Cytosolic 5'-Nucleotidase III and Nucleoside Triphosphate Diphosphohydrolase 1 Dephosphorylate the Pharmacologically Active Metabolites of Gemcitabine and Emtricitabine.

Gemcitabine (dFdC) and emtricitabine (FTC) are first-line drugs that are used for the treatment of pancreatic cancer and human immunodeficiency virus, respectively. The above drugs must undergo sequential phosphorylation to become pharmacologically active. Interindividual variability associated with the responses of the above drugs has been reported. The molecular mechanisms underlying the observed variability are yet to be elucidated. Although this could be multifactorial, nucleotidases may be involved in the dephosphorylation of drug metabolites due to their structural similarity to endogenous nucleosides. With these in mind, we performed in vitro assays using recombinant nucleotidases to assess their enzymatic activities toward the metabolites of dFdC and FTC. From the above in vitro experiments, we noticed the dephosphorylation of dFdC-monophosphate in the presence of two 5'-nucleotidases (5'-NTs), cytosolic 5'-nucleotidase IA (NT5C1A) and cytosolic 5'-nucleotidase III (NT5C3), individually. Interestingly, FTC monophosphate was dephosphorylated only in the presence of NT5C3 enzyme. Additionally, nucleoside triphosphate diphosphohydrolase 1 (NTPDase 1) exhibited enzymatic activity toward both triphosphate metabolites of dFdC and FTC. Enzyme kinetic analysis further revealed Michaelis-Menten kinetics for both NT5C3-mediated dephosphorylation of monophosphate metabolites, as well as NTPDase 1-mediated dephosphorylation of triphosphate metabolites. Immunoblotting results confirmed the presence of NT5C3 and NTPDase 1 in both pancreatic and colorectal tissue that are target sites for dFdC and FTC treatment, respectively. Furthermore, sex-specific expression patterns of NT5C3 and NTPDase 1 were determined using mass spectrometry-based proteomics approach. Based on the above results, NT5C3 and NTPDase 1 may function in the control of the levels of dFdC and FTC metabolites. SIGNIFICANCE STATEMENT: Emtricitabine and gemcitabine are commonly used drugs for the treatment of human immunodeficiency virus and pancreatic cancer. To become pharmacologically active, both the above drugs must be phosphorylated. The variability in the responses of the above drugs can lead to poor clinical outcomes. Although the sources of drug metabolite concentration variability are multifactorial, it is vital to understand the role of nucleotidases in the tissue disposition of the above drug metabolites due to their structural similarities to endogenous nucleosides.

Solubility Data, Solubility Parameters and Thermodynamic Behavior of an Antiviral Drug Emtricitabine in Different Pure Solvents: Molecular Understanding of Solubility and Dissolution.

The solubility values, various Hansen solubility parameters (HSPs) and thermodynamic behavior of emtricitabine (ECT) in twelve different pure solvents (PS) were estimated using various experimental as well as computational methods. Experimental solubility values (xe) of ECT in twelve different PS were obtained at T = 298.2 K to 318.2 K and p = 0.1 MPa. The xe values of ECT were correlated by "van't Hoff, Apelblat and Buchowski-Ksiazaczak λh models". Various HSPs for ECT and twelve different PS were also calculated using "HSPiP software". The xe values of ECT were estimated maximum in polyethylene glycol-400 (PEG-400; 1.41 × 10-1), followed by ethylene glycol, Transcutol-HP, propylene glycol, methanol, water, isopropanol, ethanol, 1-butanol, dimethyl sulfoxide, 2-butanol and EA (1.28 × 10-3) at T = 318.2 K. "Apparent thermodynamic analysis" showed an "endothermic and entropy-driven dissolution" of ECT. Overall, PEG-400 was found as the best/ideal solvent for solubility/miscibility of ECT compared to other solvents studied.

Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance.

Human immunodeficiency virus 1 (HIV-1) infection is a global health issue since neither a cure nor a vaccine is available. However, the highly active antiretroviral therapy (HAART) has improved the life expectancy for patients with acquired immunodeficiency syndrome (AIDS). Nucleoside reverse transcriptase inhibitors (NRTIs) are in almost all HAART and target reverse transcriptase (RT), an essential enzyme for the virus. Even though NRTIs are highly effective, they have limitations caused by RT resistance. The main mechanisms of RT resistance to NRTIs are discrimination and excision. Understanding the molecular mechanisms for discrimination and excision are essential to develop more potent and selective NRTIs. Using protein X-ray crystallography, we determined the first crystal structure of RT in its post-catalytic state in complex with emtricitabine, (-)FTC or stavudine (d4T). Our structural studies provide the framework for understanding how RT discriminates between NRTIs and natural nucleotides, and for understanding the requirement of (-)FTC to undergo a conformation change for successful incorporation by RT. The crystal structure of RT in post-catalytic complex with d4T provides a "snapshot" for considering the possible mechanism of how RT develops resistance for d4T via excision. The findings reported herein will contribute to the development of next generation NRTIs.

Solubility, Hansen Solubility Parameters and Thermodynamic Behavior of Emtricitabine in Various (Polyethylene Glycol-400 + Water) Mixtures: Computational Modeling and Thermodynamics.

This study was aimed to find out the solubility, thermodynamic behavior, Hansen solubility parameters and molecular interactions of an antiviral drug emtricitabine (ECT) in various "[polyethylene glycol-400 (PEG-400) + water]" mixtures. The solubility of ECT in mole fraction was determined at "T = 298.2 to 318.2 K" and "p = 0.1 MPa" using an isothermal method. The experimental solubilities of ECT in mole fraction were validated and correlated using various computational models which includes "Van't Hoff, Apelblat, Yalkowsky-Roseman, Jouyban-Acree and Jouyban-Acree-Van't Hoff models". All the models performed well in terms of model correlation. The solubility of ECT was increased with the raise in temperature in all "PEG-400 + water" mixtures studied. The highest and lowest solubility values of ECT were found in pure PEG-400 (1.45 × 10-1) at "T = 318.2 K" and pure water (7.95 × 10-3) at "T = 298.2 K", respectively. The quantitative values of activity coefficients indicated higher interactions at molecular level in ECT and PEG-400 combination compared with ECT and water combination. "Apparent thermodynamic analysis" showed an "endothermic and entropy-driven dissolution" of ECT in all "PEG-400 + water" combinations studied. The solvation nature of ECT was found an "enthalpy-driven" in each "PEG-400 + water" mixture studied.

Synthesis and characterization of a long-acting emtricitabine prodrug nanoformulation.

PURPOSE: A palmitoylated prodrug of emtricitabine (FTC) was synthesized to extend the drug's half-life, antiretroviral activities and biodistribution. METHODS: A modified FTC prodrug (MFTC) was synthesized by palmitoyl chloride esterification. MFTC's chemical structure was evaluated by nuclear magnetic resonance. The created hydrophobic prodrug nanocrystals were encased into a poloxamer surfactant and the pharmacokinetics (PK), biodistribution and antiretroviral activities of the nanoformulation (NMFTC) were assessed. The conversion of MFTC to FTC triphosphates was evaluated. RESULTS: MFTC coated with poloxamer formed stable nanocrystals (NMFTC). NMFTC demonstrated an average particle size, polydispersity index and zeta potential of 350 nm, 0.24 and -20 mV, respectively. Drug encapsulation efficiency was 90%. NMFTC was readily taken up by human monocyte-derived macrophages yielding readily detected intracellular FTC triphosphates and an extended PK profile. CONCLUSION: NMFTC shows improved antiretroviral activities over native FTC. This is coordinate with its extended apparent half-life. The work represents an incremental advance in the development of a long-acting FTC formulation.

Synthesis of a long acting nanoformulated emtricitabine ProTide.

While antiretroviral therapy (ART) has revolutionized treatment and prevention of human immunodeficiency virus type one (HIV-1) infection, regimen adherence, viral mutations, drug toxicities and access stigma and fatigue are treatment limitations. These have led to new opportunities for the development of long acting (LA) ART including implantable devices and chemical drug modifications. Herein, medicinal and formulation chemistry were used to develop LA prodrug nanoformulations of emtricitabine (FTC). A potent lipophilic FTC phosphoramidate prodrug (M2FTC) was synthesized then encapsulated into a poloxamer surfactant (NM2FTC). These modifications extended the biology, apparent drug half-life and antiretroviral activities of the formulations. NM2FTC demonstrated a >30-fold increase in macrophage and CD4+ T cell drug uptake with efficient conversion to triphosphates (FTC-TP). Intracellular FTC-TP protected macrophages against an HIV-1 challenge for 30 days. A single intramuscular injection of NM2FTC, at 45 mg/kg native drug equivalents, into Sprague Dawley rats resulted in sustained prodrug levels in blood, liver, spleen and lymph nodes and FTC-TP in lymph node and spleen cells at one month. In contrast, native FTC-TPs was present for one day. These results are an advance in the transformation of FTC into a LA agent.

Structural insights into the recognition of nucleoside reverse transcriptase inhibitors by HIV-1 reverse transcriptase: First crystal structures with reverse transcriptase and the active triphosphate forms of lamivudine and emtricitabine.

The retrovirus HIV-1 has been a major health issue since its discovery in the early 80s. In 2017, over 37 million people were infected with HIV-1, of which 1.8 million were new infections that year. Currently, the most successful treatment regimen is the highly active antiretroviral therapy (HAART), which consists of a combination of three to four of the current 26 FDA-approved HIV-1 drugs. Half of these drugs target the reverse transcriptase (RT) enzyme that is essential for viral replication. One class of RT inhibitors is nucleoside reverse transcriptase inhibitors (NRTIs), a crucial component of the HAART. Once incorporated into DNA, NRTIs function as a chain terminator to stop viral DNA replication. Unfortunately, treatment with NRTIs is sometimes linked to toxicity caused by off-target side effects. NRTIs may also target the replicative human mitochondrial DNA polymerase (Pol γ), causing long-term severe drug toxicity. The goal of this work is to understand the discrimination mechanism of different NRTI analogues by RT. Crystal structures and kinetic experiments are essential for the rational design of new molecules that are able to bind selectively to RT and not Pol γ. Structural comparison of NRTI-binding modes with both RT and Pol γ enzymes highlights key amino acids that are responsible for the difference in affinity of these drugs to their targets. Therefore, the long-term goal of this research is to develop safer, next generation therapeutics that can overcome off-target toxicity.

How broadly can poly(urethane)-based implants be applied to drugs of varied properties?

Implants offer the opportunity to improve patient adherence and real-world outcomes. However, most polymers used today are hydrophobic and limit drug properties suitable for development. Thermoplastic poly(urethanes) (TPUs) form pores upon hydration and may facilitate the development of implants containing drugs exhibiting broadly different properties. We sought to investigate the effect of drug physicochemical properties on permeability through membranes of varying TPU mixture composition; leverage imaging to visualize microstructural changes to the membrane across the TPU mixture composition range; and quantitatively characterize the membrane microstructure using equivalent pore analysis. We observed a correlation between drug hydrophobicity and its permeability through hydrophobic-rich TPU membranes. Conversely, all compounds diffused through hydrophilic-rich TPU membranes at similar rates, regardless of drug properties. Imaging revealed significant microstructure differences between hydrophobic-rich and hydrophilic-rich TPU membranes, supporting hypotheses proposed in our previous study. The hydrated hydrophilic TPU membrane pore area was determined to be 0.583% and its equivalent pore radius was found to be 128 nm, suggesting that hydrophilic TPU membranes may be used to modify the release of small molecular weight drugs and macromolecules. These findings highlight the benefits of hydrophilic TPUs as rate-controlling membranes to modulate the release rate of drugs with varying physicochemical properties.

Semi-solid prodrug nanoparticles for long-acting delivery of water-soluble antiretroviral drugs within combination HIV therapies.

The increasing global prevalence of human immunodeficiency virus (HIV) is estimated at 36.7 million people currently infected. Lifelong antiretroviral (ARV) drug combination dosing allows management as a chronic condition by suppressing circulating viral load to allow for a near-normal life; however, the daily burden of oral administration may lead to non-adherence and drug resistance development. Long-acting (LA) depot injections of nanomilled poorly water-soluble ARVs have shown highly promising clinical results with drug exposure largely maintained over months after a single injection. ARV oral combinations rely on water-soluble backbone drugs which are not compatible with nanomilling. Here, we evaluate a unique prodrug/nanoparticle formation strategy to facilitate semi-solid prodrug nanoparticles (SSPNs) of the highly water-soluble nucleoside reverse transcriptase inhibitor (NRTI) emtricitabine (FTC), and injectable aqueous nanodispersions; in vitro to in vivo extrapolation (IVIVE) modelling predicts sustained prodrug release, with activation in relevant biological environments, representing a first step towards complete injectable LA regimens containing NRTIs.

Using artificial neural network and multivariate calibration methods for simultaneous spectrophotometric analysis of Emtricitabine and Tenofovir alafenamide fumarate in pharmaceutical formulation of HIV drug.

Spectrophotometric analysis method based on artificial neural network (ANN), partial least squares regression (PLS) and principal component regression (PCR) models was proposed for the simultaneous determination of Emtricitabine (ETB) and Tenofovir alafenamide fumarate (TAF) in human immunodeficiency virus (HIV) drug. An artificial neural network consisting of two, five, and seven layers with 2,3,5,7, and 9 neurons was trained by applying a feed forward back-propagation learning. In this method, Levenberg-Marquardt (LM) and gradient descent with momentum and adaptive learning rate back propagation (GDX) algorithms were used. Statistical parameters indicated that the ability of LM was better than GDX algorithm. Also, root mean square error (RMSE) and recovery (%) of the PLS and PCR methods showed that PLS has worked better than PCR. The proposed models were compared to the high- performance liquid chromatography (HPLC) as a reference method. Furthermore, the obtained results of the one-way analysis of variance (ANOVA) test at the 95% confidence level represented that there was no significant difference between the proposed and reference methods.

3D printed, controlled release, tritherapeutic tablet matrix for advanced anti-HIV-1 drug delivery.

PURPOSE: A 3D-Bioplotter® was employed to 3D print (3DP) a humic acid-polyquaternium 10 (HA-PQ10) controlled release fixed dose combination (FDC) tablet comprising of the anti-HIV-1 drugs, efavirenz (EFV), tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC). METHODS: Chemical interactions, surface morphology and mechanical strength of the FDC were ascertained. In vitro drug release studies were conducted in biorelevant media followed by in vivo study in the large white pigs, in comparison with a market formulation, Atripla®. In vitro-in vivo correlation of results was undertaken. RESULTS: EFV, TDF and FTC were successfully entrapped in the 24-layered rectangular prism-shaped 3DP FDC with a loading of ∼12.5 mg/6.3 mg/4 mg of EFV/TDF/FTC respectively per printed layer. Hydrogen bonding between the EFV/TDF/FTC and HA-PQ10 was detected which was indicative of possible drug solubility enhancement. The overall surface of the tablet exhibited a fibrilla structure and the 90° inner pattern was determined to be optimal for 3DP of the FDC. In vitro and in vivo drug release profiles from the 3DP FDC demonstrated that intestinal-targeted and controlled drug release was achieved. CONCLUSION: A 3DP FDC was successfully manufactured with the aid of a 3D-Bioplotter in a single step process. The versatile HA-PQ10 entrapped all drugs and achieved an enhanced relative bioavailability of EFV, TDF, and FTC compared to the market formulation for potentially enhanced HIV treatment.

New resistance mutations to nucleoside reverse transcriptase inhibitors at codon 184 of HIV-1 reverse transcriptase (M184L and M184T).

Mutations at HIV-1 reverse transcriptase (RT) codon 184 such as M184V confer resistance to two nucleos(t)ide RT inhibitors (NRTI), lamivudine (3TC) and emtricitabine (FTC). The prevalence of mutations at HIV-1 RT codon 184 was evaluated using three independent RT sequence databases from treatment-experienced (TE) and treatment-naïve (TN) individuals. Data were collected retrospectively from three centers: one in Italy and two in France between 1997 and 2016. In order to highlight the role of these mutations in conferring drug resistance, structural and thermodynamic analyses were conducted by means of computational approaches. Among 32,440 RT sequences isolated from TE and 12,365 isolated from TN patients, the prevalence of HIV-1 RT codon 184 substitutions in each group was 31.21% and 0.72%, respectively. The mutations M184L and M184T have been observed only in TE patients. In all cases but four, M184L and M184T mutations were present during NRTI treatment. Molecular recognition studies on M184L and M184T structures showed both FTC and 3TC thermodynamic profiles unfavorable in comparison with the wild-type sequence, corroborated by molecular dynamic simulations (MDS). In this study, we highlighted two new resistance mutations in vivo for NRTI resistance. The low frequency of this pathway can be related to high impairment of replicative capacity mediated by these mutations.

Can drug release rate from implants be tailored using poly(urethane) mixtures?

Hydrophobic and hydrophilic thermoplastic poly(urethane) (TPU) mixtures offer the opportunity to tune water swelling capacity and diffusion rate for drugs exhibiting broadly different properties. We sought to (1) assess the range of drug diffusion rates achieved by varying hydrophilic-to-hydrophobic TPU ratio relative to varying ethylene vinyl acetate (EVA) crystallinity; (2) investigate the effect of mixture ratio on permeability of emtricitabine; and (3) investigate the impact of the extrusion process on mixing of the two TPUs and the resulting impact on drug diffusion. The permeability of water-soluble emtricitabine exhibited a 736-fold range across the blends of TPU, but only a 3.4-fold range across the EVA grades investigated. Varying hydrophilic content of the TPU mixture from 0% to 25% (w/w) led to a negligible permeability change, while changing hydrophilic content from 55% to 100% resulted in a linear 3-fold increase in drug permeability. Interestingly, an 123-fold permeability change occurred between 50% and 55% hydrophilic polymer. Extrusion process parameters exhibited minimal impact on homogeneity and drug diffusion. These findings suggest that hydrophilic polymer domains form a continuous network at levels above 55% hydrophilic TPU, thus facilitating a water-filled porous network when exposed to water that provides a mechanism for accelerated drug diffusion.

Injectable long-acting human immunodeficiency virus antiretroviral prodrugs with improved pharmacokinetic profiles.

While highly active antiretroviral therapy (HAART) has significantly reduced mortality rates in patients with human immunodeficiency virus type 1 (HIV-1), its efficacy may be impeded by emergence of drug resistance caused by lack of patient adherence. A therapeutic strategy that requires infrequent drug administration as a result of sustained release of antiretroviral drugs would put less burden on the patient. Long-acting antiretroviral prodrugs for HIV therapy were synthesized through modification of the active drugs, emtricitabine (FTC) and elvitegravir (EVG), with docosahexaenoic acid (DHA) in one-step, one-pot, high-yielding reactions. The in vitro drug release profiles of these synthetic conjugates demonstrated sustained and controlled release of the active drug over a period of 3-4 weeks attributable to the hydrolysis of the chemical linker in conjunction with the hydrophilicity of the parent drug. Both conjugates exhibited superior antiviral activities in tissue culture models of HIV replication as compared to those of the free drugs, strengthening their role as potent prodrugs for HIV therapy. Pharmacokinetic analysis in CD1 mice further confirmed the long-acting aspect of these conjugates with released drug concentrations in plasma detected at their respective IC90/IC95 values over a period of 2 weeks and discernable amounts of active drug even at 6 weeks. Our findings suggest that the injectable small molecule conjugates could be used as long-acting controlled release of FTC and EVG in attempts to mitigate adherence-related HIV resistance.

Efficacy of single-tablet darunavir, cobicistat, emtricitabine, and tenofovir alafenamide in the treatment of HIV-1.

INTRODUCTION: HIV eradication is not feasible and lifelong treatment is warranted to manage HIV infection. In this scenario, the advent of single-tablet, once-daily, fixed-dose co-formulations is important for reducing pill burden and maximize long-term drug adherence. Cobicistat-boosted darunavir along with emtricitabine and tenofovir alafenamide co-formulation (DRV/c/FTC/TAF or the trade name Symtuza®) is the first marketed protease inhibitor-based fixed-dose combination regimen for the treatment of HIV infection. It was approved in late 2017 by the European Medical Agency both for naïve patients and treatment-experienced patients with viral suppression. Areas covered: PubMed, ClinicalTrials.gov and presentations at scientific meetings were searched with the terms 'darunavir/cobicistat' and 'tenofovir alafenamide and emtricitabine' for clinical trials either conducted to date or ongoing as well as a review of abstracts from major HIV/AIDS and infectious diseases conferences from 2015 to up to date. Expert opinion: DRV/c/FTC/TAF is a novel unique antiretroviral drug co-formulation that exhibits a convenient dosing, satisfactory safety profile, and high antiviral efficacy, even in patients harboring viruses with resistance to antivirals other than darunavir in the short-midterm. It represents the first fixed-dose combination therapy including a protease inhibitor given as one single pill once daily for drug-naïve patients and as second-line antiretroviral therapy.

Simultaneous determination and validation of emtricitabine, rilpivirine and tenofovir from biological samples using LC and CE methods.

A combination of antiretroviral agents is frequently used in effective treatment of the human immunodeficiency virus infection. In this study, two different separation methods are presented for the simultaneous determination of emtricitabine, rilpivirine and tenofovir from raw materials and urine samples. Developed liquid chromatography and capillary electrophoresis methods were thoroughly optimized for high analytical performances. Optimization of multiple variables at the same time by performing a minimum number of experiments was achieved by the Box-Behnken design, which is an experimental design in response surface methodology, in capillary electrophoresis. The results of the experimental design ensure minimum analysis time with well-separated analytes. Separation conditions, such as different stationary phases, pH level, organic modifiers and temperatures in liquid chromatography method, were also optimized. In particular, among stationary phases, the core-shell column especially enhanced the effectiveness of separation in liquid chromatography. Both methods were fully validated and applied to real samples. The main advantage of the developed methods is the separation of the drug combination in a short time with high efficiency and without any time-consuming steps.

Development, validation and clinical application of a method for the simultaneous quantification of lamivudine, emtricitabine and tenofovir in dried blood and dried breast milk spots using LC-MS/MS.

OBJECTIVES: To present the validation and clinical application of a LC-MS/MS method for the quantification of lamivudine (3TC), emtricitabine (FTC) and tenofovir (TFV) in dried blood spots (DBS) and dried breast milk spots (DBMS). METHODS: DBS and DBMS were prepared from 50 and 30µL of drug-spiked whole blood and human breast milk, respectively. Following extraction with acetonitrile and water, chromatographic separation utilised a Synergi polar column with a gradient mobile phase program consisting of 0.1% formic acid in water and 0.1% formic acid in acetonitrile. Detection and quantification was performed using a TSQ Quantum Ultra triple quadrupole mass spectrometer. The analytical method was used to evaluate NRTI drug levels in HIV-positive nursing mothers-infant pairs. RESULTS: The assay was validated over the concentration range of 16.6-5000ng/mL for 3TC, FTC and TFV in DBS and DBMS except for TFV in DBMS where linearity was established from 4.2-1250ng/mL. Intra and inter-day precision (%CV) ranged from 3.5-8.7 and accuracy was within 15% for all analytes in both matrices. The mean recovery in DBS was >61% and in DBMS >43% for all three analytes. Matrix effect was insignificant. Median AUC0-8 values in maternal DBS and DBMS, respectively, were 4683 (4165-6057) and 6050 (5217-6417)ngh/mL for 3TC, 3312 (2259-4312) and 4853 (4124-6691)ngh/mL for FTC and 1559 (930-1915) and 56 (45-80)ngh/mL for TFV. 3TC and FTC were quantifiable (>16.6ng/mL) in DBS from 2/6 and 1/6 infants respectively whereas TFV was undetectable in all infants. CONCLUSIONS: DBS and DBMS sampling for bioanalysis of 3TC, FTC and TFV is straightforward, robust, accurate and precise, and ideal for use in low-resource settings.

Structural basis for the D-stereoselectivity of human DNA polymerase ß.

Nucleoside reverse transcriptase inhibitors (NRTIs) with L-stereochemistry have long been an effective treatment for viral infections because of the strong D-stereoselectivity exhibited by human DNA polymerases relative to viral reverse transcriptases. The D-stereoselectivity of DNA polymerases has only recently been explored structurally and all three DNA polymerases studied to date have demonstrated unique stereochemical selection mechanisms. Here, we have solved structures of human DNA polymerase ß (hPolß), in complex with single-nucleotide gapped DNA and L-nucleotides and performed pre-steady-state kinetic analysis to determine the D-stereoselectivity mechanism of hPolß. Beyond a similar 180° rotation of the L-nucleotide ribose ring seen in other studies, the pre-catalytic ternary crystal structures of hPolß, DNA and L-dCTP or the triphosphate forms of antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP) provide little structural evidence to suggest that hPolß follows the previously characterized mechanisms of D-stereoselectivity. Instead, hPolß discriminates against L-stereochemistry through accumulation of several active site rearrangements that lead to a decreased nucleotide binding affinity and incorporation rate. The two NRTIs escape some of the active site selection through the base and sugar modifications but are selected against through the inability of hPolß to complete thumb domain closure.

Structural Insights into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed by a DNA Polymerase.

DNA polymerases are essential enzymes that faithfully and efficiently replicate genomic information.1-3 The mechanism of nucleotide incorporation by DNA polymerases has been extensively studied structurally and kinetically, but several key steps following phosphodiester bond formation remain structurally uncharacterized due to utilization of natural nucleotides. It is thought that the release of pyrophosphate (PPi) triggers reverse conformational changes in a polymerase in order to complete a full catalytic cycle as well as prepare for DNA translocation and subsequent incorporation events. Here, by using the triphosphates of chain-terminating antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine ((-)FTC-TP), we structurally reveal the correct sequence of post-chemistry steps during nucleotide incorporation by human DNA polymerase ß (hPolß) and provide a structural basis for PPi release. These post-catalytic structures reveal hPolß in an open conformation with PPi bound in the active site, thereby strongly suggesting that the reverse conformational changes occur prior to PPi release. The results also help to refine the role of the newly discovered third divalent metal ion for DNA polymerase-catalyzed nucleotide incorporation. Furthermore, a post-chemistry structure of hPolß in the open conformation, following incorporation of (-)3TC-MP, with a second (-)3TC-TP molecule bound to the active site in the absence of PPi, suggests that nucleotide binding stimulates PPi dissociation and occurs before polymerase translocation. Our structural characterization defines the order of the elusive post-chemistry steps in the canonical mechanism of a DNA polymerase.