Group presentation 2 for project ddd.pptx

group presentation

1. In Silico and Biological Activity Studies of the Aminothiazole Series Against Histone Deacetylase Enzyme as Antifungal Treatment for Eumycetoma Muhammad Reza Al Faathiansyah MSc Drug Discovery and Development Group Presentation Part 2 11/07/2024

2. Introduction Eumycetoma, a neglected tropical disease, predominantly impacts individuals residing in tropical and subtropical areas, resulting in significant problems and incapacity if not adequately treated. Existing antifungal therapies are expensive, entail notable adverse reactions, and frequently prove unsuccessful, particularly in areas with low resources. Considering the pressing requirement for treatments that are safer, more efficient, and less expensive, it is essential to investigate new therapeutic targets, such as the HDAC enzyme. Aminothiazole compounds, renowned for their wide range of pharmacological activity, including their ability to suppress the growth of fungi, present a highly attractive opportunity for the development of HDAC inhibitors. The objective of this study is to examine the capacity of these substances to hinder HDAC activity in Madurella mycetomatis , therefore offering a new therapeutic alternative for eumycetoma.

3. Aims and Objective Aim: The aim of this project is to explore the potential of aminothiazole based compounds as inhibitor of histone deacetylase (HDAC) enzyme for the treatment of eumycetoma, particularly caused by Madurella mycetomatis through a combination of in silico and biological activity study. Objective: To develop and validate the homology protein model for the target protein using homology modelling tools To perform molecular docking studies of the aminothiazole derived compounds to identify the interaction and screen the potential inhibitor To evaluate the biological activity study which is the enzymatic activity of the HDAC by determining the inhibitory activity of the compounds against the enzyme

4. Result

5. Sequence Alignment Based on this sequence alignment with sequence similarity 67.12%: The query sequence has a similar amino acid compared with the template marked with “*”. Also it has conserved amino acids with substitution into other amino acids with similar properties (marked with “:“) Most amino acids in this box are conserved showing the amino acids which building the binding pocket of the target protein is similar as the template

6. Model Validation Green: target protein Blue: protein template RMSD: 0.053 A Docking validation of target protein using ligand crystal structure from template ( Vorinostat ) The protein model was superimposed with the template and showing RMSD <2 A indicating the structure is similar with the human crystal structure which act as template. This also supported by the docking validation of the modelled protein using the ligand from protein template as shown at the figure on the right side Metal chelation Zinc binding region

7. Protein Stereochemical and Geometry This Ramachandran plot indicates that the protein in question has a significant presence of alpha-helical and beta-sheet structures, with most residues falling within sterically allowed regions. The few outliers may warrant further investigation but do not necessarily indicate a problem with the overall protein structure. The geometry of the protein indicating a good protein structure as compared to the crystal structure from PDB. The MolProbity score represents the quality of the protein structure on a scale equivalent to X-ray resolution

8. In Silico Result Protein: modelled protein Protein: 4LXZ (human HDAC) Interacting amino acids of the modelled protein Amino acid which anchoring the Zinc ion

9. The in silico result of 21 aminothiazole based compounds and SAHA ( Vorinostat ) indicate that: SAHA shows consistent binding affinity across both proteins, validating the comparative analysis. While some compounds show variations in their binding affinities between the modeled and 4LXZ protein, overall, the trend and ranking are similar, suggesting the modeled protein is a good representation of the 4LXZ protein in terms of binding affinity prediction. Based on this we also know that the binding pocket especially the tunnel is mostly involved hydrophobic interaction showed by the compound that has low binding affinity are mostly having many aromatic ring such as in MYOS610, MYOS604, and MYOS600 The modeled protein appears to provide a reliable prediction of binding affinities compared to the actual human HDAC protein, with similar trends and top binders identified in both cases.

10. Enzymatic Activity Assay Result Found 7 compounds that have inhibitory activity against HDAC which are: MYOS592, MYOS429, MYOS597, MYOS598, MYOS440, MYOS606, and MYOS612 with MYOS429 has the higher %inhibition among them Based on the docking interaction data, all of 7 compounds have interaction with the zinc ion and only MYOS429 that showed high inhibition against the HDAC enzyme. This compound could become a potential HDAC inhibitor but further study is required such as in vitro and in vivo assay. As for other compounds, optimization of the chemical structure is required to increase the potency

11. MYOS429 interaction with amino acids in the target protein MYOS429 conformation inside the catalytic tunnel and interact with zinc ion with distance 2.01 Angstrom Interaction between MYOS429 compound and the target (modelled protein) The aminothiazole structure interact with the important amino acid in the binding pocket such as HIS285 which also anchoring the zinc ion

12. Interaction of the MYOS Compounds with Human Crystal Structure (PDB ID: 4LXZ) In comparison with this image, the MYOS429 did not have any interaction with the Zinc ion due to the functional group is far away from the Zinc ion. In terms of binding affinity, it has good binding affinity compared to the one with modelled protein due to it fits well into the catalytic tunnel Zinc atom

13. MYOS592 MYOS597 MYOS598 MYOS440 MYOS606 MYOS612

14. THANK YOU