Effects of metal ions on the structural and biochemical properties of trypanosomatid phosphoglycerate mutases

Flagellate protozoa from the order Trypanosomatida have developed a range of strategies to survive in their mammalian hosts. A consequence is that the glycolytic pathway has assumed an important role, especially in bloodstream-form Trypanosoma brucei, where it is essential as the sole producer of ATP. The seventh enzyme in the pathway, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is particularly attractive as a drug target because it shares no common properties with the corresponding enzyme in humans. This enzyme catalyses the conversion of 3PGA to 2PGA, with the requirement for metal ions to assist the catalytic function. In this study, two important biochemical and structural aspects of the enzyme were investigated: i) The in vitro and in vivo requirements for biologically relevant metal ions to support the activity of iPGAM, and ii) The ability of trypanosomatid iPGAM to exist in multiple conformations and oligomeric states in solution. The maximum activity of iPGAM in vitro requires Co2+, but this cannot be the case in vivo where ICP-OES analyses confirmed that Co2+ was essentially undetectable in T. brucei cytosolic fractions. The activity of iPGAM in vivo is therefore one of the lowest among the glycolytic enzymes. By contrast, Mg2+ and Zn2+ were found to be the most abundant metals in both cytosolic fractions and in purified bacterially expressed iPGAM. Our newly-developed multimode-plate reader discontinuous assay further revealed that of the biologically relevant metals, only Mg2+ can support iPGAM activity, but at less than 50% of the level of Co2+. By contrast, Zn2+ strongly inhibits iPGAM. This assay which was developed with minimal metal interference on the coupling enzymes, also showed that in solution, the ratio of the concentrations of 3PGA:2PGA (substrate:product) at equilibrium is not 1:1 as observed in the crystal structure, but is in fact 12:1, which may be due to the tighter binding of 2PGA to the enzyme. A series of biophysical analyses, notably by SEC-MALS showed that iPGAM from Leishmania mexicana, another trypanosomatid protozoan parasite exists in different forms and oligomeric states in solution, either as the closed-form monomer, openiii form monomer, or closed/open-form dimer which can be successfully separated by ion-exchange chromatography. The open-form LmiPGAM is particularly relevant for drug development, as the catalytic site in the closed-form structure is poorly inaccessible. Both virtual and high-throughput screening approaches were used to identify novel potential inhibitors. Out of a collection of 11 compounds tested at 1 mM, two showed substantial inhibition with 49% and 14% remaining activity. Taken together, the findings from this study demonstrated the potential of iPGAM to be a key modulator in controlling glycolytic flux in trypanosomes, and thus further validated it as an important drug target

Enhanced expression and purification strategy for recombinant bacterially-expressed human hexokinase II

Dengue virus hijacks the host cellular mechanism to propagate and survive during viral infection, in which the central carbon mechanism plays a crucial role to upregulate DENV infection through the increase of human hexokinase II (HKII) activity. Since the enzyme governs the glycolytic pathway, it has potentials as a target for anti-dengue (DENV) drug development. In this study, the production of human hexokinase II protein has been enhanced by using bacterial system for anti-dengue therapeutic purpose. The HKII gene was cloned into pET28b vector and transformed into the E. coli strain BL21 (DE3) for HKII expression. In order to obtain soluble recombinant HKII in an active form, we optimized protein expression under specific conditions at 18°C for 19 hours using Terrific Broth media, in the presence of 0.5 mM isopropyl-2-D-thiogalactopyranoside (IPTG). The pET28b-HKII construct expressed in BL21(DE3) system exhibited adequate protein expression, thus, this construct was subsequently proceeded to purification process. The expressed protein was purified to homogeneity by a combination of Immobilized Metal Ion Affinity Chromatography (IMAC)and size exclusion chromatography (SEC), resulting in pure, active bacterially-expressed HKII with a specific activity of 56. 67U.mg-1. The amount of HKII obtained from 2 L culture is 80 mg, with a yield percentage of 10.5%. Hence in this study, human HKII has successfully been cloned and expressed as a soluble protein that can be utilized for further therapeutic studies

Interrogating novel compounds for improved anti-dengue therapies via inhibition of human hexokinase II (HKII)

Dengue is one of the most fatal infectious diseases in the world, which is caused by dengue virus (DENV). Regrettably until now, specific treatment for the disease has not been established. It has been reported that a human glycolytic enzyme, the human hexokinase II (HKII) has a great impact in supporting viral replication in the host cell, thus the enzyme has been proposed as an anti-DENV drug target. The main aim of this research is to identify novel anti-DENV agents for the treatment of dengue disease through in silico screening and HKII enzymatic inhibition studies

Expression and purification of soluble bacterially-expressed human hexokinase II in E.coli system

Human hexokinase II (HKII) is one of the key enzymes in the glycolytic pathway. It has been postulated that HKII is a potential target for anti-dengue (DENV) drug development, as well as involved in cancer and tumor cell growth. In this work, the human hexokinase II (HKII) gene was cloned into pETite N-His SUMO vector and transformed into the E.coli strain HI-control 10G for the propagation of clones. Two different expression hosts, E.coli HI-controlTM BL21 (DE3) and BL21 (DE3) pLysS were used to optimize HKII expression. In order to obtain the soluble recombinant HKII in a functional form, we optimized protein expression at three different temperatures; 17°C, 25°C and 37°C, at 24 hours incubation time. The soluble protein was expressed in the presence of 0.5 mM isopropyl-2-Dthiogalactopyranoside (IPTG) in TB media at 17°C for 24 hrs. The expressed protein was then purified to homogeneity by a combination of Immobilized Metal Ion Affinity Chromatography (IMAC), size exclusion chromatography (SEC) and ion-exchange chromatography (IEX), resulting in pure bacterially-expressed HK2. Taken together, this study has successfully produced soluble bacterially-expressed human HKII that can be utilized for further therapeutic studies

Identifying analogues of 2-deoxyglucose, alpha-d-glucose and beta-d-glucose-6-phosphate as potential inhibitors of human hexokinase ii for the development of anti-dengue therapeutics

The human hexokinase isoform II (HKII) is one of the important enzymes for dengue virus (DENV) replication and thus has been suggested as a potential therapeutic target for DENV drug development. In this work, compounds were identified using Ultrafast Shape Recognition with CREDO Atom Types (USRCAT) by utilizing both HKII’s substrate and product; alpha-D-glucose (GLC) and beta-D-glucose-6-phosphate (BG6), as well as a known HKII’s inhibitor, 2-deoxyglucose (2DG), as the query molecules. The analogues of the three query molecules were subsequently docked against the HKII’s crystal structure (PDB ID: 2NZT) by using Auto Dock 4 program on Chain B, where the active sites and strong bonds were located. Among the top-ranked compounds, Compound 4 (ZINC26898487), which was the most similar to 2DG, showed the best binding energy (-7.63 kcal/mol) and contained two H bonds. Compound 9 (ZINC16930948), an analogue of GLC emerged as the best inhibitor candidate because it had six H bonds. Similarly, among the molecules similar to BG6, Compound 14 (ZINC4403351) had been suggested as a potential inhibitor because it contained four strong H bonds. All compounds were predicted to be non-toxic, based on Toxicity Estimation Software Tool (TEST) analysis. By providing these valuable findings, this study has paved the way for the discovery of compounds that should be further tested for the development of anti-dengue drugs. © 2019, Universiti Putra Malaysia Press. All rights reserved

Cloning and characterisation of Lactate Dehydrogenase Gene from Plasmodium knowlesi in bacterial system

Glycolysis is essential for Plasmodium survival during its intra-erythrocytic stage in the human host. As a consequence, enzymes in the glycolytic pathway have been proposed as ideal therapeutic targets for malaria pharmaceuticals. Specifically, lactate dehydrogenase, which is the final enzyme in glycolysis, has been validated as a good drug target. We have cloned and characterised recombinant lactate dehydrogenase from Plasmodium knowlesi in a bacterial system. Synthetic P. knowlesi lactate dehydrogenase (Pk-LDH) gene was obtained from GenScript®. Pk-LDH gene was successfully amplified from the pUC57 vector and a PCR product with the size of 951bp was cloned into pEASY-Blunt E1 expression vector. The ligated product was subsequently transformed into Trans1-T1 Phage Resistant Chemically Competent Cell. A sequence alignment analysis, which was conducted to compare the sequence similarity of Pk-LDH to LDH from other human malaria parasites revealed open reading frame of 316 amino acids of Pk-LDH and showed 97.8% homology to P. vivax LDH and 90% homology to P. malariae, P. falciparum, and P. ovale LDHs, respectively. The purified recombinant Pk-LDH will later be utilised for inhibition studies in future antimalarial drug design and discovery research, specifically for P. knowlesi

Identifying potential inhibitors of human hexokinase II for the development of anti-dengue therapeutics via virtual screening approaches

The human hexokinase II (HK2) has been suggested as a potential therapeutic target for the development of drugs against dengue virus (DENV) infection. In this paper, compounds with potential HK2 inhibitory activity have been identified using ligandbased and structure-based virtual screening approaches. Ligand-based drug design was performed by using Ultra-Fast Shape Recognition with Atom Types (UFSRAT) and Ultrafast Shape Recognition with CREDO Atom Types (USRCAT) programmes by utilising 2-Deoxyglucose (2-DG) as the query molecule, which is a known HK2 inhibitor. The molecules identified from the programmes showed great similarity to 2-DG with scores ranged from 0.78-0.85 and 0.88-0.97 for UFSRAT and USRCAT, respectively. The analogues were docked against the crystal structure of HK2 (PDB ID: 2NZT) in complex with alpha-D-glucose (GLC) and beta-D-glucose-6-phosphate (BG6) by using AutoDock Vina programme, on both A and B chains where the active sites were located. The docking hits for molecules from UFSRAT showed binding energies ranged from -7.1 to -4.8 kcal/mol when docked on chain A, while the hits for chain B showed scores ranged from -6.7 to -4.8 kcal/mol. On the other hand, the binding energies for molecules from USRCAT when docked on both A and B chains were similar, which ranged from -7.0 to - 5.2 kcal/mol. The hits bind firmly at the cavities, where both GLC and BG6 were oriented towards the active sites of HK2. Taken together, this study has successfully discovered compounds which have potentials as potent inhibitors of HK2, thus pave the path towards the development of dengue therapeutics

Plasmodial enzymes in metabolic pathways as therapeutic targets and contemporary strategies to discover new antimalarial drugs: a review

Malaria continues to pose imminent threat to the world population, as the mortality rate associated with this disease remains high. Current treatment relies on antimalarial drugs such as Artemisinin Combination Therapy (ACT) are still effective throughout the world except in some places, where ACT-resistance has been reported, thus necessitating novel approaches to develop new anti-malarial therapy. In the light of emerging translational research, several plasmodial targets, mostly proteins or enzymes located in the parasite’s unique organelles, have been extensively explored as potential candidates for the development of novel antimalarial drugs. By targeting the metabolic pathways in mitochondrion, apicoplast or cytoplasm of Plasmodium, the possibility to discover new drugs is tremendous, as they have potentials as antimalarial therapeutic targets. This literature review summarizes pertinent information on plasmodial targets, especially enzymes involved in specific metabolic pathways, and the strategies used to discover new antimalarial drugs. © 2019, University of Malaya. All rights reserved

Effects of Daidzin and analogue of Ganoderma sinense on bacterially-expressed human hexokinase isoform 2 for anti-dengue drug design

Dengue disease, which is caused by dengue virus (DENV) has been a major worldwide concern, with increased number of cases each year. Currently, there are no specific medications to treat the disease. Hence, there is a dire need to develop novel drugs for disease treatment. Glycolysis is a metabolic pathway that serves as the main source of energy for DENV replication and targeting the pathway is one of the ideal approach to discover new anti-DENV drugs. This paper focuses on the inhibition of the human hexokinase isoform 2 (HK2) enzyme, which is one of the important enzymes in glycolysis, in the quest to disrupt DENV replication. In order to search for potential inhibitors, two methods were conducted, which are ligand-based screening and structure-based screening approaches. The docking of Daidzin, which was derived from Kudzu, a Japanese plant, has shown the nearest binding affinity score (-7.94 kcal/mol) to Glucose‘s (GLC), which is -8.15 kcal/mol. Meanwhile, from the ligand-based screening, Ethyl (2R)-2-[[3-[2-[(4-methylbenzoyl)amino]ethyl]-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl]butanoate, a compound which is the analogue of Ganoderma sinense with a binding score of -8.43 kcal/mol was chosen for the subsequent inhibition studies. These compounds were further analysed in an inhibition assay to determine the effects of of the potential naturally-derived inhibitors on the activity of HK2. The outcome from the inhibition study shows that both compounds exhibited substantial inhibition on HK2 enzyme, where Daidzin, at 0.5 mM, resulted in HK2 remaining activity of 88.98%, while Ethyl (2R)-2-[[3-[2-[(4-methylbenzoyl)amino]ethyl]-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl]butanoate (Ethyl (2R)) resulted in 69.58% of HK2 remaining activity, also at 0.5 mM concentration. In conclusion, this study has served as a platform for the development of anti-dengue drugs based on naturally-derived compounds, which is anticipated to be a safer option for dengue treatmen