Dataset on double mutation in PGIP of Glycine max improves defense to PG of Sclerotinia sclerotiorum.

The cell wall of the Glycine max altered by the polygalacturonases (PGs) secreted by the fungus Sclerotinia sclerotiorum, causes disease and quality losses. In soybeans, a resistance protein called polygalacturonases-inhibiting proteins (PGIPs) binds to the PG to block fungal infection. The active site residues of PGIP3, VAL170 and GLN242 are mutated naturally by various amino acids in different types of PGIPs. Therefore, the mutation of VAL170 to GLY is ineffective but the GLN242 amino acid mutation by LYS significantly alters the structure and is crucial for interacting with the PG protein. Docking and Molecular Dynamics simulation provide a comprehensive evaluation of the interactions between gmPGIP and ssPG. By elucidating the structural basis of the interaction between gmPGIP and ssPG, this investigation lays a foundation for the development of targeted strategies in-order to enhance soybean resistance against Sclerotinia sclerotiorum. By leveraging this knowledge, researchers can potentially engineer soybean varieties with improved resistance to the fungus, thereby reducing disease incidence and improving crop yields.

Targeting Pyrimidine Pathway of Plasmodium knowlesi: New Strategies Towards Identification of Novel Antimalarial Chemotherapeutic Agents.

AIM AND OBJECTIVE: Plasmodium knowlesi has been recently recognized as a human malarial parasite, particularly in the region of south-east Asia. Unlike human host, P. knowlesi cannot salvage pyrimidine bases and relies solely on nucleotides synthesized from de novo pyrimidine pathway. The enzymes involved in this are also unique in terms of their structure and function to its human counterpart. Thus, targeting Dihydroorotase, an enzyme involved in the pyrimidine biosynthesis, provides a promising route for novel drug development. MATERIALS AND METHODS: The 3D structure of P. knowlesi Dihydroorotase was predicted, refined and validated. Multiple docking was performed and the resultant complex was used for 3D structurebased pharmacophore modelling. A combinatorial library of 2,664,779 molecules was generated and used for structure based virtual screening. The stability of resultant compounds was checked using simulation studies. RESULTS: The modelled 3D structure of P. knowlesi Dihydroorotase enzyme is relaxed by running an MD simulation of 20 ns, and structure is validated by using Ramachandran plot and G-factor analysis. A five point based pharmacophore model was created and used as a query for screening in house database. The stability of two negatively charged compounds was studied, and ZINC22066495-DHOase complex was more stable throughout the simulation. CONCLUSION: The present study shows that ZINC22066495 compound has a high potential for disrupting P. knowlesi DHOase enzyme and may be used as a potential lead molecule for effective pyrimidine biosynthesis inhibition in P. knowlesi.

In silico drug re-purposing against African sleeping sickness using GlcNAc-PI de-N-acetylase as an experimental target.

Trypanosoma brucei is a protozoan that causes African sleeping sickness in humans. Many glycoconjugate compounds are present on the entire cell surface of Trypanosoma brucei to control the infectivity and survival of this pathogen. These gycoconjugates are anchored to the plasma membrane with the help of glycosyl phosphatidyl inositol (GPI) anchors. This type of anchor is much more common in protozoans than in other eukaryotes. The second step of glycosyl phosphatidyl inositol (GPI) anchor biosynthesis is catalyzed by an enzyme, which is GlcNAc-PI de-N-acetylase. GlcNAc-PI de-N-acetylase has a conserved GPI domain, which is responsible for the functionality of this enzyme. In this study, the three-dimensional structure of the target is modelled by I-TASSER and the ligand is modelled by PRODRG server. It is found that the predicted active site residues of the GPI domain are ultra-conserved for the Trypanosomatidae family. The predicted active site residues are His41, Pro42, Asp43, Asp44, Met47, Phe48, Ser74, Arg80, His103, Val144, Ser145, His147 and His150. Two hydrogen bond acceptors and four hydrogen bond donors are found in the modelled pharmacophore. All compounds of the Drugbank database and twenty three known inhibitors have been considered for structure based virtual screening. This work is focused on approved drugs because they are already tested for safety and effectiveness in humans. After the structure-based virtual screening, seventeen approved drugs and two inhibitors are found, which interact with the ligand on the basis of the designed pharmacophore. The docking has been performed for the resultant seventeen approved drugs and two known inhibitors. Two approved drugs have negative binding energy and their pKa values are similar to the selected known inhibitors. The result of this study suggests that the approved drugs Ethambutol (DB00330) and Metaraminol (DB00610) may prove useful in the treatment of African sleeping sickness.

Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias.

UNLABELLED: It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA). ABBREVIATIONS: CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.