Abstract:Xanthine oxidoreductase (XOR) is an enzyme found in various organisms. It converts hypoxanthine to xanthine and urate, which are crucial steps in purine elimination in humans. Elevated uric acid levels can lead to conditions like gout and hyperuricemia. Therefore, there is significant interest in developing drugs that target XOR for treating these conditions and other diseases. Oxipurinol, an analogue of xanthine, is a well-known inhibitor of XOR. Crystallographic studies have revealed that oxipurinol directly… Show more
“…1 B and C. The Amber FF14SB force field 40 , 41 were used for proteins, and the TIP3P water model 42 , 43 was added for these systems. The parameterization protocol applied for the flavin adenine dinucleotide (FAD), molybdenum cofactor (MOA) and Fe 2 S 2 cluster (FES) have been described previously 44 , 45 . Figure 1 ( A ) 3D structure of one subunit of XO, the close-up represents the XO’s active region.…”
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynamics simulations for the Apo, LWM, and ALPM systems. The results reveal a stronger binding affinity of the LWM peptide to XO, potentially due to increased hydrogen bond formation. Notable changes were observed in the XO tunnel upon inhibitor binding, particularly with LWM, which showed a thinner, longer, and more twisted configuration compared to ALPM. The study highlights the importance of residue F914 in the allosteric pathway. Methodologically, we utilized the perturbed response scan (PRS) based on Python, enhancing tools for MD analysis. These findings deepen our understanding of food-derived anti-XO inhibitors and could inform the development of food-based therapeutics for reducing uric acid levels with minimal side effects.
“…1 B and C. The Amber FF14SB force field 40 , 41 were used for proteins, and the TIP3P water model 42 , 43 was added for these systems. The parameterization protocol applied for the flavin adenine dinucleotide (FAD), molybdenum cofactor (MOA) and Fe 2 S 2 cluster (FES) have been described previously 44 , 45 . Figure 1 ( A ) 3D structure of one subunit of XO, the close-up represents the XO’s active region.…”
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynamics simulations for the Apo, LWM, and ALPM systems. The results reveal a stronger binding affinity of the LWM peptide to XO, potentially due to increased hydrogen bond formation. Notable changes were observed in the XO tunnel upon inhibitor binding, particularly with LWM, which showed a thinner, longer, and more twisted configuration compared to ALPM. The study highlights the importance of residue F914 in the allosteric pathway. Methodologically, we utilized the perturbed response scan (PRS) based on Python, enhancing tools for MD analysis. These findings deepen our understanding of food-derived anti-XO inhibitors and could inform the development of food-based therapeutics for reducing uric acid levels with minimal side effects.
“…Calculating the average energies of nonbonded intermolecular interactions (Coulomb + van der Waals) with respect to specific reference residue(s) can provide insight into the role of individual residues. EDA has been proven effective in exploring MD simulations and QM/MM calculations for various protein systems. − EDA was calculated using the AMBER-EDA code on the precatalytic stage of the polymerization reaction by the WT and Y432S systems. The analysis was run on 25,000 snapshots of the last 500 ns of the MD simulations.…”
Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S using classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our findings suggest that Y432S induces structural alterations in domains responsible for nucleotide addition and ternary complex stabilization while retaining structural features consistent with possible catalysis in the active site. Calculations of the minimum energy path associated with the reaction mechanism of the wild type (WT) and Y432S Pol κ indicate that, while both enzymes are catalytically competent (in terms of energetics and the active site's geometries), the cancer mutation results in an endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on nonbonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP 3− over dCTP 4− .
“…In addition to the computational efficiency of MM/GBSA, several studies have shown that this method results in comparable or even more accurate data in ranking ligand affinities compared to the molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA). − The offset and surface tension default values were used to correct the nonpolar contribution to the solvation free energy, and the salt concentration in the GB equation was set to 150 mM. Previous studies have shown that the MM/GB(PB)SA can satisfactorily compare the relative ligand-binding affinities, particularly when dealing with similar ligands. − Since the only difference between the Matched and MM5 is a C to G and G to C mutations in the fifth position of the ligand (t-DNA and nt-DNA, respectively) from the PAM, the entropic effect is not expected to be highly determinant.…”
The clustered regularly interspaced short palindromic
repeats (CRISPR)
technology is an RNA-guided targeted genome-editing tool using Cas
family proteins. Two magnesium-dependent nuclease domains of the
Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the
target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH
domain is believed to determine the DNA cleavage activity of both
endonuclease domains and is sensitive to complementary RNA-DNA base
pairing. However, the underlying molecular mechanisms of CRISPR-Cas9,
by which it rebukes or accepts mismatches, are poorly understood.
Thus, investigation of the structure and dynamics of the catalytic
state of Cas9 with either matched or mismatched t-DNA can provide
insights into improving its specificity by reducing off-target cleavages.
Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical
molecular dynamics and coupled quantum mechanics/molecular mechanics
simulations to study two possible mechanisms of t-DNA cleavage reaction
catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA
structure called MM5 (C to G at the fifth position from the protospacer
adjacent motif region), the impact of single-guide RNA (sgRNA) and
t-DNA complementarity on the catalysis process was investigated. Based
on these simulations, our calculated binding affinities, minimum energy
paths, and analysis of catalytically important residues provide atomic-level
details of the differences between matched and mismatched cleavage
reactions. In addition, several residues exhibit significant differences
in their catalytic roles for the two studied systems, including K253,
K263, R820, K896, and K913.
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