Molecular docking
I) Dioncophyllin - A: The binding affinity of dioncophyllin-A to the malaria hexokinase-1 protein was evaluated using a docking score of -7.7, as shown in Table 1. This docking score serves as a quantitative measure of the compound's ability to bind to the target protein. The experimental results revealed a distance range of 1.94226 Å to 5.32012 Å. The crucial role that strong hydrogen bonds, particularly HIS467, PHE67 and the hydrophobic bonds LEU463, VAL459, ILE163 and LEU463, play in determining the molecular affinity of a system. The first hydrogen bond exhibits remarkable robustness, as demonstrated by its bond length of 3.4 Å. In addition, we observed a second hydrogen bond that, although less impressive, still has a bond length of 3.8 Å (Fig. 2).
II) Hugorosenone: Molecular docking analysis was performed to evaluate the binding affinity of hugorosenone toward the malaria hexokinase-1 protein. The obtained docking score of -7.7 indicates a strong interaction between hugorosenone and the target protein, as shown in Table 1. In the present study, a novel finding was made regarding the interaction between hugorosenone and specific amino acid residues of the malaria pathogen (Fig. 3). Hydrogen bonds were observed to occur specifically at the amino acid residues ARG69 within the studied system. Furthermore, in the present study, the formation of hydrophobic bonds between amino acid residues ILE470 and HIS467 was observed. The experimental results gave a distance spectrum of 1.87757 Å to 5.37953 Å. The above value serves as a quantitative assessment of the affinity between the compound under study and its intended target molecule.
III) Marmesin: Molecular docking analysis to examine the binding affinity of marmesin to the malaria hexokinase-1 protein. The docking score obtained for this interaction was -7.6, as shown in Table 1. The present study demonstrates a convincing correlation between marmesine and the malaria hexokinase-1 protein and suggests a possible avenue to investigate the ability of marmesine as an inhibitor or modulator of the functionality of the malaria hexokinase-1 protein. Our results show that marmesine forms hydrogen bonds with four specific amino acid residues, namely ARG69 and SER70. These observations provide valuable insights into the molecular interactions of marmesine with amino acids and shed light on its potential biological activities and mechanisms of action. Further studies are required to investigate the functional implications of these interactions and their significance in the context of the biological properties of marmesine. The measured values were 2.05256 Å and 2.28493 Å, respectively. In this study, we successfully identified five hydrophobic interaction bonds between marmesine and specific amino acid residues, namely VAL68, VAL459, VAL456, ILE163, and LEU463. The distances between marmesin and these residues were measured to be 3.98606 Å, 3.75715 Å, 5.31584 Å, 4.8324 Å, and 5.35527 Å, respectively (Fig. 4). These results provide valuable insights into the molecular interactions between marmesine and the target amino acid residues and shed light on the possible mechanisms underlying their binding affinity.
IV) Oxyprotostemonine: Molecular docking analysis, a docking score of -8.6 was obtained for the binding of oxyprotostemonine to malaria hexokinase-1 protein, as shown in Table 1. This finding suggests a possible interaction between oxyprotostemonine and malaria hexokinase-1 protein highlights the possibility of oxyprotostemonine as a potential inhibitor or modulator of malaria hexokinase-1 protein function. Through molecular model analysis, oxyprotostemonine was observed to form hydrogen bonds with four amino acid residues, namely ARG69, HIS467, ASP814, and ASP814. The distances oxyprotostemonine and these residues were measured to be 2.84867 Å, 2.64886 Å, 3.3784 Å, 3.3784 Å respectively. Furthermore, two hydrophobic interaction bonds were identified between oxyprotostemonine and amino acid residues LEU463, ILE470 with distances of 5.37888 Å, 5.19227 Å (Fig. 5).
V) Pachyrrhizin: The binding affinity of pachyrrhizin to the malaria hexokinase-1 protein was evaluated using a docking score of -9.9, as shown in Table 1. This docking score serves as a quantitative measure of the compound's ability to bind to the target protein. The experimental results revealed a distance range of 2.2091 Å to 5.33502 Å. The crucial role that strong hydrogen bonds, particularly SER70, ILE163, SER70 and the hydrophobic bonds ILE163, VAL459, LYS162, PHE67, LEU463, VAL68, VAL456, ARG69 play in determining the molecular affinity of a system (Fig. 6). This score indicates a strong binding affinity between pachyrrhizin and the target protein, suggesting that pachyrrhizin is a promising candidate for further research to develop antimalarial drugs.
VI) Plumbagin: The binding affinity of plumbagin to the malaria hexokinase-1 protein was evaluated using a docking score of -6.6, as shown in Table 1. This docking score serves as a quantitative measure of the compound's ability to bind to the target protein. The experimental results revealed a distance range of 3.55171 Å to 5.12241 Å. The crucial role that strong hydrophobic bonds LEU318, MET313, LYS21, ILE22 play in determining the molecular affinity of a system (Fig. 7).
VII) Stemocurtisine: The binding affinity of stemocurtisine to the malaria hexokinase-1 protein was evaluated using a docking score of -7.8, as shown in Table 1. This docking score serves as a quantitative measure of the compound's ability to bind to the target protein. The experimental results revealed a distance range of 1.88868 Å to 4.3109 Å. The crucial role that strong hydrogen bond HIS467, ASP814 and hydrophobic bonds LEU463 play in determining the molecular affinity of a system (Fig. 8).
Yu et al. (2018), the authors investigated the central role of hexokinases as essential glycolytic enzymes responsible for the activation of glucose and various hexoses. Plasmodium parasites, belonging to the phylum Apicomplexa, are obligate intracellular parasites responsible for the development of malaria in humans. These parasites have evolved unique metabolic adaptations to survive within their host and successfully complete their life cycle. Through a comprehensive analysis of existing literature and experimental data, this research article examines the role of the Krebs cycle of aerobic fermentation in Leishmania and Trypanosoma and highlights its potential importance in the survival and adaptation of these parasites. Leishmania and Trypanosoma are parasitic protozoa belonging to the order Kinetoplastida. These organisms are responsible for causing debilitating diseases in humans and animals, including leishmaniasis and trypanosis.
Given the existence of the tricarboxylic acid cycle (TCA) and the availability of oxygen (O2) in cellular environments, glucose molecules have been observed to undergo rapid conversion into mono- and dicarboxylic acids (Urbina et al., 1994). The enzymatic process of glucose phosphorylation is facilitated by the enzyme hexokinase. The present study investigates the affinity of hexokinase isozymes I, II and III towards glucose and their inhibitory effect on glucose-6-phosphate as a product. Consistent with the findings of Nederlof et al. (2014) it was observed that hexokinase IV has minimal affinity for glucose molecules and does not exert a significant influence on product inhibition under conditions of typical glucose-6-phosphate concentrations.
Physicochemical properties of dengue protein
Table 2 provides an overview of the key properties of the malaria hexokinase-1 protein. The table provided contains comprehensive data on various interesting properties of a number of molecules. These features include the number of amino acids, molecular weight, molecular formula, theoretical pI (isoelectric point), total number of negatively charged residues (Asp + Glu), total number of positively charged residues (Arg + Lys), and total number of atoms. In addition, the table contains information on Instability Index (II), Aliphatic Index, Grand Average Hydropathy (GRAVY), allergenicity and toxicity.
Structure validation
The study aimed to validate the tertiary structure of the malaria hexokinase-1 protein using the PROCHECK server. The ERRAT server served as a computational tool to predict the quality of the malaria hexokinase-1 protein. The overall quality score of the protein in this study was 91.4%. A detailed examination of the data revealed that a significant proportion of 8.4% of the residues were located in additional approved regions, suggesting their favourable conformation. Furthermore, our analysis revealed that approximately 0.3% of the residues were located in regions considered generously permitted by established conformational standards. This finding suggests that these residues adopt a slightly less favourable conformation compared to the majority of the protein structure. The results showed that only 0.1% of residues were identified in these regions, suggesting the presence of an unfavourable conformation.
These results highlight the importance of further studying the structural features and implications of these rejected regions to gain a comprehensive understanding of their impact on the overall conformation. The numerical representation of the residues is given in parentheses. In this study, individuals are identified and appropriately labelled that have an unfavourable conformation, as determined by a value below -3.00. The shading in Figure 9 represents the favourable conformations derived from an analysis of 163 structures at a resolution of 2.0 Å or higher. The study aims to quantify in percent the proportion of proteins for which the calculated error value is below the 95% exclusion limit. In general, high-resolution structures are characterized by values that typically exceed or reach 95% or more. At lower resolutions, particularly in the 2.5 to 3 angstrom (Å) range, the average overall quality factor is around 91% (Fig. 10).
Pharmacokinetics Properties of phytochemicals
In the early stages of pharmaceutical development, researchers used physicochemical parameters to identify the key characteristics that influence the biological activities of drugs, particularly absorption, distribution, metabolism, and excretion (ADME), as shown in Table 3. The assessment of screening status regarding the use of antimalarial phytochemicals in drug development heavily relies on pharmacokinetic assessment (Table 4). The current investigation aimed to explore several crucial physicochemical properties, including permeability, solubility, lipophilicity, integrity, and stability. The mentioned properties are of utmost importance for elucidating the behaviour and characteristics of various substances. Through careful measurement and comprehensive analysis of these inherent properties, numerous invaluable insights can be gained about the potential applications and limitations of the substances under investigation.
The ADME paradigm has been expanded to include the assessment of toxicity aspects. Since the inception of pharmaceutical research, scientists have employed the in silico approach to accurately predict the pharmacokinetic properties of drugs, encompassing immediate absorption, distribution, metabolism, excretion, and toxicity (Table 5).
Pathway analysis
This study highlights the importance of these pathways as viable avenues for the further development of innovative antimalarial therapeutics. Transition state analogs are widely used in scientific research to specifically target and inhibit critical enzymes involved in various metabolic pathways. These analogs have demonstrated remarkable efficacy by exhibiting strong inhibitory properties coupled with high affinity for their target enzymes. The development of effective therapeutic strategies against parasitic infections remains a major challenge due to the high similarity between parasite enzymes and their homologous counterparts in the human host (KEGG pathway). Achieving selectivity for parasite enzymes while sparing human host enzymes is critical to the development of targeted therapies (Fig. 11).
Parasitic infections pose a major threat to global health, affecting millions of people worldwide. The enzymes produced by parasites play a crucial role in their survival and pathogenesis, making them attractive targets for therapeutic interventions. However, the high structural similarity between parasite enzymes and their homologous counterparts in the human host poses a significant challenge in the development of selective enzymes. It is noteworthy that these substances have minimal affinity for the corresponding enzymes in the human host. This selective binding is achieved by mimicking the transition state of the enzymatic reaction. The critical importance of selectivity in the development of therapeutic strategies against parasitic diseases lies in its ability to specifically inhibit parasitic enzymes while leaving host enzymes unaffected. This targeted inhibition enables the effective treatment of parasitic diseases without affecting the essential functions of the host enzymes.
Transition state mimicry has emerged as a promising strategy in the search for novel and effective therapeutics against parasitic enzymes, representing a potential route to the treatment of parasitic diseases. The development of novel antimalarial drugs with reduced toxicity and increased effectiveness against antibiotic resistance can be achieved through further investigation. Studies on the tight binding and specificity of transition state analogue inhibitors will facilitate this.
Malaria, a life-threatening disease, is primarily caused by the parasite P. falciparum. Our findings highlight the urgent need for effective interventions to combat this global health burden. Malaria, caused by various species of Plasmodium, remains a significant public health concern, particularly in regions with high transmission rates. Throughout this intricate process, the parasite induces a multitude of deleterious effects, including the onset of severe complications and the development of anemia, primarily attributed to the obstruction of blood vessels. The potential antimalarial activity of any lead compound can be attributed to its ability to inhibit the aforementioned pathway. The impediment of hexose transport and glucose analogs, including 2-deoxyglucose, by small molecules derived from various sources has been investigated (Saliba et al., 2014). The transport of hexose and glucose analogs is a crucial process in cellular metabolism. Small molecules originating from different sources have been observed to interfere with this transport mechanism. Understanding the inhibitory effects of these compounds on hexose transport and glucose analogs is essential for comprehending their impact on cellular glucose uptake pathways.
In this study, we conducted an evaluation of the antiparasitic properties of seven lead compounds against the erythrocyte parasite stage of Plasmodium falciparum. Our results showed that several compounds showed significant effectiveness in controlling these parasites. The catalytic activity of the hexokinase enzyme in glycolysis has attracted great interest due to its surprising inability to generate a functional recombinant protein in in vitro classification experiments. Despite extensive research efforts, a comprehensive understanding of this phenomenon remains unclear (Olafsson et al., 1992).