A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network

Fluorinated derivatives of tetrahydroaltersolanol molecule on COVID-19, HIV, and HTLV protease by DFT and molecular docking approaches

Structural, optoelectronic, and biological properties of tetrahydroaltersolanol (C₁₆H₂₀O₇) and fluorinated derivatives are calculated using density functional theory (DFT) and molecular docking approaches. It is shown that the pure C₁₆H₂₀O₇ molecule has a direct HOMO-LUMO energy gap about 3.1 eV. The substitution of F atom at A category decreases the electronic energy gap, while it is constant at B category. In A category, the behavior of the pure molecule changed from insulator to semiconductor with various substitution of F atom. The electronic properties were depended on the F sites in the pure molecule. The molecular electrical transport properties and charge-transfer possibilities increase with decreasing energy gap. The pure C₁₆H₂₀O₇ molecule with high energy gap has low chemical reactivity and substitution of F atom at considered molecule increases chemical reactivity. Obtained results show that F-O bonds in trifurcation bonds of C₁₆H₁₉O₇(F14), C₁₆H₁₉O₇(F16), and C₁₆H₁₉O₇(F17) molecules play a key role in confronting with COVID-19, HIV, and HTLV proteases, respectively. Optical spectra, such as the dielectric functions, electron energy-loss spectroscopy, refractive index, extinction coefficient, and reflection spectra show that fluorinated derivatives of C₁₆H₂₀O₇ at B category can be used in the new drugs.

Human T lymphotropic virus type 1 and risk of cardiovascular disease: High-density lipoprotein dysfunction versus serum HDL-C concentrations

High-density lipoprotein (HDL) is thought to be protective against cardiovascular disease (CVD), and HDL dysfunction is considered to be a risk factor for CVD. It is unclear whether there is an association between Human T lymphotropic virus type 1 (HTLV1) infection and CVD risk. We have assessed HDL lipid peroxidation (HDLox) as a marker of HDL dysfunction and CVD risk in a subgroup of the MASHAD cohort study. One hundred and sixty two individuals including 50 subjects positive for HTLV1 infection and 112 individuals negative for HTLV1 infection were recruited. Anthropometric and biochemical parameters including serum hs-CRP, fasted lipid profile (HDL-C, LDL, triglycerides, and cholesterol), and fasting blood glucose were determined. Serum HDLox was also measured in the study participants. Multivariate analyses were used to evaluate the association between serum HDLox and HTLV1 infection. None of the traditional CVD risk factors were associated with HTLV1 infection, including serum HDL-C. However, serum HDLox was independently associated with the presence of HTLV1 infection. Logistic regression analysis showed that subjects who were positive for HTLV1 infection were also significantly more likely than uninfected individuals to have higher HDLox (odds ratio 9.35, 95%CI: 3.5-24.7; P < 0.001). HDLox was increased approximately 20% (P < 0.001) in infected subjects compared to the uninfected group. Serum HDLox is a marker of CVD risk factor and increased in individuals affected by HTLV1 infection compared to healthy subjects. © 2019 BioFactors, 45(3):374-380, 2019.

Cardiovascular risk profile in patients with myelopathy associated with HTLV-1

HAM/TSP (HTLV-1-associated myelopathy/tropical spastic paraparesis) is a slowly progressive disease, characterized by a chronic spastic paraparesis. It is not known if the disease carries an independent risk for cardiovascular disease. The objective of this study was to evaluate the cardiovascular risk profile related to HAM/TSP and compare it with the general population.

METHODS

This was a cross-sectional study, with a control group. HAM/TSP patients were evaluated using cardiovascular risk scores (ASCVD RISK, SCORE and Framingham) and inflammatory markers (ultrasensitive CRP and IL-6), and compared with a control group of healthy individuals. We also evaluated the correlation between cardiovascular risk and the functional status of patients with HAM/TSP evaluated by the FIM scale.

RESULTS

Eighty percent of patients in this study were females, mean age of 51 years (11.3). The control group showed an increased cardiovascular event risk in 10 years when ASCVD was analyzed (cardiovascular risk ≥7.5% in 10 years seen in 43% of patients in the control group vs. 23% of patients with HAM/TSP; p=0.037). There was no difference in ultrasensitive CRP or IL-6 values between the groups, even when groups were stratified into low and high risk. There was no correlation between the functional status of HAM/TSP patients and the cardiovascular risk.

CONCLUSIONS

In this study, the cardiovascular risk profile of patients with HAM/TSP was better than the risk of the control group.

Molecular insights on analogs of HIV PR inhibitors toward HTLV-1 PR through QM/MM interactions and molecular dynamics studies: comparative structure analysis of wild and mutant HTLV-1 PR

Retroviruses HTLV-1 and HIV-1 are the primary causative agents of fatal adult T-cell leukemia and acquired immune deficiency syndrome (AIDS) disease. Both retroviruses are similar in characteristics mechanism, and it encodes for protease that mainly involved in the viral replication process. On the basis of the therapeutic success of HIV-1 PR inhibitors, the protease of HTLV-1 is mainly considered as a potential target for chemotherapy. At the same time, structural similarities in both enzymes that originate HIV PR inhibitors can also be an HTLV-1 PR inhibitor. But the expectations failed because of rejection of HIV PR inhibitors from the HTLV-1 PR binding pocket. In this present study, the reason for the HIV PR inhibitor rejection from the HTLV-1 binding site was identified through sequence analysis and molecular dynamics simulation method. Functional analysis of M37A mutation in HTLV PR clearly shows that the MET37 specificity and screening of potential inhibitors targeting MET37 is performed by using approved 90% similar HIV PR inhibitor compounds. From this approach, we report few compounds with a tendency to accept/donate electron specifically to an important site residue MET37 in HTLV-1 PR binding pocket.

Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease

Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy simulations have been conducted to study the proton transfer reaction between the catalytic residues of HTLV-1 protease using a combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulation. The free energy profiles for the reaction in the apo-enzyme and in an enzyme - substrate complex have been obtained. In the apo-enzyme, the two catalytic residues are chemically equivalent and are expected to be both unprotonated. Upon substrate binding, the catalytic residues of HTLV-1 protease evolve to a singly protonated state, in which the OD1 of Asp32 is protonated and forms a hydrogen bond with the OD1 of Asp32', which is unprotonated. The HTLV-1 protease-substrate complex structure obtained from this simulation can serve as the Michaelis complex structure for further mechanistic studies of HTLV-1 protease while providing a receptor structure with the correct protonation states for the active site residues toward the design of novel HTLV-1 protease inhibitors through virtual screening.

Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors

Retroviruses HIV-1 and HTLV-1 are chiefly considered to be the most dangerous pathogens in Homo sapiens. These two viruses have structurally unique protease (PR) enzymes, which are having common function of its replication mechanism. Though HIV PR drugs failed to inhibit HTLV-1 infections, they emphatically emphasise the need for designing new lead compounds against HTLV-1 PR. Therefore, we tried to understand the binding level interactions through the charge environment present in both ligand and protein active sites. The domino effect illustrates that libraries of purvalanol-A are attuned to fill allosteric binding site of HTLV-1 PR through molecular recognition and shows proper binding of ligand pharmacophoric features in receptor contours. Our screening evaluates seven compounds from purvalanol-A libraries, and these compounds' pharmacophore searches for an appropriate place in the binding site and it places well according to respective receptor contour surfaces. Thus our result provides a platform for the progress of more effective compounds, which are better in free energy calculation, molecular docking, ADME and molecular dynamics studies. Finally, this research provided novel chemical scaffolds for HTLV-1 drug discovery.

Molecular modeling studies and comparative analysis on structurally similar HTLV and HIV protease using HIV-PR inhibitors

Retroviruses are most perilous viral family, which cause much damage to the Homo sapiens. HTLV-1 mechanism found to more similar with HIV-1 and both retroviruses are causative agents of severe and fatal diseases including adult T-cell leukemia (ATL) and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease (PR) that is essential for replication and therefore represents a key target for drugs interfering with viral infection. In this work, the comparative study of HIV-1 and HTLV-1 PR enzymes through sequence and structural analysis is reported along with approved drugs of HIV-PR. Conformation of each HIV PR drugs have been examined with different parameters of interactions and energy scorings parameters. MD simulations with respect to timescale event of 20 ns favors that, few HIV-PR inhibitors can be more active inside the HTLV-1 PR binding pocket. Overall results suggest that, some of HIV inhibitors like Tipranavir, Indinavir, Darunavir and Amprenavir are having good energy levels with HTLV-1. Due to absence of interactions with MET37, here we report that derivatives of these compounds can be much better inhibitors for targeting HTLV-1 proteolytic activity.

Small molecule regulation of protein conformation by binding in the Flap of HIV protease

The fragment indole-6-carboxylic acid (1F1), previously identified as a flap site binder in a fragment-based screen against HIV protease (PR), has been cocrystallized with pepstatin-inhibited PR and with apo-PR. Another fragment, 3-indolepropionic acid (1F1-N), predicted by AutoDock calculations and confirmed in a novel inhibition of nucleation crystallization assay, exploits the same interactions in the flap site in two crystal structures. Both 1F1 and 1F1-N bind to the closed form of apo-PR and to pepstatin:PR. In solution, 1F1 and 1F1-N raise the Tm of apo-PR by 3.5-5 °C as assayed by differential scanning fluorimetry (DSF) and show equivalent low-micromolar binding constants to both apo-PR and pepstatin:PR, assayed by backscattering interferometry (BSI). The observed signal intensities in BSI are greater for each fragment upon binding to apo-PR than to pepstatin-bound PR, consistent with greater conformational change in the former binding event. Together, these data indicate that fragment binding in the flap site favors a closed conformation of HIV PR.