Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation

Determining the unbinding pathways of potential small molecule compounds from their target proteins is of great significance for designing efficacious treatment solutions. One of these potential compounds is the approved HIV-1 protease inhibitor, Indinavir, which has a weak effect on the HTLV-1 protease. In this work, by employing the SuMD method, we reconstructed the unbinding pathways of Indinavir from HIV and HTLV-1 proteases to compare and understand the mechanism of the unbinding and to discover the reasons for the lack of inhibitory activity of Indinavir against the HTLV-1 protease. We achieved multiple unbinding events from both HIV and HTLV-1 proteases in which the RMSD values of Indinavir reached over 40 Å. Also, we found that the mobility and fluctuations of the flap region are higher in the HTLV-1 protease, making the drug less stable. We realized that critically positioned aromatic residues such as Trp98/Trp98′ and Phe67/Phe67′ in the HTLV-1 protease could make strong π-Stacking interactions with Indinavir in the unbinding pathway, which are unfavorable for the stability of Indinavir in the active site. The details found in this study can make a reasonable explanation for the lack of inhibitory activity of this drug against HTLV-1 protease. We believe the details discovered in this work can help design more effective and selective inhibitors for the HTLV-1 protease.

Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by Supervised Molecular Dynamics simulation

Determining the unbinding pathways of potential small molecule compounds from their target proteins is of great significance for designing efficacious treatment solutions. One of these potential compounds is the approved HIV-1 protease inhibitor, indinavir, which has a weak effect on the HTLV-1 protease. In this work, by employing SuMD method, we reconstructed the unbinding pathways of indinavir from HIV and HTLV-1 proteases in order to compare and to understand the mechanism of the unbinding, and also to discover the reasons for the lack of inhibitory activity of indinavir against the HTLV-1 protease. We achieved multiple unbinding events from both HIV and HTLV-1 proteases in which the RMSD values of indinavir reached over 4 nm. Also, we found that the mobility and the fluctuations of the flap region is higher in the HTLV-1 protease which makes the drug less stable. We realized that critically positioned aromatic residues such as Trp98/Trp98' and Phe67/Phe67' in the HTLV-1 protease can make strong pi-Stacking interactions with indinavir in the unbinding pathway which are unfavorable for the stability of indinavir in the active site. The details found in this study can make a good explanation for the lack of inhibitory activity of this drug against HTLV-1 protease. We believe the details discovered in this work can be a great assist for designing more effective and more selective inhibitors for the HTLV-1 protease.

BACE1 Inhibitor, Neuroprotective, and Neuritogenic Activities of Melatonin Derivatives

Alzheimer’s disease (AD) is a common chronic neurodegenerative disorders. Melatonin (MLT) has been reported to be neuroprotective agent, and its modified structures exhibit potent antioxidant and anti-inflammation activities. Therefore, the activity of MLT and its derivatives against AD was investigated. Herein, the targeted enzymes, such as β-secretase (BACE1) and acetylcholinesterase (AChE), as well as the neuroprotective and neuritogenic effects on P19-derived neurons were evaluated. All the derivatives (1–5), including MLT, displayed potent inhibitory activity for BACE1, with inhibition values of more than 75% at 5 µM. A molecular docking study predicted that MLT, 5-MT, and 5 bound with BACE1 at catalytic amino acids Asp32 and the flap region, whereas 1–4 interacted with allosteric residue Thr232 and the flap region. The additional π-π interactions between 2, 3, and 5 with Tyr71 promoted ligand-enzyme binding. In addition, MLT, 1, 3, and 5 significantly protected neuron cells from oxidative stress by increasing the cell viability to 97.95, 74.29, 70.80, and 69.50% at 1 nM, respectively. Moreover, these derivatives significantly induced neurite outgrowth by increasing the neurite length and number. The derivatives 1, 3, and 5 should be thoroughly studied as potential AD treatment and neuroprotective agents.

Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants

ABSTRACTWe generated two novel nonpeptidic HIV-1 protease inhibitors (PIs), GRL-001-15 and GRL-003-15, which contain unique crown-like tetrahydropyranofuran (Crn-THF) and P2′-cyclopropyl-aminobenzothiazole (Cp-Abt) moieties as P2 and P2′ ligands, respectively. GRL-001-15 and GRL-003-15 havemeta-monofluorophenyl andpara-monofluorophenyl at the P1 site, respectively, exert highly potent activity against wild-type HIV-1 with 50% effective concentrations (EC50s) of 57 and 50 pM, respectively, and have favorable cytotoxicity profiles with 50% cytotoxic concentrations (CC50s) of 38 and 11 μM, respectively. The activity of GRL-001-15 against multi-PI-resistant HIV-1 variants was generally greater than that of GRL-003-15. The EC50of GRL-001-15 against an HIV-1 variant that was highly resistant to multiple PIs, including darunavir (DRV) (HIV-1DRVRP30), was 0.17 nM, and that of GRL-003-15 was 3.3 nM, while DRV was much less active, with an EC50of 216 nM. The emergence of HIV-1 variants resistant to GRL-001-15 and GRL-003-15 was significantly delayed compared to that of variants resistant to selected PIs, including DRV. Structural analyses of wild-type protease (PRWT) complexed with the novel PIs revealed that GRL-001-15’smeta-fluorine atom forms halogen bond interactions (2.9 and 3.0 Å) with Gly49 and Ile50, respectively, of the protease flap region and with Pro81′ (2.7 and 3.2 Å), which is located close to the protease active site, and that two fluorine atoms of GRL-142-13 form multiple halogen bond interactions with Gly49, Ile50, Pro81′, Ile82′, and Arg8′. In contrast, GRL-003-15 forms halogen bond interactions with Pro81′ alone, suggesting that the reduced antiviral activity of GRL-003-15 is due to the loss of the interactions with the flap region.

Structural Adaptation of Darunavir Analogs Against Primary Resistance Mutations in HIV-1 Protease

HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82 and I84 that line the S1/S1’ pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogs to primary S1’ mutations. The analogs had modifications at the hydrophobic P1’ moiety to better occupy the unexploited space in the S1’ pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analog with the largest P1’ moiety, indicating interdependency between the S1’ subsite and the flap region. Collective analysis of protease-inhibitor van der Waals (vdW) interactions in the crystal structures using principle component analysis indicated I84V mutation underlying the largest variation in the vdW contacts. Interestingly, the principle components were able to distinguish inhibitor identity and relative potency solely based on vdW interactions of active site residues in the crystal structures. Our results reveal the interplay between inhibitor P1’ moiety and primary S1’ mutations, as well as suggesting a novel method for distinguishing the interdependence of resistance through principle component analyses.

Drag Characterization Study of Variable Camber Continuous Trailing Edge Flap

A Reynolds-averaged Navier–Stokes (RANS) computational study was conducted to investigate the effect of various variable camber continuous trailing edge flap (VCCTEF) configurations on the lift and drag of a NASA generic transport model (GTM) wing section. Out of the five two-dimensional (2D) VCCTEF configurations considered with varying camber in the three-segment flap region, with a total deflection of 6 deg, the best stall performance was exhibited by the circular and parabolic arc camber flaps. Both circular and parabolic arc flaps give similar lift performance, with the circular arc yielding a higher lift coefficient and parabolic arc resulting in the lowest drag and hence the best L/D performance at design Cl. Analysis of results based on linear theory shows excellent agreement between computed and theoretical incremental lift.

Unsteady two-dimensional jet with flexible flaps at the channel exit

The present work studies the effect of passive exit flexibility on a two-dimensional starting jet. The exit flexibility is introduced by attaching two flexible (deformable) flaps at the jet exit of a high aspect ratio rectangular duct with the flaps initially being parallel to the channel walls. A controlled piston motion is used to generate the starting jet, which is composed of a rapid acceleration to a constant velocity ($U_{p}$) that is maintained for a given duration of time, after which it is brought to rest impulsively. The parameters which are varied include the flexural rigidity ($EI$) of the flaps, flap length ($L_{f}$) and piston speed ($U_{p}$), with measurements of the flap kinematics and flow field in each case. The flaps initially bulge due to the acceleration of the piston from rest, with this bulge growing in size and moving downstream as the flow develops, culminating in a large opening at the flap exit. Subsequently, the flaps return to their initial parallel position and remain there as long as the piston is in motion. Once the piston stops, the flaps collapse inwards due to fluid deceleration causing additional flow out of the flap region in the form of a jet that adds to the net amount of fluid pushed by the piston. We find that the flap kinematics is affected by the flap $EI$ and $L_{f}$ besides $U_{p}$. We define a non-dimensional flexural rigidity $EI^{\ast }=EI_{eq}/(1/2\unicode[STIX]{x1D70C}U_{p}^{2}L_{f}^{2}d)$, where $EI_{eq}$ is an equivalent flexural rigidity which takes the self-weight of the flaps into account ($d=\text{channel width}$; $\unicode[STIX]{x1D70C}=$ fluid density). We find that across different $EI_{eq}$, $L_{f}$, and piston speeds, the maximum opening of the flap tip and the time taken to reach this maximum opening in terms of $L/L_{f}$ (where $L=\text{fluid slug length}$) fall on a single curve for all the cases studied, when plotted with $EI^{\ast }$. Particle image velocimetry measurements show that the motion of the flaps results in the formation of additional pairs of vortices when compared to the single vortex pair formed in the absence of flaps. The total final circulation coming out of the flap region remains nearly the same as that of the rigid exit case. However, the final fluid impulse is always found to be higher in the flap cases, with the fluid impulse in most flap cases being approximately two times the fluid impulse of the rigid exit case. This increase in impulse is shown to be linked to the fact that the centroids of vorticity get spread out more in the lateral direction due to the opening of the flaps. The increased impulse and the higher time rate of change of impulse, which is linked with force, suggest that introduction of flexible flaps can help improve thrust performance when looked at from a propulsion point of view.