Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase

The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined. Therefore, the detailed reaction mechanism at the molecular level is unclear. Here, we developed a computational protocol to analyze the free-energy profile for the glycine phosphorylation process catalyzed by PurD, which examines the free-energy change along a minimum energy path based on a perturbation method combined with the quantum mechanics and molecular mechanics hybrid model. Further analysis revealed that during the formation of glycyl-phosphate, the partial atomic charge distribution within the substrate molecules was not localized according to the formal charges, but was delocalized overall, which contributed significantly to the interaction with the charged amino acid residues in the ATP-grasp domain of PurD.

POSSIBILITY OF NEW LYMPHATIC PATHWAY CREATION THROUGH NEO-LYMPHANGIOGENESIS INDUCED BY SUBDERMAL DISSECTION

Surgical intervention and subsequent wound healing process are known to induce neo-lymphangiogenesis, but few studies have been reported to utilize this mechanism for lymphedema treatment. The aim of this study was to evaluate feasibility of subdermal dissection for neo-lymphangiogenesis induction (SDN) to treat lower extremity lymphedema (LEL). Medical records of secondary LEL patients who had undergone ICG lymphography and SDN procedure were reviewed. SDN was performed by dissecting fat tissues just below the dermis from the most proximal area showing dermal backflow through abdominal-toaxillary lymphatic pathways. Perioperative lymphedematous conditions were evaluated with lymphedema quality of life score (LeQOLiS) and LEL index. Seventeen female patients were included. SDN could be performed in 10 minutes on average without postoperative complication. Postoperative ICG lymphography showed new lymphatic pathways in 6 (35.3%) cases. Postoperative LeQOLiS ranged from 9 to 66, which was statistically lower than preoperative LeQOLiS (32.9 ± 19.2 vs. 36.6 ± 19.3, p = 0.048), whereas there was no statistically significant difference between pre- and post-operative LEL index (275.2 ± 23.3 vs. 270.5 ± 20.8, P = 0.073). Subdermal dissection, although its probability is not high, has a potential to induce neo-lymphangiogenesis. Further studies are required to improve and demonstrate efficacy of the procedure for new lymphatic pathway creation.

Theoretical insights into the molecular mechanism of I117V mutation in neuraminidase mediated reduction of oseltamivir drug susceptibility in A/H5N1 influenza virus

The substitution of Ile to Val at residue 117 (I117V) of neuraminidase (NA) reduces the susceptibility of the A/H5N1 influenza virus to oseltamivir (OTV). However, the molecular mechanism by which the I117V mutation affects the intermolecular interactions between NA and OTV has not been fully elucidated. In this study, we performed molecular dynamics (MD) simulations to analyze the characteristic conformational changes that contribute to the reduced binding affinity of NA to OTV after the I117V mutation. The results of MD simulations revealed that after the I117V mutation in NA, the changes in the secondary structure around the mutation site had a noticeable effect on the residue interactions in the OTV-binding site. In the case of the WT NA-OTV complex, the positively charged side chain of R118, located in the β-sheet region, frequently interacted with the negatively charged side chain of E119, which is an amino acid residue in the OTV-binding site. This can reduce the electrostatic repulsion of E119 toward D151, which is also a negatively charged residue in the OTV-binding site, so that both E119 and D151 simultaneously form hydrogen bonds with OTV more frequently, which greatly contributes to the binding affinity of NA to OTV. After the I117V mutation in NA, the side chain of R118 interacted with the side chain of E119 less frequently, likely because of the decreased tendency of R118 to form a β-sheet structure. As a result, the electrostatic repulsion of E119 toward D151 is greater than that of the WT case, making it difficult for both E119 and D151 to simultaneously form hydrogen bonds with OTV, which in turn reduces the binding affinity of NA to OTV. Hence, after the I117V mutation in NA, influenza viruses are less susceptible to OTV because of conformational changes in residues of R118, E119, and D151 around the mutation site and in the binding site.

Predictive value of QRS duration normalized to left ventricular volume for responding to cardiac resynchronization therapy in patients with mid-QRS duration enrolled in the multicenter registry

Background

For cardiac resynchronization therapy (CRT), patients with chronic heart failure (HF) and wide (>150msec) QRS duration (QRSd) received class I/A indication. However, its beneficial effect seemed to be limited for those with mid- (120–150msec) QRSd. Recent studies demonstrated that QRSd normalized to left ventricular end-diastolic volume (QRSd/ LVEDV) improved prediction of clinical outcome in patients with CRT. Therefore, we sought to investigate predictive value of QRSd/LVEDV for responding to CRT in patients with mid-QRSd.

Methods

This was retrospective multi-center observational cohort study. A total 506 consecutive patients who underwent CRT implantation in Tohoku University Hospital and National Cerebral and Cardiovascular Center were evaluated. Exclusion criteria were QRSd less than 120ms, upgrade procedures from other implanted non-CRT devices and bradycardia requiring pacing. We evaluated clinical variables, data of electrocardiogram and transthoracic echocardiography at baseline and 6 months after CRT implantation. Primary endpoint was a HF hospitalization after CRT implantation. Distribution of free from HF hospitalization during follow-up was calculated using Kaplan-Meier curves, and the effects of covariate on the time to endpoint were investigated using a Cox proportional hazards model.

Results

After 199 patients were excluded based on exclusion criterion, remaining 307 patients were included for the analysis. Mean age was 62±14 [SD] years, and 238 (77%) were male. Mean LVEF and LVEDV were 25±9% and 234±82ml, respectively, and 24% of patients had ischemic etiology of HF. During the median 948 days of follow-up, CRT patients with mid QRSd (n=126; 136±10msec), as compared with those with wide QRSd (n=181; 174±17msec), tended to have higher incidence of HF hospitalization (Wilcoxon p=0.03). Multivariate analysis showed that QRSd and QRSd/LVEDV were significant predictors for HF hospitalization in CRT patients with mid QRSd, and cut-off values (137msec of QRSd and 0.65 of QRSd/LVEDV), which was calculated by receiver operative curve analysis, was used for risk stratification. QRSd<137msec was significant negative predictors for HF hospitalization (p=0.005), and Mid-QRSd patients with QRSd≥137msec demonstrated equivalent clinical outcome with those with wide QRSd. Moreover, patients with QRSd/LVEDV≥0.65 tended to have lower incidence of HF hospitalization as compared with those without it among patients with QRSd<137msec (n=64, Figure).

Conclusion

The present study demonstrates that QRSd normalized to left ventricular end-diastolic volume (QRSd/ LVEDV) could be clinical value in predicting outcome in CRT patients with mid-QRSd. These findings indicate normalized QRSd reflects myocardial conduction properties and contribute to risk stratification.

Funding Acknowledgement

Type of funding sources: None.

Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus

Background

Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated.

Methods

In this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site.

Results

dRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions.

Nivolumab with carboplatin, paclitaxel, and bevacizumab for first-line treatment of advanced nonsquamous non-small-cell lung cancer

BACKGROUND

This international, randomized, double-blind phase III study (ONO-4538-52/TASUKI-52) evaluated nivolumab with bevacizumab and cytotoxic chemotherapy as first-line treatment for nonsquamous non-small-cell lung cancer (NSCLC).

PATIENTS AND METHODS

Between June 2017 and July 2019, this study enrolled treatment-naïve patients with stage IIIB/IV or recurrent nonsquamous NSCLC without sensitizing EGFR, ALK, or ROS1 alterations. They were randomly assigned in a 1 : 1 ratio to receive nivolumab or placebo in combination with carboplatin, paclitaxel, and bevacizumab every 3 weeks for up to six cycles, followed by nivolumab/placebo with bevacizumab until progressive disease or unacceptable toxicity. The primary endpoint was progression-free survival (PFS) assessed by an independent radiology review committee (IRRC).

RESULTS

Overall, 550 patients from Japan, Korea, and Taiwan were randomized; of these patients, 273 and 275 received the nivolumab and placebo combinations, respectively. In the present preplanned interim analysis with a median follow up of 13.7 months, the IRRC-assessed median PFS was significantly longer in the nivolumab arm than in the placebo arm (12.1 versus 8.1 months; hazard ratio 0.56; 96.4% confidence interval 0.43-0.71; P < 0.0001). The PFS benefit was observed across all patients with any programmed death-ligand 1 (PD-L1) expression levels including PD-L1-negative patients. The IRRC-assessed objective response rates were 61.5% and 50.5% in the nivolumab and placebo arms, respectively. The incidence of treatment-related adverse events of grade 3 or 4 was comparable between the two arms; treatment-related adverse events leading to death were observed in five and four patients in the nivolumab and placebo arms, respectively.

CONCLUSION

The TASUKI-52 regimen should be considered a viable new treatment strategy for treatment-naïve patients with advanced nonsquamous NSCLC.

Path Ensembles for Pin1-Catalyzed Cis-Trans Isomerization of a Substrate Calculated by Weighted Ensemble Simulations

Pin1 enzyme protein recognizes specifically phosphorylated serine/threonine (pSer/pThr) and catalyzes the slow interconversion of the peptidyl-prolyl bond between cis and trans forms. Structural dynamics between the cis and trans forms are essential to reveal the underlying molecular mechanism of the catalysis. In this study, we apply the weighted ensemble (WE) simulation method to obtain comprehensive path ensembles for the Pin1-catalyzed isomerization process. Associated rate constants for both cis-to-trans and trans-to-cis isomerization are calculated to be submicroseconds time scales, which are in good agreement with the calculated free energy landscape where the cis form is slightly less favorable. The committor-like analysis indicates the shift of the transition state toward trans form (at the isomerization angle ω ∼ 110°) compared to the intrinsic position for the isolated substrate (ω ∼ 90°). The calculated structural ensemble clarifies a role of both the dual-histidine motif, His59/His157, and the basic residues, Lys63/Arg68/Arg69, to anchor both sides of the peptidyl-prolyl bond, the aromatic ring in Pro, and the phosphate in pSer, respectively. The rotation of the torsion angle is found to be facilitated by relaying the hydrogen-bond partner of the main-chain oxygen in pSer from Cys113 in the cis form to Arg68 in the trans form, through Ser154 at the transition state, which is really the cause of the shift in the transition state. The role of Ser154 as a driving force of the isomerization is confirmed by additional WE and free energy calculations for S154A mutant where the isomerization takes place slightly slower and the free energy barrier increases through the mutation. The present study shows the usefulness of the WE simulation for substantial path samplings between the reactant and product states, unraveling the molecular mechanism of the enzyme catalysis.