts with pABG; however, DHFR inhibition is not cooperative. The biguanides competitively inhibit the activity of ecDHFR, with the phenformin inhibition constant being 100-fold lower than that of metformin. This inhibition may be significant at concentrations present in the gut of treated individuals, and inhibition of DHFR in intestinal mucosal cells may also occur if accumulation levels are sufficient. Perturbation of folate homeostasis can alter the pyridine nucleotide redox ratios that are important regulators of cellular metabolism.
Collapse
Affiliation(s)
- Scott A. Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Michael R. Duff
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Eugene F. DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | | | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Robert E. London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| |
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
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
|
20
|
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]
|
21
|
Abstract
The biguanide metformin is widely prescribed for Type II diabetes and has anti-neoplastic activity in laboratory models. Despite evidence that inhibition of mitochondrial respiratory complex I by metformin is the primary cause of its cell-lineage-specific actions and therapeutic effects, the molecular interaction(s) between metformin and complex I remain uncharacterized. In the present paper, we describe the effects of five pharmacologically relevant biguanides on oxidative phosphorylation in mammalian mitochondria. We report that biguanides inhibit complex I by inhibiting ubiquinone reduction (but not competitively) and, independently, stimulate reactive oxygen species production by the complex I flavin. Biguanides also inhibit mitochondrial ATP synthase, and two of them inhibit only ATP hydrolysis, not synthesis. Thus we identify biguanides as a new class of complex I and ATP synthase inhibitor. By comparing biguanide effects on isolated complex I and cultured cells, we distinguish three anti-diabetic and potentially anti-neoplastic biguanides (metformin, buformin and phenformin) from two anti-malarial biguanides (cycloguanil and proguanil): the former are accumulated into mammalian mitochondria and affect oxidative phosphorylation, whereas the latter are excluded so act only on the parasite. Our mechanistic and pharmacokinetic insights are relevant to understanding and developing the role of biguanides in new and existing therapeutic applications, including cancer, diabetes and malaria.
Collapse
|
22
|
Basuki S, Fitriah, Riyanto S, Budiono, Dachlan YP, Uemura H. Two novel mutations of pfdhps K540T and I588F, affecting sulphadoxine-pyrimethamine-resistant response in uncomplicated falciparum malaria at Banjar district, South Kalimantan Province, Indonesia. Malar J 2014; 13:135. [PMID: 25187019 PMCID: PMC4222776 DOI: 10.1186/1475-2875-13-135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/25/2014] [Indexed: 11/10/2022] Open
Abstract
Background Mutations in pfdhfr and pfdhps genes have been shown to associate with sulphadoxine-pyrimethamine (SP) resistance of Plasmodium falciparum parasites. However, pfdhfr, pfdhps genotypes and the correlations to SP treatment outcome in Indonesia has not yet been well analysed. Methods After obtaining informed consent, 61 uncomplicated falciparum malaria patients were recruited in Banjar district, South Kalimantan Province, Indonesia, from October 2009 to August 2010. They were treated by a single oral dose of SP and its effects on clinical and parasitological status were followed until day 28 after treatment. Occasionally, a thick smear blood film for microscopy observation and blood spot on a filter paper for pfdhfr and pfdhps genotype analysis were collected. Results Pfdhfr and pfdhps genotypes from 24 P. falciparum-infected patients consisting of adequate clinical parasitological response (ACPR) (n = 6; 25.0%) and early treatment failure (ETF) (n = 10; 41.7%) or late parasitological failure (LPF) (n = 8; 33.3%) were obtained by sequencing. Two novel mutations of pfdhps gene, K540T and I588F, were determined in ten and five isolates, respectively. These mutations were present in the pfdhfr/pfdhps combined haplotypes of ANRNI/SGTGA (n = 6), ANRNL/SGTGA (n = 4), and ANRNI/SGEAA(588F) (n = 5), (mutation codons are bold typed); these haplotypes were mostly belonging to parasitological failure (ETF or LPF). The parasites acquiring five mutations in pfdhfr/pfdhps haplotypes and four mutations with additional I588F did not respond adequately to SP treatment. Conclusion Many of Plasmodium falciparum infected patients in Banjar district, South Kalimantan, Indonesia did not respond adequately to SP treatment and these low ineffectiveness of SP in this area was associated with two novel mutations of pfdhps, K540T and I588F.
Collapse
Affiliation(s)
| | | | | | | | | | - Haruki Uemura
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.
| |
Collapse
|
23
|
Folate metabolism in human malaria parasites—75 years on. Mol Biochem Parasitol 2013; 188:63-77. [DOI: 10.1016/j.molbiopara.2013.02.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/15/2013] [Accepted: 02/19/2013] [Indexed: 12/21/2022]
|