Parameterization and Application of the General Amber Force Field to Model Fluoro Substituted Furanose Moieties and Nucleosides.

Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.

Structural modeling and analysis of the SARS-CoV-2 cell entry inhibitor camostat bound to the trypsin-like protease TMPRSS2.

The type II transmembrane serine protease TMPRSS2 facilitates the entry of coronaviruses, such as SARS-CoV-2, into host cells by cleaving the S1/S2 interface of the viral spike protein. Based on structural data derived from X-ray crystallographic data of related trypsin-like proteases, a homology model of TMPRSS2 is described and validated using the broad spectrum COVID-19 drug candidate camostat as a probe. Both active site recognition and catalytic function are examined using quantum mechanics/molecular mechanics molecular dynamic (QM/MM MD) simulations of camostat and its active metabolite, 4-(4-guanidinobenzoyloxy) phenylacetate (GBPA). Substrate binding is shown to be primarily stabilized through salt bridge formation between the shared guanidino pharmacophore and D435 in pocket A (flanking the catalytic S441). Based on the binding mode of GBPA, residues K342 and W461 have been identified as potential contacts involved in TMPRSS2 selective binding and activity. Additional data is reported that indicates the transition state structure is stabilized through H-bonding interactions with the backbone N-H groups within an oxyanion hole following bottom-side attack of the carbonyl by S441. This is supported by prior work on related serine proteases suggesting further strategies to exploit in the design of more potent inhibitors. Taken overall, the proposed structure along with the key contact sites and mechanistic features identified should prove highly advantageous to the design and rational development of safe and effective therapeutics that target TMPRSS2 and avoid inhibition of other trypsin-dependent processes.

Prediction of Ligand Transport along Hydrophobic Enzyme Nanochannels.

Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the model makes it applicable to any hydrophobic channel/ligand combination.

Role of Water Hydrogen Bonding on Transport of Small Molecules inside Hydrophobic Channels.

We conducted a systematic analysis of water networking inside smooth hyperboloid hydrophobic structures (cylindrical, barrel, and hourglass shapes) to elucidate the role of water hydrogen bonding on the transport of small hydrophobic molecules (ligands). Through a series of molecular dynamics simulations, we established that a hydrogen-bonded network forming along the centerline resulted in a water exclusion zone adjacent to the walls. The size of the exclusion zone is a function of the geometry and the nonbonded interaction strength, defining the effective hydrophobicity of the structure. Exclusion of water molecules from this zone results in lower apparent viscosity, leading to acceleration of ligand transport up to 7 times faster than that measured in the bulk. Transport of ligands into and out of the hydrophobic structures was shown to be controlled by a single water molecule that capped the narrow regions in the structure. This mechanism provides physical insights into the behavior and role of water in the bottleneck regions of hydrophobic enzyme channels. These findings were then used in a sister publication [ Escalante , D. E. , Comput. Struct. Biotechnol. J. 2019 17 757 760 ] to develop a model that can accurately predict the transport of ligands along nanochannels of broad-substrate specificity enzymes.

Simulation of the Bottleneck Controlling Access into a Rieske Active Site: Predicting Substrates of Naphthalene 1,2-Dioxygenase.

Naphthalene 1,2-dioxygenase (NDO) has been computationally understudied despite the extensive experimental knowledge obtained for this enzyme, including numerous crystal structures and over 100 demonstrated substrates. In this study, we have developed a substrate prediction model that moves away from the traditional active-site-centric approach to include the energetics of substrate entry into the active site. By comparison with experimental data, the accuracy of the model for predicting substrate oxidation is 92%, with a positive predictive value of 93% and a negative predictive value of 98%. Also, the present analysis has revealed that the amino acid residues that provided the largest energetic barrier for compounds entering the active site are residues F224, L227, P234, and L235. In addition, F224 is proposed to play a role in controlling ligand entrance via π-π stacking stabilization as well as providing stabilization via T-shaped π-π interactions once the ligand has reached the active-site cavity. Overall, we present a method capable of being scaled to computationally discover thousands of substrates of NDO, and we present parameters to be used for expanding the prediction method to other members of the Rieske non-heme iron oxygenase family.

In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products.

Emerging contaminants are principally personal care products not readily removed by conventional wastewater treatment and, with an increasing reliance on water recycling, become disseminated in drinking water supplies. Carbamazepine, a widely used neuroactive pharmaceutical, increasingly escapes wastewater treatment and is found in potable water. In this study, a mechanism is proposed by which carbamazepine resists biodegradation, and a previously unknown microbial biodegradation was predicted computationally. The prediction identified biphenyl dioxygenase from Paraburkholderia xenovorans LB400 as the best candidate enzyme for metabolizing carbamazepine. The rate of degradation described here is 40 times greater than the best reported rates. The metabolites cis-10,11-dihydroxy-10,11-dihydrocarbamazepine and cis-2,3-dihydroxy-2,3-dihydrocarbamazepine were demonstrated with the native organism and a recombinant host. The metabolites are considered nonharmful and mitigate the generation of carcinogenic acridine products known to form when advanced oxidation methods are used in water treatment. Other recalcitrant personal care products were subjected to prediction by the Pathway Prediction System and tested experimentally with P. xenovorans LB400. It was shown to biodegrade structurally diverse compounds. Predictions indicated hydrolase or oxygenase enzymes catalyzed the initial reactions. This study highlights the potential for using the growing body of enzyme-structural and genomic information with computational methods to rapidly identify enzymes and microorganisms that biodegrade emerging contaminants.

Efficacy of combined antiparasitic therapy with praziquantel and albendazole for neurocysticercosis: a double-blind, randomised controlled trial.

BACKGROUND: Neurocysticercosis causes a substantial burden of seizure disorders worldwide. Treatment with either praziquantel or albendazole has suboptimum efficacy. We aimed to establish whether combination of these drugs would increase cysticidal efficacy and whether complete cyst resolution results in fewer seizures. We added an increased dose albendazole group to establish a potential effect of increased albendazole concentrations. METHODS: In this double-blind, placebo-controlled, phase 3 trial, patients with viable intraparenchymal neurocysticercosis were randomly assigned to receive 10 days of combined albendazole (15 mg/kg per day) plus praziquantel (50 mg/kg per day), standard albendazole (15 mg/kg per day), or increased dose albendazole (22·5 mg/kg per day). Randomisation was done with a computer generated schedule balanced within four strata based on number of cysts and concomitant antiepileptic drug. Patients and investigators were masked to group assignment. The primary outcome was complete cyst resolution on 6-month MRI. Enrolment was stopped after interim analysis because of parasiticidal superiority of one treatment group. Analysis excluded patients lost to follow-up before the 6-month MRI. This trial is registered with ClinicalTrials.gov, number NCT00441285. FINDINGS: Between March 3, 2010 and Nov 14, 2011, 124 patients were randomly assigned to study groups (41 to receive combined albendazole plus praziquantel [39 analysed], 43 standard albendazole [41 analysed], and 40 increased albendazole [38 analysed]). 25 (64%) of 39 patients in the combined treatment group had complete resolution of brain cysts compared with 15 (37%) of 41 patients in the standard albendazole group (rate ratio [RR] 1·75, 95% CI 1·10-2·79, p=0·014). 20 (53%) of 38 patients in the increased albendazole group had complete cyst resolution at 6-month MRI compared with 15 (37%) of 41 patients in the standard albendazole group (RR 1·44, 95% CI 0·87-2·38, p=0·151). No significant differences in adverse events were reported between treatment groups (18 in combined treatment group, 11 in standard albendazole group, and 19 in increased albendazole group). INTERPRETATION: Combination of albendazole plus praziquantel increases the parasiticidal effect in patients with multiple brain cysticercosis cysts without increased side-effects. A more efficacious parasiticidal regime without increased treatment-associated side-effects should improve the treatment and long term prognosis of patients with neurocysticercosis. FUNDING: National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health.

[Wilson'S disease: dominant neuropsychiatric form. Case presentation and its physiopathologic interpretation based upon magnetic resonance of the encephalon]. / Enfermedad de Wilson: Forma Neuropsiquiátrica dominante presentación de un caso y su interpretación fisiopatológica basada en resonancia magnética del encéfalo.

This is a presentation of a clinical case of Wilson s disease. The patient is a 26 year old woman who began to evidence psychological symptoms, which were later accompanied by neurological manifestations such as asymmetrical hand tremor, parkinsonism, dystonia and later on, dysphagia and mutism. The ophthalmological examination found a Kayser Fleischer ring in Descemet s membrane. There was disturbance of copper metabolism documented with reduction of serum ceruloplasmin and increase of the urinary excretion of copper. Cirrhosis was demonstrated through laparoscopy and liver biopsy. The brain magnetic resonance showed frontotemporal atrophy and a degenerative process at the basal ganglia, cerebellum and brain stem. This information could suggest probable neuropsychiatric physiopathology. The stenosis and intense cervical dysphagia, associated with the crycopharyngeal membrane, has not been mentioned previously.

Enfermedad de Wilson: forna neuropsiquiátrica dominante presentación de un caso y su interpretación fisiopatológica basada en resonancia magnética del encéfalo / Disease of Wilson: it forms dominant neuropsiquiatrica presentation of a case and its fisiopatologica interpretation based on magnetic resonance of encephalon

Se presenta un caso clínico de la efermedad de Wilson. Una mujer de 26 años de edad, comenzó a mostrar trastornos psíquicos, a los que se añadieron signos neurológicos, tales como temblor asimétrico de las manos, parkinsonismo, distonia; últimamente, presentó mutismo y disfagia. La exploración oftalmológica demostró la presencia del anillo de Kayser - Fleischer en la membrana de Descemet. Se comprobó alteración del metabolismo del cobre en cuanto a reducción de la ceruloplasmina sérica y aumento de la excreción urinaria de cobre. Mediante laparoscopía y biopsias puso en evidencia cirrosis hepática. La investigación de las estructuras del encéfalo con resoncia magnética (IRM) reveló atrofia frontotemporal del cerebro, y proceso degenerativo de los ganglios basales, el cerebelo y el tronco encefálico, datos que puden ser utilizados para sugerir la probable fisiopatología neuropsiquiátrica. La asociación con membrana cricofaríngea causante de estenosis y disfagia cervical intensa no ha sido mencionada anteriormente.