Closed genomes of four multidrug resistance Salmonella enterica serotype Infantis isolated in Costa Rica.

Here, we report the complete genome of four S. enterica Infantis isolated in Costa Rica from human, poultry rinse, and raw chicken meat from 2017 to 2019. All genomes belonged to ST32 and carried a 310-kb plasmid with many antimicrobial resistance genes including the bla CTX-M65 gene.

A Chemical Approach to Introduce 2,6-Diaminopurine and 2-Aminoadenine Conjugates into Oligonucleotides without Need for Protecting Groups.

We report a simple, postsynthetic strategy for synthesis of oligonucleotides containing 2,6-diaminopurine nucleotides and 2-aminoadenine conjugates using 2-fluoro-6-amino-adenosine. The strategy allows introduction of 2,6-diaminopurine and other 2-amino group-containing ligands. The strongly electronegative 2-fluoro deactivates 6-NH2 obviating the need for any protecting group on adenine, and simple aromatic nucleophilic substitution of fluorine makes reaction with aqueous NH3 or R-NH2 feasible at the 2-position.

Permanent maxillary central incisor and first molar rotations in the mixed dentition in repaired complete unilateral cleft lip and palate and their relationship with absence of teeth in their vicinity.

OBJECTIVES: To describe qualitatively and quantitatively the directions and magnitudes of rotations of permanent maxillary central incisors and first molars in the mixed dentition in repaired complete unilateral cleft lip and palate (UCLP) and study their associations with absence of teeth in their vicinity. MATERIALS AND METHODS: Dental casts and orthodontic records taken prior to orthodontic preparation for alveolar bone grafting of 74 children with repaired UCLP (53 male, 21 female; aged 8.9 ± 1.0 years) were studied. Directions and magnitudes of permanent maxillary central incisor and first molar rotations were recorded. Tooth absence was confirmed from longitudinal radiographic records. Incisor and molar rotations were analyzed in relation to the absence of teeth in their vicinity. RESULTS: Distolabial rotation of the permanent maxillary central incisor was noted in 77.14% on the cleft side, while distopalatal rotation was noted in 82.19% on the noncleft side. Incisor rotation was greater when a permanent tooth was present distal to the cleft side central incisor, in the greater segment. The permanent maxillary first molar showed mesiopalatal rotation, which was greater on the cleft side and when there was absence of one or more teeth in the buccal segment. CONCLUSIONS: Presence and absence of teeth were associated with the severity of incisor and molar rotations in UCLP. Crowding of anterior teeth in the greater segment was associated with a greater magnitude of rotation of the cleft side permanent central incisor. Absence of one or more buccal segment teeth was associated with greater magnitude of rotation of the molar.

Incisor and molar overjet, arch contraction, and molar relationship in the mixed dentition in repaired complete unilateral cleft lip and palate: A qualitative and quantitative appraisal.

OBJECTIVE: To compare the mixed dentition incisor and molar overjet, severity of contraction of the dental arch, and the sagittal molar relationship on the cleft side vs the noncleft side in children with repaired complete unilateral cleft of the lip and palate (UCLP). MATERIALS AND METHODS: Orthodontic records taken prior to orthodontic preparation for alveolar bone grafting were screened to select study casts from patients with nonsyndromic repaired complete UCLP who did not have mandibular skeletal or dental asymmetry. The study sample comprised dental casts from 74 children aged 8.9 ± 1 years. Standardized digital photographs were acquired at 1:1 magnification. A coordinate system was developed using digital image-processing software (Photoshop CS4 and Adobe Illustrator). Incisor and molar overjet, Angle's classification, and arch contraction were recorded. Descriptive statistics, paired t-tests, and kappa statistics were used to compare the cleft and noncleft sides. RESULTS: A negative overjet of -1 to -5 mm was often present at the incisors, with greater frequency and magnitude on the cleft side. Class II molar relation was more frequent on the cleft side (61.1%) than on the noncleft side (47.2%). Significantly greater contraction of the cleft side deciduous canine and deciduous first molar was noted, while the difference was very minor at the first permanent molar. CONCLUSIONS: Cleft side maxillary arch contraction was most severe in the deciduous canine and first deciduous molar region and progressively less severe in the posterior region of the arch. A greater frequency and severity of negative overjet and Class II molar relationship was seen on the cleft side.

Discovery and Synthesis of a Phosphoramidate Prodrug of a Pyrrolo[2,1-f][triazin-4-amino] Adenine C-Nucleoside (GS-5734) for the Treatment of Ebola and Emerging Viruses.

The recent Ebola virus (EBOV) outbreak in West Africa was the largest recorded in history with over 28,000 cases, resulting in >11,000 deaths including >500 healthcare workers. A focused screening and lead optimization effort identified 4b (GS-5734) with anti-EBOV EC50 = 86 nM in macrophages as the clinical candidate. Structure activity relationships established that the 1'-CN group and C-linked nucleobase were critical for optimal anti-EBOV potency and selectivity against host polymerases. A robust diastereoselective synthesis provided sufficient quantities of 4b to enable preclinical efficacy in a non-human-primate EBOV challenge model. Once-daily 10 mg/kg iv treatment on days 3-14 postinfection had a significant effect on viremia and mortality, resulting in 100% survival of infected treated animals [ Nature 2016 , 531 , 381 - 385 ]. A phase 2 study (PREVAIL IV) is currently enrolling and will evaluate the effect of 4b on viral shedding from sanctuary sites in EBOV survivors.

Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys.

The most recent Ebola virus outbreak in West Africa, which was unprecedented in the number of cases and fatalities, geographic distribution, and number of nations affected, highlights the need for safe, effective, and readily available antiviral agents for treatment and prevention of acute Ebola virus (EBOV) disease (EVD) or sequelae. No antiviral therapeutics have yet received regulatory approval or demonstrated clinical efficacy. Here we report the discovery of a novel small molecule GS-5734, a monophosphoramidate prodrug of an adenosine analogue, with antiviral activity against EBOV. GS-5734 exhibits antiviral activity against multiple variants of EBOV and other filoviruses in cell-based assays. The pharmacologically active nucleoside triphosphate (NTP) is efficiently formed in multiple human cell types incubated with GS-5734 in vitro, and the NTP acts as an alternative substrate and RNA-chain terminator in primer-extension assays using a surrogate respiratory syncytial virus RNA polymerase. Intravenous administration of GS-5734 to nonhuman primates resulted in persistent NTP levels in peripheral blood mononuclear cells (half-life, 14 h) and distribution to sanctuary sites for viral replication including testes, eyes, and brain. In a rhesus monkey model of EVD, once-daily intravenous administration of 10 mg kg(-1) GS-5734 for 12 days resulted in profound suppression of EBOV replication and protected 100% of EBOV-infected animals against lethal disease, ameliorating clinical disease signs and pathophysiological markers, even when treatments were initiated three days after virus exposure when systemic viral RNA was detected in two out of six treated animals. These results show the first substantive post-exposure protection by a small-molecule antiviral compound against EBOV in nonhuman primates. The broad-spectrum antiviral activity of GS-5734 in vitro against other pathogenic RNA viruses, including filoviruses, arenaviruses, and coronaviruses, suggests the potential for wider medical use. GS-5734 is amenable to large-scale manufacturing, and clinical studies investigating the drug safety and pharmacokinetics are ongoing.

Soft-tissue profile growth in patients with repaired complete unilateral cleft lip and palate: A cephalometric comparison with normal controls at ages 7, 11, and 18 years.

INTRODUCTION: In this retrospective longitudinal study, we aimed to study differences in the soft-tissue profiles in growing children with clefts in comparison with controls through the period of facial growth from 7 to 18 years. METHODS: Lateral cephalometric measurements made at 7 years (T1), 11.1 years (T2), and 17.9 years (T3) of age of 70 white children (35 boys, 35 girls) with complete unilateral cleft lip and palate (UCLP) who received primary lip and palate repair surgeries at The Hospital for Sick Children, Toronto, were compared with those of a control group of similar ages, sexes, and racial backgrounds, and having skeletal Class I facial growth, selected from the Burlington Growth Study. None of the included subjects had received any surgeries other than the primary lip and palate repairs, and none had undergone nasal septum surgery or nasal molding during infancy. Between-group comparisons were made at each time point using generalized linear models adjusted for age and sex effects. Longitudinal comparisons across all time points were conducted using the mixed model approach, adjusting for these effects and their interactions with time. RESULTS: Bimaxillary retrognathism, progressive maxillary retrognathism, and increasing lower anterior face height with downward and backward growth rotation of the mandible in the UCLP group were seen. Unlike the hard-tissue face height ratio, their soft-tissue face height ratio was not affected. The upper lips in the UCLP group were shorter by 1.81 mm at T2 (P <0.001) and by 1.16 mm at T3 (P = 0.018), whereas their lower lips were 2.21 mm longer at T3 (P = 0.003). A reduced upper lip to lower lip length ratio at T2 and T3 (P <0.001) resulted. Their upper lips were relatively retruded by 1.44 mm at T1, 1.66 mm at T2, and 1.86 mm at T3 (all, P <0.001), and their lower lips were relatively protruded by 1.07 mm at T1 (P = 0.003), 1.40 mm at T2 (P <0.001), and 1.62 mm at T3 (P <0.001). Nose depths in the UCLP group were shallower by at least 1 mm from T1 to T3, and columellar length was shorter by almost 2 mm (all, P <0.001). Their columellae and nose tips rotated downward with growth, with the most significant rotations experienced from T2 to T3, and progressive reductions in their soft-tissue profile convexity were seen from T1 to T3 (P <0.001). CONCLUSIONS: Key attributes of the imbalance in the soft-tissue profile in children with repaired UCLP were identified in the lip and nose regions. Although many profile differences were visible as early as 7 years of age, they became more apparent by 11 years of age and increased in severity thereafter. The short upper lip combined with a long lower lip resulted in the characteristic lip length imbalance, whereas the progressively retruding upper lip and protruding lower lip led to developing a step relationship in the sagittal lip profile during the adolescent growth period. Their columellae and nose tips rotated downward during this time.

ß-D-2'-α-F-2'-ß-C-Methyl-6-O-substituted 3',5'-cyclic phosphate nucleotide prodrugs as inhibitors of hepatitis C virus replication: a structure-activity relationship study.

The 3',5'-cyclic phosphate prodrug 9-[ß-d-2'-deoxy-2'-α-fluoro-2'-ß-C-methylribofuranosyl]-2-amino-6-ethoxypurine, PSI-352938 1, has demonstrated promising anti-HCV efficacy in vitro and in human clinical trials. A structure-activity relationship study of the nucleoside 3',5'-cyclic phosphate series of ß-d-2'-deoxy-2'-α-fluoro-2'-ß-C-methylribofuranosyl nucleoside prodrugs was undertaken and the anti-HCV activity and in vitro safety profile were assessed. Cycloalkyl 3',5'-cyclic phosphate prodrugs were shown to be significantly more potent as inhibitors of HCV replication than branched and straight chain alkyl 3',5'-cyclic phosphate prodrugs. No cytotoxicity and mitochondrial toxicity for prodrugs 12, 13 and 19 were observed at concentrations up to 100 µm in vitro. Cycloalkyl esters of 3',5'-cyclic phosphate nucleotide prodrugs demonstrated the ability to produce high levels of active triphosphate in clone-A cells and primary human hepatocytes. Compounds 12, 13 and 19 also demonstrated the ability to effectively deliver in vivo high levels of active nucleoside phosphates to rat liver.

Rapid differentiation of nucleotide phosphoramidate diastereomers by electrospray ionization tandem mass spectrometry.

RATIONALE: Nucleotide phosphoramidates are prodrugs which effectively deliver the active nucleotide to target tissues. It was shown that the individual phosphoramidate diastereomers have different antiviral activity, although the active nucleotide is the same. Therefore, a fast and simple analytical method is needed to characterize the individual diastereomeric phosphoramidate prodrugs. METHODS: Stock solutions of diastereomeric nucleotide phosphoramidate prodrugs, i.e., 5'-phosphate derivatives of the ß-D-2'-deoxy-2'-α-fluoro-2'-ß-C-methyluridine nucleotide, were made in 25% acetonitrile to achieve a final concentration of 10 µg/mL. The samples were studied using high-performance liquid chromatography (HPLC) coupled with electrospray ionization tandem mass spectrometry (ESI-MS/MS). RESULTS: The MS/MS spectra of diastereomeric pairs showed substantial differences in the relative abundances of a characteristic ion in negative mode, which is proposed to be a cyclic phosphoramidate ion. Results were confirmed by the MS/MS spectrum of an analog without the NH proton and deuterium exchange experiment. Furthermore, the diastereomer-specific fragmentation behavior in negative ESI-MS was used to characterize a series of nucleotide phosphoramidates with different amino acid and aromatic substituents. CONCLUSIONS: An HPLC/MS/MS method was developed for the differentiation of the diastereomers of phosphoramidate prodrugs. In negative mode MS/MS spectra, the cyclic phosphoramidate ions yielded unambiguous distinction. This method presented a rapid and simple way for the characterization of nucleotide phosphoramidates.

Phosphoramidate prodrugs of (-)-ß-D-(2R,4R)-dioxolane-thymine (DOT) as potent anti-HIV agents.

BACKGROUND: Nucleoside reverse transcriptase inhibitors (NRTIs) are an effective class of agents that has played a vital role in the treatment of HIV infections. (-)-ß-D-(2R,4R)-dioxolane-thymine (DOT) is a thymidine analogue that is active against wild-type and NRTI-resistant HIV-1 mutants. It has been shown that the anti-HIV activity of DOT is limited due to poor monophosphorylation. METHODS: To further enhance the anti-HIV activity of DOT, an extensive structure-activity relationship analysis of phosphoramidate prodrugs of DOT monophosphate was undertaken. These prodrugs were evaluated for anti-HIV activity using Hela CD4 ß-gal reporter cells (P4-CCR5 luc cells). RESULTS: Among the synthesized prodrugs, the 4-bromophenyl benzyloxy l-alanyl phosphate derivative of DOT was the most potent, with a 50% effective concentration of 0.089 µM corresponding to a 75-fold increase in activity relative to the parent nucleoside DOT with no increased cytotoxicity. The metabolic stability of a selected number of potent DOT phosphoramidates was also evaluated in simulated gastric fluid, simulated intestinal fluid, human plasma and liver S9 fractions. CONCLUSIONS: A series of new phosphoramidate prodrugs of DOT were prepared and evaluated as inhibitors of HIV replication in vitro. Metabolic stability studies indicated that these DOT phosphoramidate derivatives have the potential to show acceptable stability in the gastrointestinal tract, but they metabolize rapidly in the liver.

Characteristics of lower extremity clonus after human cervical spinal cord injury.

Clonus can interfere with self-care and rehabilitation of people with spinal cord injury. Our aim was to characterize clonus and to evaluate factors that influence clonus duration in muscles paralyzed chronically by spinal cord injury. Electromyographic activity was recorded from soleus and 7 other limb muscles (5 ipsilateral, 2 contralateral) during clonus. In 14 subjects, clonus frequency in soleus averaged 5.4±0.9 Hz and was slower when the reflex path was longer. Contraction frequency slowed at the beginning and end of clonus (sometimes by 2 Hz). The magnitude of one cycle changed the timing and magnitude of the next cycle. These data suggest that afferent input influences the frequency and maintenance of clonus. Recording from many muscles revealed that clonus was prolonged (>40 sec) when only ipsilateral triceps surae or triceps surae and tibialis anterior were involved. Therefore, localized inputs to spinal circuits were important to sustain clonus. Clonus was intermediate (median: 21 sec) with activation of three or four ipsilateral muscles and these contractions were associated with greater activation of ipsilateral flexors. Clonus was short (<5 sec) when ipsilateral and contralateral muscles were activated (five or six muscles). Activation of extraneous afferent input, particularly contralateral muscles, may provide a way to shorten clonus after spinal cord injury.

A liquid chromatography-tandem mass spectrometry method for the quantitative determination of diastereomers of a phosphoramidate nucleotide prodrug (PSI-7851) in human plasma.

A rapid and stereospecific method using high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) for the separation and determination of PSI-7851 diastereomers in human K2EDTA plasma has been developed. The analytical method involves direct protein precipitation with acetonitrile, followed by separation of the diastereomers on a Luna C18 column, positive mode electrospray ionization and selected reaction monitoring mode mass spectrometry detection. The mobile phase composition and pH were investigated for the resolution of the two diastereomers of PSI-7851. The optimized method showed good resolution (R(s) = 4.8) within short analysis time (approximately 8 min). The assay range was 5-2500 ng/mL for both diastereomers using a 1/x² weighted linear regression analysis for standard curve fitting. Replicate sample analysis indicated that intra- and inter-day accuracy and precision were within ±15.0%. The recovery of diastereomers from human plasma was greater than 85% and no significant matrix effect was observed. The method was demonstrated to be sensitive, selective and robust, and was successfully used to support clinical studies.

Synthesis of stable isotope labeled analogs of the anti-hepatitis C virus nucleotide prodrugs PSI-7977 and PSI-352938.

In order to support bioanalytical LC/MS method development and plasma sample analysis in preclinical and clinical studies of the anti-hepatitis C-virus nucleotides, PSI-7977 and PSI-352938, the corresponding stable isotope labeled forms were prepared. These labeled compounds were prepared by addition reaction of the freshly prepared Grignard reagent (13)CD(3)MgI to the corresponding 2 '-ketone nucleosides followed by fluorination of the resulting carbinol with DAST. As expected, these 2 '-C-(trideuterated-(13)C-methyl) nucleotide prodrugs showed similar anti-HCV activity to that of the corresponding unlabeled ones.

Synthesis of diastereomerically pure nucleotide phosphoramidates.

Prodrugs of therapeutic nucleoside monophosphates masked as phosphoramidate derivatives have become an increasingly important class of antiviral drugs in pharmaceutical research for delivering nucleotides in vitro and in vivo. Conventionally, phosphoramidate derivatives are prepared as a mixture of two diastereomers. We report a class of stable phosphoramidating reagents containing an amino acid ester and two phenolic groups, one unsubstituted and the other with electron-withdrawing substituents. The reagents can be isolated as single diastereomers and reacted with the 5'-hydroxyl group of nucleosides through selective nucleophilic displacement of the substituted phenol to prepare single diastereomer phosphoramidate products. This method has been used to prepare the HCV clinical candidate PSI-7977 in high yield and high diastereomeric purity.

Activity and the metabolic activation pathway of the potent and selective hepatitis C virus pronucleotide inhibitor PSI-353661.

PSI-353661, a phosphoramidate prodrug of 2'-deoxy-2'-fluoro-2'-C-methylguanosine-5'-monophosphate, is a highly active inhibitor of genotype 1a, 1b, and 2a HCV RNA replication in the replicon assay and of genotype 1a and 2a infectious virus replication. PSI-353661 is active against replicons harboring the NS5B S282T or S96T/N142T amino acid alterations that confer decreased susceptibility to nucleoside/tide analogs as well as mutations that confer resistance to non-nucleoside inhibitors of NS5B. Replicon clearance studies show that PSI-353661 was able to clear cells of HCV replicon RNA and prevent a rebound in replicon RNA. PSI-353661 showed no toxicity toward bone marrow stem cells or mitochondrial toxicity. The metabolism to the active 5'-triphosphate involves hydrolysis of the carboxyl ester by cathepsin A (Cat A) and carboxylesterase 1 (CES1) followed by a putative nucleophilic attack on the phosphorus by the carboxyl group resulting in the elimination of phenol and the alaninyl phosphate metabolite, PSI-353131. Histidine triad nucleotide-binding protein 1 (Hint 1) then removes the amino acid moiety, which is followed by hydrolysis of the methoxyl group at the O(6)-position of the guanine base by adenosine deaminase-like protein 1 (ADAL1) to give 2'-deoxy-2'-fluoro-2'-C-methylguanosine-5'-monophosphate. The monophosphate is phosphorylated to the diphosphate by guanylate kinase. Nucleoside diphosphate kinase is the primary enzyme involved in phosphorylation of the diphosphate to the active triphosphate, PSI-352666. PSI-352666 is equally active against wild-type NS5B and NS5B containing the S282T amino acid alteration.

Stereoselective synthesis of PSI-352938: a ß-D-2'-deoxy-2'-α-fluoro-2'-ß-C-methyl-3',5'-cyclic phosphate nucleotide prodrug for the treatment of HCV.

PSI-352938 is a novel 2'-deoxy-2'-α-fluoro-2'-ß-C-methyl 3',5'-cyclic phosphate nucleotide prodrug currently under investigation for the treatment of hepatitis C virus (HCV) infection. PSI-352938 demonstrated superior characteristics in vitro that include broad genotype coverage, superior resistance profile, and high levels of active triphosphate in vivo in the liver compared to our first and second generation nucleoside inhibitors of this class. Consequently, PSI-352938 was selected for further development and an efficient and scalable synthesis was sought to support clinical development. We report an improved, diastereoselective synthesis of a key 1'-ß-nucleoside intermediate 13 via S(N)2 displacement of 1-α-bromo ribofuranose sugar 16 with the potassium salt of 6-chloro-2-amino purine and an efficient method to prepare cis-Rp cyclic phosphate (PSI-352938) in a highly stereoselective manner without any chromatographic purification. The 1-α-bromo sugar 16 was stereospecifically prepared from the corresponding 1-ß-lactol in high yield under mild bromination conditions using CBr(4)/PPh(3) (Appel reaction). The desired cis-Rp 3',5'-cyclic phosphate construction was accomplished using isopropyl phosphorodichloridate readily obtained from POCl(3) and isopropyl alcohol. The base combination of Et(3)N/NMI was identified as a key factor for producing PSI-352938 as the major (>95%) diastereomer (cis-Rp) in high yield after the final cyclization step. The current route described in this article was successfully used to produce PSI-352938 on multikilogram scale.

Discovery of PSI-353661, a Novel Purine Nucleotide Prodrug for the Treatment of HCV Infection.

Hepatitis C virus afflicts approximately 180 million people worldwide, and the development of direct acting antivirals may offer substantial benefit compared to the current standard of care. Accordingly, prodrugs of 2'-deoxy-2'-fluoro-2'-C-methylguanosine monophosphate analogues were prepared and evaluated for their anti-HCV efficacy and tolerability. These prodrugs demonstrated >1000 fold greater potency than the parent nucleoside in a cell-based replicon assay as a result of higher intracellular triphosphate levels. Further optimization led to the discovery of the clinical candidate PSI-353661, which has demonstrated strong in vitro inhibition against HCV without cytotoxicity and equipotent activity against both the wild type and the known S282T nucleoside/tide resistant replicon. PSI-353661 is currently in preclinical development for the treatment of HCV.

2'-deoxy-2'-α-fluoro-2'-ß-C-methyl 3',5'-cyclic phosphate nucleotide prodrug analogs as inhibitors of HCV NS5B polymerase: discovery of PSI-352938.

A series of novel 2'-deoxy-2'-α-fluoro-2'-ß-C-methyl 3',5'-cyclic phosphate nucleotide prodrug analogs were synthesized and evaluated for their in vitro anti-HCV activity and safety. These prodrugs demonstrated a 10-100-fold greater potency than the parent nucleoside in a cell-based replicon assay due to higher cellular triphosphate levels. Our structure-activity relationship (SAR) studies provided compounds that gave high levels of active triphosphate in rat liver when administered orally to rats. These studies ultimately led to the selection of the clinical development candidate 24a (PSI-352938).