R521C and R521H mutations in FUS result in weak binding with Karyopherinβ2 leading to Amyotrophic lateral sclerosis: a molecular docking and dynamics study

<p>Fused in sarcoma (FUS) gene encodes the RNA binding protein FUS. This gene is mapped to chromosome 16p11.2. The FUS protein binds with karyopherineβ2 (Kapβ2) through its proline/tyrosine nuclear localization signal (PY-NLS) that helps in the localization of FUS protein within the nucleus. Arginine residue in 521 position (R521) of PY-NLS plays a vital role in the binding of FUS protein with Kapβ2. Mutations in this position (R521C and R521H) are the most predominant mutations associated with amyotrophic lateral sclerosis (ALS). However, the mechanism by which these mutations lead to ALS is poorly understood. We examined the binding behaviour of the mutants FUS (R521C) and FUS (R521H) with Kapβ2 through protein–protein docking and molecular dynamics simulation. The binding patterns of mutants were compared with the binding behaviour of wild FUS–Kapβ2. Our results suggest that these mutants have relatively weak binding affinity with Kapβ2 when compared with wild FUS–Kapβ2 as indicated by the lesser number of interactions found between the mutant FUS and Kapβ2. Hence, these mutations weakens the binding and this results in the cytoplasmic mislocalization of mutant FUS; and thereby it increases the severity of ALS.</p

Computational study of the piperidine and FtsZ interaction in <i>Salmonella</i> Typhi: implications for disrupting cell division machinery

FtsZ, a bacterial cell division protein, is essential for assembling the contractile Z-ring crucial in bacterial cytokinesis. Consequently, inhibiting FtsZ could impede proto-filaments, disrupting FtsZ and other associated proteins vital for cell division machinery. Conduct an in-silico drug interaction study to identify novel drug candidates that inhibit the FtsZ protein, aiming to prevent Multi-Drug Resistant (MDR) Salmonella Typhi. Data mining was performed based on piperidine compounds, which were subsequently screened for safe pharmacokinetic profiles. Compounds that met favorable drug-likeness criteria underwent virtual screening against the FtsZ drug target. Two compounds were chosen for molecular docking and molecular dynamic simulation to verify the binding affinity and stability between the target protein and the potential compounds. The 400 isoforms of piperidine analogues were curated, among them potent compound ZINC000000005416 found to possess high binding affinity (-8.49 kcal/mol) and low dissociation constant (0.597 µM). The highest binding affinity shown by ZINC000000005416 was validated by hydrogen bonds, hydrophobic interaction, and salt bridges with the functional domain of the cell division regulatory protein. Docking profiles, when correlated with molecular dynamic simulation (MDS) depicted stable trajectories and compatible conformational changes in the FtsZ-ZINC000000005416 complex. The stable simulated trajectories were validated through free-energy calculations using the Molecular Mechanics-Poisson Boltzmann Surface Area (MM/PBSA) module. Low energy conformations, although the simulation trajectory confirmed the stable ZINC000000005416-FtsZ interaction, which encouraged experimental validations. This study encourages further exploration of the compound ZINC000000005416 as a drug candidate inhibiting FtsZ protein against MDR Salmonella Typhi. Communicated by Ramaswamy H. Sarma</p

H-bond interaction and bond length obtained for Tigecycline and Ceftazidime with <i>bla</i>OXA-1.

<p>H-bond interaction and bond length obtained for Tigecycline and Ceftazidime with <i>bla</i>OXA-1.</p

Final model structure for <i>bla</i>OXA-1 from <i>K. pneumoniae</i>.

<p>The α-helix is represented in red color, β-sheet by yellow arrows and loops by green lines. Acitve site is obtained by Q-siteFinder and shown in magenta color surface model.</p

Molecular docking result of tigecycline.

<p>(A) Binding pose of tigecycline in the binding site of <i>bla</i>OXA-1 (B) A close-up view of the binding pose of tigecycline; Protein structure is shown in surface model and the ligand is shown in stick model. (C) H-bond network with protein residues are shown.</p

Comparison of binding energy and percentage of resistance.

<p>Comparison of binding energy and percentage of resistance.</p

Backbone RMSDs are shown for tigecycline-<i>bla</i>OXA1 complex at 300K.

<p>Backbone RMSDs are shown for tigecycline-<i>bla</i>OXA1 complex at 300K.</p

Antibiotic resistance pattern by Kirby Bauer method Vs E-test (MIC) (n = 59).

<p>Ampicillin (AMP), Cefotaxime (CTX), Ceftazidime (CZD), Piperacillin/Tazobactam (TZP), Cefepime (FEP), Cefpirome (CPO), Levofloxacin (LEVO), Amikacin (AK), Cefoxitin (FOX), Ertapenem (ETP), Meropenem (MEM), Imipenem (IMP), and Tigecycline (TIG).</p

Gel picture of <i>bla</i>OXA-1.

<p>Lane 1: 3MB09 (Positive <i>bla</i>OXA-1 (427 bp), Lane 2: 3ADB28 (Negative), Lane 3: Negative control (sterile water), Lane 4 : Ladder 100 bp.</p

Molecular docking result of ceftazidime.

<p>(A) Binding pose of ceftazidime in the binding site of <i>bla</i>OXA-1 (B) A close-up view of the binding pose of ceftazidime; Protein structure is shown in surface model and the ligand is shown in stick model. (C) H-bond network with protein residues are shown.</p