Deciphering complex mechanisms of resistance and loss of potency through coupled molecular dynamics and machine learning [preprint]

Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially involving those distal from the active site, alter drug binding to confer resistance are poorly understood and thus difficult to counteract. A strategy coupling parallel molecular dynamics simulations and machine learning to identify conserved mechanisms underlying resistance was developed. A series of 28 HIV-1 protease variants with up to 24 varied substitutions were used as a rigorous model of this strategy. Many of the mutations were distal from the active site and the potency to darunavir varied from low pM to near μM. With features extracted from molecular dynamics simulations, elastic network machine learning was applied to correlate physical interactions at the molecular level with potency loss. This fit to within 1 kcal/mol of experimental potency for both the training and test sets, outperforming MM/GBSA calculations. Feature reduction resulted in a model with 4 specific features that correspond to interactions critical for potency regardless of enzyme variant. These predictive features throughout the enzyme would not have been identified without dynamics and machine learning and specifically varied with potency. This approach enables capturing the conserved dynamic molecular mechanisms by which complex combinations of mutations confer resistance and identifying critical interactions which serve as bellwethers over a wide range of inhibitor potency. Machine learning models leveraging molecular dynamics can thus elucidate mechanisms that confer loss of affinity due to variations distal from the active site, such as in drug resistance

Comparison of the accelerated and classic vaccination schedules against Hepatitis B: three-week Hepatitis B vaccination schedule provides immediate and protective immunity

BACKGROUND: Hepatitis B virus infection although preventable by vaccination remains an important health issue throughout the world due to its morbidity, mortality and economical losses. Early seroprotection is desirable for people at high risk of exposure. The aim of this study was to determine whether three-week hepatitis B vaccination (on days 0, 10 and 21) provide seroprotection or not. METHODS: The 120 subjects enrolled into the study were divided into two groups and vaccinated by the classic (months 0, 1, and 2) or the accelerated (days 0, 10, and 21) schedules and antibody response determined on days 30, 60, and 90 and, if below 10 mIU/ml(-1), again on day 180. For each individual in the classic group (B) three subjects were enrolled in the accelerated group (A). Recombinant hepatitis B vaccine (Gen-Hevac B, Pasteur) was given as 20 micrograms intramuscular injections via the deltoid muscle. A booster dose on day 365 was administered for each group. Family members of hepatitis B carriers and volunteer health personnel were enrolled into group A. To the B group only volunteers who wanted vaccination against hepatitis B were included. RESULTS: After three doses of vaccine, Anti-HBs titers reached protective levels in both groups. The number of vaccinees with seroprotective levels of Anti-HBs (≥10 mIU/ml(-1)) on day 30 was 53 (58.9%) in group A and 9 (30.0%) in group B (p < 0.05). On day 60, there was no difference between group A and B, with response rates of 84.4% (n = 76) and 80.0% (n = 24) respectively (p > 0.05). On day 90 there was no difference between group B and group A; with 26 (86.7%) and 79 (87.7%) responders respectively. In both groups those with Anti-HBs levels <10 mIU/ml(-1 )attained protective levels by day 180. CONCLUSION: In this study, the three-week vaccination provided protective antibody titers within a shorter time compared to the classic schedule. Therefore, in order to provide rapid antibody production against hepatitis B virus, the accelerated vaccination schedule seems to be a good preference

HIV-1 protease-substrate coevolution in nelfinavir resistance

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30\u27s interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. IMPORTANCE: Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations

Interdependence of Inhibitor Recognition in HIV-1 Protease

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1\u27 and S2\u27 subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1\u27 subsite highly influences other subsites: the extension of the hydrophobic P1\u27 moiety results in 1) reduced van der Waals contacts in the P2\u27 subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor

Medicinal powders made of fresh milk for pediatric use

Communication presented at the 1st International Congress of CiiEM - From Basic Sciences to Clinical Research. 27-28 November 2015, Egas Moniz, Caparica, Portugal"Nowadays, the need to formulate medicines specifically designed for children is imperative [1] and solid dosage forms are the first choice for providing the required drug stability and dose accuracy. Milk, as a worldwide accepted food, is proposed in this study as a platform to deliver drugs orally in pediatrics. Therefore, the main goals of this project are: (a) to assess the properties of spray-dried milk powders, (b) to evaluate drug-milk interactions and (c) to ascertain the stability of the spray-dried milk powders."Fundação para a Ciência e a Tecnologi

Spray-dried fresh milk powders for oral drug delivery in pediatrics

Poster presented at the 10th World Meeting on Pharmaceutics, Biopharmaceutics and Pharmaceutical Technology. 4-7 April 2016, Glasgow, UKN/

Serum Endothelin-1 and Transforming Growth Factor-β Levels in the Newborns With Respiratory Distress

The purpose of this present study was to evaluate the serum levels of ET-1 and TGF-β in the newborns with respiratory distress. In this study, newborns with respiratory distress hospitalized into the Newborn Intensive Care Unit were included. The highest values of ET-1 and TGF-β were obtained from newborns with diagnosis as meconium aspiration syndrome (5.70 ± 5.87 pg/mL and 3.75 ± 1.94 pg/mL, resp) in the sample obtained in the first six hours after birth, and these are statistically different from control group (P < .05). Also, same results were obtained for newborns with respiratory distress syndrome (3.37 ± 1.59 pg/mL and 2.05 ± 0.98 pg/mL, resp). After oxygen treatment, ET-1 values obtained in the first six hours of life were decreased regularly in the following days (P < .05). In the differentiating diagnosis of the respiratory distress of newborns, the investigation of ET-1 and TGF-β levels is meaningful. The ET-1 levels investigated in the first six hours is more useful in determining the prognosis, and repeating ET-1 levels in the following days is more meaningful to determine clinical response

Milk as a drug delivery platform in paediatrics

Communication presented at the PSSRC − 9th Annual Symposium. 16-18 September 2015, Ghent, Belgium"Purpose: to assess the physical properties of spray dried milk powders and evaluate drug-milk interactions.

Serum IL-1β, IL-6, IL-8, and TNF-α Levels in Early Diagnosis and Management of Neonatal Sepsis

Aim. To determine serum IL-1β, IL-6, IL-8, and TNF-α levels in neonatal sepsis at the time of diagnosis and after therapy, and to show the meaningful on the follow up. Methods. This prospective study was performed on newborns who were hospitalized for neonatal sepsis and who were classified as culture-proven sepsis (n=12), as culture-negative sepsis (n=21), and as healthy newborns (n=17). Results. At the time of diagnosis, serum IL-1β, IL-6, IL-8, and TNF-α levels of culture-proven sepsis were significantly higher than those of the control groups (P<.05). At the time of diagnosis, IL-1β, IL-6, IL-8, and TNF-α levels of culture-proven sepsis and culture-negative sepsis were significantly higher than levels at the seventh day after antibiotic treatment. Conclusion. Serum IL-1β, IL-6, IL-8, and TNF-α are mediators of inflammation and can be used at the diagnosis and at the evaluation of the therapeutic efficiency in neonatal sepsis