Comparison of potential inhibitors and targeting fat mass and obesity-associated protein causing diabesity through docking and molecular dynamics strategies

Elucidation of the CadA Protein 3D Structure and Affinity for Metals

The mitigation of cadmium (Cd) pollution, a significant ecological threat, is of paramount importance. Pseudomonas aeruginosa harbors 2 Cd resistance genes, namely, cadR and cadA. Presently, our focus is on the identification and characterization of the cation-transporting P-type ATPase (cadA) in Pseudomonas aeruginosa BC15 through in silico methods. The CadA protein and its binding capacities remain poorly understood, with no available structural elucidation. The presence of the cadA gene in P aeruginosa was confirmed, showing a striking 99% sequence similarity with both P aeruginosa and P putida. Phylogenetic analysis unveiled the evolutionary relationship between CadA protein sequences from various Pseudomonas species. Physicochemical analysis demonstrated the stability of CadA, revealing a composition of 690 amino acids, a molecular weight of 73 352.85, and a predicted isoelectric point (PI) of 5.39. Swiss-Model homology modelling unveiled a 33.73% sequence homology with CopA (3J09), and the projected structure indicated that 89.3% of amino acid residues were situated favourably within the Ramachandran plot, signifying energetic stability. Notably, the study identified metal-binding sites in CadA, namely, H3, C30, C32, C35, H48, C89, and C106. Docking studies revealed a higher efficiency of Cd binding with CadA compared to other heavy metals. This underscores the crucial role of N-terminal cysteine residues in Cd removal. It is evident that CadA of P aeruginosa BC15 plays a crucial role in Cd tolerance, rendering it a potential microorganism for Cd toxicity bioremediation. The structural and functional elucidation of CadA, facilitated by this study, holds promise for advancing cost-effective strategies in the remediation of cadmium-contaminated environments.

An integrated investigation of structural and pathway alteration caused by PIK3CA and TP53 mutations identified in cfDNA of metastatic breast cancer

In peripheral blood, cell-free DNA (cfDNA) contains circulating tumor DNA (ctDNA), which indicates molecular abnormalities in metastatic breast tumor tissue. The sequencing of cfDNA of Metastatic Breast Cancer (MBC) patients allows assessment of therapy response and noninvasive treatment. In the proposed study, clinically significant alterations in PIK3CA and TP53 genes associated with MBC resulting in a missense substitution of His1047Arg and Arg282Trp from an next-generation sequencing-based multi-gene panel were reported in a cfDNA of a patient with MBC. To investigate the impact of the reported mutation, we used molecular docking, molecular dynamics simulation, network analysis, and pathway analysis. Molecular Docking analysis determined the distinct binding pattern revealing H1047R-ATP complex has a higher number of Hydrogen bonds (H-bonds) and binding affinity with a slight difference compared to the PIK3CA-ATP complex. Following, molecular dynamics simulation for 200 ns, of which H1047R-ATP complex resulted in the instability of PIK3CA. Similarly, for TP53 mutant R282W, the zinc-free state (apo) and zinc-bounded (holo) complexes were investigated for conformational change between apo and holo complexes, of which the holo complex mutant R282W was unstable. To validate the conformational change of PIK3CA and TP53, 80% mutation of H1047R in the kinase domain of p110α expressed ubiquitously in PIK3CA protein that alters PI3K pathway, while R282W mutation in DNA binding helix (H2) region of P53 protein inhibits the transcription factor in P53 pathway causing MBC. According to our findings, the extrinsic (hypoxia, oxidative stress, and acidosis); intrinsic factors (MYC amplification) in PIK3CA and TP53 mutations will provide potential insights for developing novel therapeutic methods for MBC therapy.

Deciphering the effect of mutations in MMAA protein causing methylmalonic acidemia-A computational approach

Methylmalonic acidemia (MMA) is a rare genetic disorder affecting multiple body systems. We aimed to investigate the pathogenic mutations in MMAA that are associated with isolated methylmalonic acidemia to identify the structural behavior of MMAA upon mutation. The algorithms such as PredictSNP, iStable, ConSurf, and Align GVGD were employed to analyze the consequence of the mutations. Molecular docking was carried out for the native MMAA, L89P, G274D, and R359G to interpret its interactions with the GDP substrate. The docked complexes were simulated for 200ns aiding GROMACS in apprehending the behavior of MMAA upon mutation and GDP binding. After simulation, cα disruptions were observed using the RMSF plot, which indicated that several regions of mutant MMAAs have highly fluctuated. The gyration and H-bond plots were used to understand the compactness and intermolecular interaction with the GDP molecule. The MDS analysis showed that the mutations L89P, G274D, and R359G are highly unstable even after GDP binding, with the least compactness, fewer H-bonds, and larger conformational cα motions. Our study provided structural and dynamic insights into MMAA protein, which further helps to characterize these mutants and provide potential treatment strategies for MMA patients.

Identification of potential inhibitors, conformational dynamics, and mechanistic insights into mutant Kirsten rat sarcoma virus (G13D) driven cancers

The mutations at the hotspot region of K-Ras result in the progression of cancer types. Our study aimed to explore the small molecule inhibitors against the G13D mutant K-Ras model with anti-cancerous activity from food and drug administration (FDA)-approved drug compounds. We implemented several computational strategies such as pharmacophore-based virtual screening, molecular docking, absorption, distribution, metabolism and excretion features, and molecular simulation to ensure the identified hit compounds have potential efficacy against G13D K-Ras. We found that the FDA-approved compounds, namely, azelastine, dihydrocodeine, paroxetine, and tramadol, are potential candidates to inhibit the action of G13D mutant K-Ras. All four compounds exhibited similar binding patterns of sotorasib, and a structural binding mechanism with significant hydrophobic contacts. The descriptor features from the QikProp of all four compounds are within allowable limits compared to sotorasib drug. Consequently, a molecular simulation result emphasized that the dihydrocodeine and tramadol exhibited less fluctuation, minimal basin, significant h-bonds, and potent inhibition against G13D K-Ras. As a result, the current research identifies prospective K-Ras inhibitors that could be further improved with biochemical analysis for precision medicine against K-Ras-driven cancers.

Mutations in G6PC2 gene with increased risk for development of type 2 diabetes: Understanding via computational approach

An increase in the fast blood glucose (FBG) levels has been linked to an increased risk of developing a chronic condition, type 2 diabetes (T2D). The mutation in the G6PC2 gene was identified to have a lead role in the modulation of FBG levels. The abnormal regulation of this enzyme influences glucose-stimulated insulin secretion (GSIS), which controls the insulin levels corresponding to the system's glucose level. This study focuses on the mutations at the G6PC2 gene, which cause the variation from normal expression levels and increase the risk of T2D. We examined the non-synonymous single nucleotide polymorphisms (nsSNPs) present in the G6PC2 and subjected them to pathogenicity, stability, residue conservation, and membrane simulation. The individual representation of surrounding amino acids in the mutant (I63T) model showed the loss of hydrophobic interactions compared to the native G6PC2. In addition, the trajectory results from the membrane simulation exhibited reduced stability, and the least compactness was identified for the I63T mutant model. Our study shed light on the structural and conformational changes at the transmembrane region due to the I63T mutation in G6PC2. Additionally, the Gibbs free energy landscape analysis against the two principal components showed structural differences and decreased the conformational stability of the I63T mutant model compared to the native. Like those presented in this study, dynamical simulations may indeed be crucial to comprehending the structural insights of G6PC2 mutations in cardiovascular-associated mortality and T2D.

Identification of fosaprepitant as a novel GSTP1 inhibitor through structure-based virtual screening, molecular dynamics simulation, and biological evaluation

The workflow of virtual screening for the discovery of GSTP1 inhibitors.

Computational investigation to identify potent inhibitors of the GTPase-Kirsten RAt sarcoma virus (K-Ras) mutants G12C and G12D

K-Ras mutations are frequent in various cancer types, and according to recent research, K-Ras possesses four-drug targeting sites. This increased our interest in finding potential small molecule inhibitors with anticancer activity to treat K-Ras-driven cancers. We utilized integrated bioinformatic strategies, such as XP docking, MM-GBSA, cell-line cytotoxicity prediction, ADMET, and molecular simulation, to discover potential inhibitors of G12C and G12D mutants compared to sotorasib, which is a recent FDA-approved inhibitor of G12C. We identified compounds, such as flupentixol, amlodipine, and fluvoxamine, for the G12C mutant and paroxetine, flupentixol, and zuclopenthixol for the G12D mutant with significant inhibitory functions. All five compounds bound to the H95 cryptic groove of mutant K-Ras with high efficiency and, like sotorasib, retained a novel binding mechanism with additional hydrophobic interactions at the molecular level. Furthermore, the simulation studies suggested that the binding of flupentixol and amlodipine to G12C stabilizes switch I and switch II. In contrast, paroxetine and flupentixol to G12D showed a similar trend compared to sotorasib complexes. Thus, despite the very dynamic functionality of K-Ras switches I and II, the binding of shortlisted compounds is highly stable. Therefore, the reported study provides potential drug candidates for K-Ras inhibition that can be further developed with in vitro and in vivo evidence for targeted therapy.