Malaria has continued to be a health and economic problem in Africa and the world at large. Many anti-malarial drugs have been rendered ineffective due to the emergence of resistant strains of Plamodium falciparum. A key malaria parasite enzyme in glycolytic pathway, P. falciparum lactate dehydrogenase (P fLDH) is specially targeted for anti-malarial drugs development. Thus, the aim of this investigation was to determine the in silico inhibition effects of antimalarial compounds from Hoslundia opposita Vahl. namely hoslundin, hoslundal and hoslunddiol on P fLDH enzyme. The compounds were docked to the three-dimensional structure of P fLDH as enzyme using AutoDock Vina in PyRx virtual screening software. Binding affinity and position of the inhibitors were evaluated using PyMol software. The P fLDH enzyme showed two binding sites: the cofactors binding site (Site A) and secondary binding site (Site B). In the absence of the cofactor all ligands showed higher affinity than NADH, and were bound to the cofactors binding site (Site A). When docked in the presence of the cofactor, site B was the preferred binding site. Binding to cofactor site with higher binding energy than NADH suggests that these ligands could act as preferential competitive inhibitors of P fLDH. However, the binding to site B also suggests that they may be non-competitive allosteric inhibitors. Amino acid residues Gly99, Asn140, Phe100 and Thr97 were indicated to form hydrogen bonds with Hoslundin. Hoslunddiol showed hydrogen bonding with Thr97 and Met30, while Hoslundal formed hydrogen bond with Thr101 and Asn140.
Malaria remains to be a health and economic problem in the tropical Africa and the world at large. In Africa malaria is responsible for over 430,000 children deaths every year [
Over the recent past years, chloroquine was used to treat malaria [
Enzymes of the glycolytic pathways are thought to be an important drug target due to parasitic dependence on glycolysis for energy production [
In a search for potent anti-malarial compounds, Ngadjui and co-workers isolated anti-malarial compounds namely hoslundin, hoslundal and hoslunddiol from Hoslundia opposita (
The three dimensional protein crystal structures of PfLDH (PDB ID: IT2C) with resolution of 2.01 Å, (
were performed following the procedure reported in the literature by [
The PfLDH enzyme possesses two important binding pockets, the cofactors binding pocket (Site A) and Site B (
All ligands were successfully docked to binding sites of PfLDH enzyme. All ligands showed better docking score with stable conformation than the crystalized NADH cofactor when docked in the absence of the cofactor (in the cofactor binding site). In the absence of cofactor, all ligands bound to site A which is the binding site of the cofactor. When ligands were docked in the presence of cofactor, site B was the preferred binding site for all ligands and possessed lower docking scores (
In the present study, the anti-malarial compound hoslunddiol from Hoslundia opposita had a good docking score (−8.0 kcal/mol) higher than all the other ligands to PfLDH enzyme. The best docking score was obtained in the absence of the cofactor (
Docked ligands showed higher binding affinity than NADH in absence of the cofactor, implying a possible competitive inhibition. However, on closer examination, the interaction of NADH and PfLDH indicated many more hydrogen bonds than the ligands (
Compounds | Best binding energy (kcal/mol) | |
---|---|---|
Absence of cofactor (NADH) | Presence of cofactor (NADH) | |
Hoslundal | −7.3 | −5.9 |
Hoslundin | −7.8 | −6.1 |
Hoslunddiol | −8.0 | −6.4 |
NADH | −6.8 |
Compounds | Docking run (kcal/mol) | |||
---|---|---|---|---|
1 | 2 | 3 | Mean ± SE | |
Hoslunddiol | −8.0 | −8.1 | −8.1 | −8.06 ± 0.03 |
Hoslundin | −7.8 | −7.8 | −7.8 | −7.8 ± 0.0 |
Hoslundal | −7.3 | −7.0 | −7.0 | −7.1 ± 0.1 |
PfLDH enzyme active site [
Plasmodium falciparum is an important malaria parasite in Africa and other parts of the world. The glycolytic PfLDH enzyme is thought to be one of the important anti-malarial drug targets due to the parasite dependence on glycolysis for energy production. The present study investigated the in silico inhibition effects of the three Hoslundia opposita compounds (hoslunddiol, hoslundin and hoslundal) to PfLDH enzyme. Results indicated that hoslunddiol (−8.0 kcal/mol) and hoslundin (−7.8 kcal/mol) had better interaction with the target. Hoslundal showed less binding energy (−7.3 kcal/mol) and had few interactions. The former two compounds showed four hydrogen bonds while the latter showed only two hydrogen bonds. Since hoslundal was reported to be the most active anti-malarial compound against the multi-drug resistant K1 strain yet weakly active against the chloroquine sensitive strain NF54 in vitro, the present findings further affirm that hoslundal possesses antimalarial activities with probable different modes of action. Within the limitations of the docking procedure, these findings suggest that the studied compounds could act as competitive inhibitors as they had higher binding energy than the cofactor. The pharmacokinetics and in vivo studies of these promising anti-malarial compounds are recommended. Furthermore, studies on the interaction and mode of action with other Plasmodium falciparum enzymes
H-bond forming residues | Bond length (Å) | |
---|---|---|
Hoslundal | Thr101 | 3.08 |
Asn140 | 3.26 | |
Hoslundin | Thr97 | 2.35 |
Phe100 | 3.02 | |
Asn140 | 3.05 | |
Gly99 | 3.06 | |
Hoslunddiol | Met30 | 2.38 |
Thr97 | 3.22 | |
Thr97 | 3.54 | |
Thr97 | 3.3 | |
NADH | Thr101 | 3.29 |
Gly164 | 2.99 | |
(2) Asn140 | 3.03 and 3.18 | |
(2) His195 | 2.81 and 3.38 | |
Ile31 | 3.12 | |
Ala236 | 2.8 | |
Val233 | 2.27 | |
Asn234 | 2.81 |
and any other life cycle target points are recommended for the studied and other anti-plasmodial compounds from H. opposita.
DMS express his sincerely thanks to the NAPRECA (T) for sponsorship and facilitation on In Silico studies during the 16th NAPRECA Pre-Symposium workshop. JJEM is grateful to the International Foundation for Sciences (IFS) for financial support.
Daniel M. Shadrack,Stephen S. Nyandoro,Joan J. E. Munissi,Egid B. Mubofu, (2016) In Silico Evaluation of Anti-Malarial Agents from Hoslundia opposita as Inhibitors of Plasmodium falciparum Lactate Dehydrogenase (PfLDH) Enzyme. Computational Molecular Bioscience,06,23-32. doi: 10.4236/cmb.2016.62002
Predicated binding active site in the PfLDH enzyme by 3D ligand site prediction server.
Selected letter amino acid code sequence of PfLDH in docking server.