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Chen MD, Fucci IJ, Sinha K, Rule GS. dGMP Binding to Thymidylate Kinase from Plasmodium falciparum Shows Half-Site Binding and Induces Protein Dynamics at the Dimer Interface. Biochemistry 2020; 59:694-703. [PMID: 31934749 DOI: 10.1021/acs.biochem.9b00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) is an essential enzyme for the growth of the organism because of its critical role in the de novo synthesis of deoxythymidine 5'-diphosphate (TDP), a precursor for TTP that is required for DNA replication and repair. The kinetics, thermodynamic parameters, and substrate binding properties of PfTMK for TMP, dGMP, ADP, and ATP were measured and characterized by steady-state kinetics and a combination of isothermal titration calorimetry, tryptophan fluorescence titration, and NMR. Mutational studies were performed to investigate residues that contribute to the unique ability of PfTMK to also utilize dGMP as a substrate. Isothermal titration calorimetry experiments revealed that dGMP binding exhibits a unique half-site binding mechanism. The occlusion of the empty site in the dGMP complex is supported by molecular mechanics calculations. Relaxation dispersion experiments show that the dGMP and enzyme complex is more dynamic at the dimer interface than the TMP complex on the μs-ms time scale. The unique properties of dGMP binding need to be considered in the design of guanosine-based PfTMK-specific inhibitors.
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Affiliation(s)
- Mengshen David Chen
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Ian J Fucci
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Kaustubh Sinha
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Gordon S Rule
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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Kandeel M, Kitade Y, Al-Taher A, Al-Nazawi M. The structural basis of unique substrate recognition by Plasmodium thymidylate kinase: Molecular dynamics simulation and inhibitory studies. PLoS One 2019; 14:e0212065. [PMID: 30730992 PMCID: PMC6366710 DOI: 10.1371/journal.pone.0212065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/25/2019] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) showed structural and catalytic distinctions from the host enzyme rendering it a hopeful antiprotozoal drug target. Despite the comprehensive enzymologic, structural, inhibitory and chemical synthesis approaches targeting this enzyme, the elucidation of the exact mechanism underlying the recognition of the atypical purine substrates remains to be determined. In this study, molecular dynamics (MD) simulation of a broad range of substrates and inhibitors as well as the inhibitory properties of deoxyguanosine (dG) derivatives were used to assess the PfTMK substructure molecular rearrangements. The estimated changes during the favourable binding of high affinity substrate (TMP) include lower interaction with P-loop, free residue fluctuations of the lid domain and the average RMSD value. The RMSD of TMP complex was higher and more rapidly stabilized than the dGMP complex. The lid domain flexibility is severely affected by dGMP and β-thymidine derivatives, while being partially fluctuating with other thymidine derivatives. The TMK-purine (dGMP) complex was slowly and gradually stabilized with lower over all structure flexibility and residue fluctuations especially at the lid domain, which closes the active site during its catalytic state. Thymidine derivatives allow structure flexibility of the lid domain being highly fluctuating in α- and β-thymidine derivatives and TMP. dG derivatives remains less efficient than thymidine derivatives in inhibiting TMK. The variations in the structural dynamics of the P-loop and lid domain in response to TMP or dGMP might favour thymidine-based compounds. The provided MD simulation strategy can be used for predicating structural changes in PfTMK during lead optimization.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Kafrelsheikh, Egypt
- * E-mail: ,
| | - Yukio Kitade
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Yachigusa, Yakuza, Toyota, Japan
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu, Japan
| | - Abdulla Al-Taher
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University, Hofuf, Alahsa, Saudi Arabia
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Sinha K, Rule GS. The Structure of Thymidylate Kinase from Candida albicans Reveals a Unique Structural Element. Biochemistry 2017; 56:4360-4370. [DOI: 10.1021/acs.biochem.7b00498] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kaustubh Sinha
- Department of Biological
Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gordon S. Rule
- Department of Biological
Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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A novel viral thymidylate kinase with dual kinase activity. J Bioenerg Biomembr 2015; 47:431-40. [PMID: 26315341 DOI: 10.1007/s10863-015-9622-z] [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: 03/25/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
Abstract
Nucleotide phosphorylation is a key step in DNA replication and viral infections, since suitable levels of nucleotide triphosphates pool are required for this process. Deoxythymidine monophosphate (dTMP) is produced either by de novo or salvage pathways, which is further phosphorylated to deoxythymidine triphosphate (dTTP). Thymidyne monophosphate kinase (TMK) is the enzyme in the junction of both pathways, which phosphorylates dTMP to yield deoxythymidine diphosphate (dTDP) using adenosine triphosphate (ATP) as a phosphate donor. White spot syndrome virus (WSSV) genome contains an open reading frame (ORF454) that encodes a thymidine kinase and TMK domains in a single polypeptide. We overexpressed the TMK ORF454 domain (TMKwssv) and its specific activity was measured with dTMP and dTDP as phosphate acceptors. We found that TMKwssv can phosphorylate dTMP to yield dTDP and also is able to use dTDP as a substrate to produce dTTP. Kinetic parameters K M and k cat were calculated for dTMP (110 μM, 3.6 s(-1)), dTDP (251 μM, 0.9 s(-1)) and ATP (92 μM, 3.2 s(-1)) substrates, and TMKwssv showed a sequential ordered bi-bi reaction mechanism. The binding constants K d for dTMP (1.9 μM) and dTDP (10 μM) to TMKwssv were determined by Isothermal Titration Calorimetry. The affinity of the nucleotidic analog stavudine monophosphate was in the same order of magnitude (K d 3.6 μM) to the canonical substrate dTMP. These results suggest that nucleotide analogues such as stavudine could be a suitable antiviral strategy for the WSSV-associated disease.
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Taher AA, Kandeel M, Kim HS, Kitade Y. Cleavage of DNA and Nuclease Properties of Plasmodium Nucleoside Diphosphate Kinase. INT J PHARMACOL 2014. [DOI: 10.3923/ijp.2014.334.339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kandeel M, Al-Taher A, Nakashima R, Sakaguchi T, Kandeel A, Nagaya Y, Kitamura Y, Kitade Y. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain. PLoS One 2014; 9:e94538. [PMID: 24788663 PMCID: PMC4008379 DOI: 10.1371/journal.pone.0094538] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 03/18/2014] [Indexed: 12/27/2022] Open
Abstract
Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2) is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3′-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3′-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine), whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine and Animal Resources, King Faisal University, Alhofuf, Alahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Abdullah Al-Taher
- Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine and Animal Resources, King Faisal University, Alhofuf, Alahsa, Saudi Arabia
| | - Remi Nakashima
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Tomoya Sakaguchi
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Ali Kandeel
- Department of Biology, Faculty of Sciences and Arts, Alkamil Branch, King Abdul Aziz University, Alkamil, Saudi Arabia
- Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yuki Nagaya
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
| | - Yoshiaki Kitamura
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Yukio Kitade
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, Gifu, Japan
- * E-mail:
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Synthesis of carbocyclic pyrimidine nucleosides and their inhibitory activities against Plasmodium falciparum thymidylate kinase. Parasitol Int 2013; 62:368-71. [DOI: 10.1016/j.parint.2013.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 03/01/2013] [Accepted: 03/20/2013] [Indexed: 11/24/2022]
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Abstract
Malaria, the disease caused by infection with protozoan parasites from the genus Plasmodium, claims the lives of nearly 1 million people annually. Developing nations, particularly in the African Region, bear the brunt of this malaria burden. Alarmingly, the most dangerous etiologic agent of malaria, Plasmodium falciparum, is becoming increasingly resistant to current first-line antimalarials. In light of the widespread devastation caused by malaria, the emergence of drug-resistant P. falciparum strains, and the projected decrease in funding for malaria eradication that may occur over the next decade, the identification of promising new targets for antimalarial drug design is imperative. P. falciparum kinases have been proposed as ideal drug targets for antimalarial drug design because they mediate critical cellular processes within the parasite and are, in many cases, structurally and mechanistically divergent when compared with kinases from humans. Identifying a molecule capable of inhibiting the activity of a target enzyme is generally an arduous and expensive process that can be greatly aided by utilizing in silico drug design techniques. Such methods have been extensively applied to human kinases, but as yet have not been fully exploited for the exploration and characterization of antimalarial kinase targets. This review focuses on in silico methods that have been used for the evaluation of potential antimalarials and the Plasmodium kinases that could be explored using these techniques.
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Carbocyclic thymidine derivatives efficiently inhibit Plasmodium falciparum thymidylate kinase (PfTMK). Parasitol Int 2012; 61:501-3. [PMID: 22425904 DOI: 10.1016/j.parint.2012.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/02/2012] [Accepted: 03/02/2012] [Indexed: 11/20/2022]
Abstract
During the course of our research into new anti-malaria drugs, Plasmodium falciparum thymidylate kinase (PfTMK) has emerged as an important drug target because of its unique substrate specificity. Compared with human thymidylate kinase (HsTMK), PfTMK shows broader substrate specificity, which includes both purine and pyrimidine nucleotides. PfTMK accepts both 2'-deoxyguanosine monophosphate (dGMP) and thymidine monosphosphate (TMP) as substrates. We have evaluated the inhibitory activity of seven carbocyclic thymidine analogs and report the first structure-activity relationship for these inhibitors against PfTMK. The 2',3' dideoxycarbocyclic derivative of thymidine showed the most potent inhibition of the enzyme. The K(i)(dTMP) and K(i)(dGMP) values were 20 and 7 μM respectively. Thus, further modifications of carbocyclic thymidine analogs represent a good strategy for developing more powerful thymidylate kinase inhibitors.
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