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1.
Nature ; 623(7986): 324-328, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37938708

RESUMEN

The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.

2.
Proc Natl Acad Sci U S A ; 119(43): e2204414119, 2022 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-36252020

RESUMEN

Predictions of the structures of stoichiometric, fractional, or nonstoichiometric hydrates of organic molecular crystals are immensely challenging due to the extensive search space of different water contents, host molecular placements throughout the crystal, and internal molecular conformations. However, the dry frameworks of these hydrates, especially for nonstoichiometric or isostructural dehydrates, can often be predicted from a standard anhydrous crystal structure prediction (CSP) protocol. Inspired by developments in the field of drug binding, we introduce an efficient data-driven and topologically aware approach for predicting organic molecular crystal hydrate structures through a mapping of water positions within the crystal structure. The method does not require a priori specification of water content and can, therefore, predict stoichiometric, fractional, and nonstoichiometric hydrate structures. This approach, which we term a mapping approach for crystal hydrates (MACH), establishes a set of rules for systematic determination of favorable positions for water insertion within predicted or experimental crystal structures based on considerations of the chemical features of local environments and void regions. The proposed approach is tested on hydrates of three pharmaceutically relevant compounds that exhibit diverse crystal packing motifs and void environments characteristic of hydrate structures. Overall, we show that our mapping approach introduces an advance in the efficient performance of hydrate CSP through generation of stable hydrate stoichiometries at low cost and should be considered an integral component for CSP workflows.


Asunto(s)
Agua , Cristalización , Modelos Moleculares , Conformación Molecular , Estructura Molecular , Agua/química
3.
Mol Pharm ; 21(7): 3525-3539, 2024 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-38900600

RESUMEN

The comparative crystallizability and polymorphic selectivity of ritonavir, a novel protease inhibitor for the treatment of acquired immune-deficiency syndrome, as a function of solvent selection are examined through an integrated and self-consistent experimental and computational molecular modeling study. Recrystallization at high supersaturation by rapid cooling at 283.15 K is found to produce the metastable "disappeared" polymorphic form I from acetone, ethyl acetate, acetonitrile, and toluene solutions in contrast to ethanol which produces the stable form II. Concomitant crystallization of the other known solid forms is not found under these conditions. Isothermal crystallization studies using turbidometric detection based upon classical nucleation theory reveal that, for an equal induction time, the required driving force needed to initiate solution nucleation decreases with solubility in the order of ethanol, acetone, acetonitrile, ethyl acetate, and toluene consistent with the expected desolvation behavior predicted from the calculated solute solvation free energies. Molecular dynamics simulations of the molecular and intermolecular chemistry reveal the presence of conformational interplay between intramolecular and intermolecular interactions within the solution phase. These encompass the solvent-dependent formation of intramolecular O-H...O hydrogen bonding between the hydroxyl and carbamate groups coupled with differing conformations of the hydroxyl's shielding phenyl groups. These conformational preferences and their relative interaction propensities, as a function of solvent selection, may play a rate-limiting role in the crystallization behavior by not only inhibiting to different degrees the nucleation process but also restricting the assembly of the optimal intermolecular hydrogen bonding network needed for the formation of the stable form II polymorph.


Asunto(s)
Cristalización , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Ritonavir , Solventes , Ritonavir/química , Solventes/química , Solubilidad , Etanol/química , Acetatos , Acetonitrilos
4.
Mol Pharm ; 20(11): 5811-5826, 2023 11 06.
Artículo en Inglés | MEDLINE | ID: mdl-37750872

RESUMEN

ABBV-167, a phosphate prodrug of BCL-2 inhibitor venetoclax, was recently progressed into the clinic as an alternative means of reducing pill burden for patients in high-dose indications. The dramatically enhanced aqueous solubility of ABBV-167 allowed for high drug loading within a crystalline tablet and, when administered in phase I clinical study, conferred venetoclax exposure commensurate with the equivalent dose administered as an amorphous solid dispersion. In enabling the progression into the clinic, we performed a comprehensive evaluation of the CMC development aspects of this beyond the rule of five (bRo5) prodrug. Adding a phosphate moiety resulted in excessively complex chemical speciation and solid form landscapes with significant physical-chemical stability liabilities. A combination of experimental and computational methods including microelectron diffraction (MicroED), total scattering, tablet colorimetry, finite element, and molecular dynamics modeling were used to understand CMC developability across drug substance and product manufacture and storage. The prodrug's chemical structural characteristics and loose crystal packing were found to be responsible for the loss of crystallinity during its manufacturing, which in turn led to high solid-state chemical reactivity and poor shelf life stability. The ABBV-167 case exemplifies key CMC development challenges for complex chemical matter such as bRo5 phosphate prodrugs with significant ramifications during drug substance and drug product manufacturing and storage.


Asunto(s)
Profármacos , Humanos , Profármacos/química , Fosfatos , Desarrollo de Medicamentos , Solubilidad , Comprimidos
5.
Mol Pharm ; 19(7): 2367-2379, 2022 07 04.
Artículo en Inglés | MEDLINE | ID: mdl-35481355

RESUMEN

Dasabuvir is a non-nucleoside polymerase inhibitor for the treatment of hepatitis C virus (HCV) infection. It is an extremely weak diacidic drug (pKa = 8.2 and 9.2) and a prolific solvate former. Due to its exceedingly low aqueous solubility (≤0.127 µg/mL at pH 1-6.8, dose number of 1.31 × 104), crystalline dasabuvir free acid exhibited poor oral bioavailability in initial animal pharmacokinetic (PK) assessment. This necessitated the development of enabling formulation for human clinical studies to achieve the required therapeutic in vivo concentration of dasabuvir. While salt formation has been widely used to enhance the solubility and dissolution rate of solids, this approach has rarely been applied to develop oral solid dosage forms for acidic drugs as weak as dasabuvir due to concerns of rapid disproportionation and crystallization of its free acid. In this contribution, we detail our efforts in identifying dasabuvir monosodium monohydrate as a drug substance that is stable, manufacturable, and, most importantly, significantly enhances the dissolution and oral absorption of this poorly soluble drug. The oral delivery of dasabuvir through the salt approach has enabled the commercialization of the triple-combination direct-acting antiviral HCV regimen, Viekira Pak. The methodologies and solutions identified in targeted studies to overcome technical challenges encountered along the way (i.e., incorporation of polymers to inhibit crystallization and disproportionation and species mapping to enable salt manufacturing process, etc.) can be applied to other insoluble compounds.


Asunto(s)
Hepatitis C Crónica , Hepatitis C , Animales , Antivirales/uso terapéutico , Disponibilidad Biológica , Hepacivirus , Hepatitis C/tratamiento farmacológico , Hepatitis C Crónica/tratamiento farmacológico , Preparaciones Farmacéuticas , Solubilidad
6.
J Am Chem Soc ; 143(42): 17479-17491, 2021 10 27.
Artículo en Inglés | MEDLINE | ID: mdl-34637297

RESUMEN

Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.

7.
Pharm Res ; 38(6): 971-990, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-34009625

RESUMEN

PURPOSE: Application of multi-scale modelling workflows to characterise polymorphism in ritonavir with regard to its stability, bioavailability and processing. METHODS: Molecular conformation, polarizability and stability are examined using quantum mechanics (QM). Intermolecular synthons, hydrogen bonding, crystal morphology and surface chemistry are modelled using empirical force fields. RESULTS: The form I conformation is more stable and polarized with more efficient intermolecular packing, lower void space and higher density, however its shielded hydroxyl is only a hydrogen bond donor. In contrast, the hydroxyl in the more open but less stable and polarized form II conformation is both a donor and acceptor resulting in stronger hydrogen bonding and a more stable crystal structure but one that is less dense. Both forms have strong 1D networks of hydrogen bonds and the differences in packing energies are partially offset in form II by its conformational deformation energy difference with respect to form I. The lattice energies converge at shorter distances for form I, consistent with its preferential crystallization at high supersaturation. Both forms exhibit a needle/lath-like crystal habit with slower growing hydrophobic side and faster growing hydrophilic capping habit faces with aspect ratios increasing from polar-protic, polar-aprotic and non-polar solvents, respectively. Surface energies are higher for form II than form I and increase with solvent polarity. The higher deformation, lattice and surface energies of form II are consistent with its lower solubility and hence bioavailability. CONCLUSION: Inter-relationship between molecular, solid-state and surface structures of the polymorphic forms of ritonavir are quantified in relation to their physical-chemical properties.


Asunto(s)
Química Farmacéutica/métodos , Cristalización/métodos , Inhibidores de la Proteasa del VIH/química , Conformación Molecular , Ritonavir/química , Fenómenos Químicos , Inhibidores de la Proteasa del VIH/metabolismo , Enlace de Hidrógeno , Interacciones Hidrofóbicas e Hidrofílicas , Ritonavir/metabolismo , Solubilidad , Propiedades de Superficie
8.
J Chem Inf Model ; 61(3): 1412-1426, 2021 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-33661005

RESUMEN

Drug design with patient centricity for ease of administration and pill burden requires robust understanding of the impact of chemical modifications on relevant physicochemical properties early in lead optimization. To this end, we have developed a physics-based ensemble approach to predict aqueous thermodynamic crystalline solubility, with a 2D chemical structure as the input. Predictions for the bromodomain and extraterminal domain (BET) inhibitor series show very close match (0.5 log unit) with measured thermodynamic solubility for cases with low crystal anisotropy and good match (1 log unit) for high anisotropy structures. The importance of thermodynamic solubility is clearly demonstrated by up to a 4 log unit drop in solubility compared to kinetic (amorphous) solubility in some cases and implications thereof, for instance on human dose. We have also demonstrated that incorporating predicted crystal structures in thermodynamic solubility prediction is necessary to differentiate (up to 4 log unit) between solubility of molecules within the series. Finally, our physics-based ensemble approach provides valuable structural insights into the origins of 3-D conformational landscapes, crystal polymorphism, and anisotropy that can be leveraged for both drug design and development.


Asunto(s)
Física , Agua , Humanos , Conformación Molecular , Solubilidad , Termodinámica
9.
Pediatr Transplant ; 19(6): 623-33, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-26179628

RESUMEN

OHT is the definitive therapy in end-stage heart failure. Elevated PVRI is considered a relative contraindication to isolated OHT; this assumption is re-evaluated using data from the UNOS database. A retrospective review of de-identified data from the UNOS dataset was performed. There were 1943 pediatric OHT recipients between 10/87 and 12/11 with sufficient data for analysis. Cox regression was performed to examine the effect of baseline characteristics on post-transplant survival. Patients were propensity matched, and Kaplan-Meier survival analysis was performed comparing cohorts of patients using thresholds of 6 and 9 WU × m(2) . PVRI was not a significant predictor of post-transplant outcomes in either univariate or multivariate Cox regression. Kaplan-Meier analysis revealed no difference in survival between both unmatched and propensity-matched OHT recipients. In conclusion, elevated PVRI was not associated with post-transplant mortality in pediatric OHT recipients. A prospective study assessing the current use of PVRI ≥6 as a threshold to contraindicate isolated OHT should be undertaken. Removing this potentially unnecessary restriction on transplant candidacy may make this life-saving therapy available to a greater number of patients.


Asunto(s)
Insuficiencia Cardíaca/cirugía , Trasplante de Corazón/mortalidad , Circulación Pulmonar/fisiología , Resistencia Vascular , Adolescente , Niño , Preescolar , Bases de Datos Factuales , Femenino , Humanos , Lactante , Masculino , Periodo Preoperatorio , Pronóstico , Puntaje de Propensión , Estudios Retrospectivos , Análisis de Supervivencia , Trasplante Homólogo
10.
Cardiol Young ; 25(6): 1141-7, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-25245660

RESUMEN

BACKGROUND: Although some prior studies have provided evidence to question the historical belief that pulmonary vascular resistance index ⩾6 Wood Units×m2 should be a contraindication to heart transplantation in children, no national analyses specific to the modern area have addressed this question. METHODS: Data were analysed for paediatric heart transplant recipients from 1 January, 2002 to 1 September, 2012 (n=699). The relationship between pulmonary vascular resistance and all-cause 30-day mortality was evaluated using univariate and multivariate analyses. RESULTS: The 30-day mortality included 10 patients (1.43%), which is lower than in the previous analyses. Receiver operating curve analysis of pulmonary vascular resistance index as a predictor of mortality yielded a cut-off value of 3.37 Wood Units×m2, but the area under the curve and specificity of this threshold was weaker than in previous analyses. Whereas pulmonary vascular resistance index treated as a dichotomised variable was a significant predictor of mortality in univariate (odds ratio 4.92, 95% confidence interval 1.04-23.33, p=0.045) and multivariate (odds ratio 5.26, 95% confidence interval 1.07-25.80, p=0.041) analyses, pulmonary vascular resistance index treated as a continuous variable was not a significant predictor of mortality in univariate (p=0.12) or multivariate (p=0.11) analyses. CONCLUSIONS: The relationship between pulmonary vascular resistance and post-heart transplant mortality in children is less convincing in this analysis of a comprehensive, contemporary database than in previous series. This suggests the possibility that modern improvements in the management of post-transplant right ventricular dysfunction have mitigated the contribution of pulmonary hypertension to early mortality.


Asunto(s)
Trasplante de Corazón/efectos adversos , Trasplante de Corazón/mortalidad , Hipertensión Pulmonar/etiología , Resistencia Vascular , Adolescente , Niño , Preescolar , Femenino , Humanos , Lactante , Modelos Logísticos , Masculino , Análisis Multivariante , Oportunidad Relativa , Factores de Riesgo , Índice de Severidad de la Enfermedad
11.
Transfusion ; 54(2): 300-5, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23710629

RESUMEN

BACKGROUND: Glanzmann thrombasthenia (GT) is an autosomal recessive disorder in which the platelet (PLT) glycoprotein IIb/IIIa complex is either deficient or dysfunctional. In its most severe form, GT may result in spontaneous bleeding, although most cases are first detected in the setting of an invasive procedure. CASE REPORT: A 59-year-old male with Type I GT and a history of transfusion reactions to PLT infusions developed severe aortic stenosis secondary to bicuspid valve disease. He successfully underwent open aortic valve replacement with cardiopulmonary bypass without perioperative bleeding complications. RESULTS: A multidisciplinary team (anesthesia, hematology, cardiac surgery, and transfusion medicine) was established to optimize perioperative hematologic management. Bleeding risk was assessed given the patient's prior history and a dosing timeline for administration of blood products and recombinant clotting factors was established. Successful management was achieved during the operation by prophylactic administration of HLA-matched PLTs and Factor VIIa. Prophylactic PLT administration was continued through the immediate postoperative period and no bleeding complications occurred. Thromboelastograms (TEGs) were used in conjunction with traditional hematologic laboratory analysis to optimize clinical management. CONCLUSION: Patients with GT requiring cardiac surgical procedures are at high risk for perioperative bleeding complications. This case report illustrates the importance of multidisciplinary planning, TEG analysis, and the judicious use of recombinant factors to minimize operative bleeding risk.


Asunto(s)
Estenosis de la Válvula Aórtica/complicaciones , Estenosis de la Válvula Aórtica/cirugía , Pérdida de Sangre Quirúrgica/prevención & control , Implantación de Prótesis de Válvulas Cardíacas , Trombastenia/complicaciones , Humanos , Masculino , Persona de Mediana Edad , Grupo de Atención al Paciente , Periodo Perioperatorio , Trombastenia/sangre , Resultado del Tratamiento
12.
J Card Surg ; 29(5): 733-6, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25039539

RESUMEN

Vena cava superior syndrome is a serious complication after heart transplantation, leading to low cardiac output, cerebral edema, and multi-organ dysfunction. We report three adult patients who underwent heart and heart-lung transplantation and required immediate postoperative balloon angioplasty and stent placement by interventional radiology. The observed obstructions were located at sites of intraoperatively removed pacemaker or defibrillator wires. Percutaneous stent placement immediately improved the hemodynamic condition of the patients. Early recognition of the complication and availability of immediate intervention are essential to prevent further deterioration.


Asunto(s)
Remoción de Dispositivos/efectos adversos , Procedimientos Endovasculares/métodos , Trasplante de Corazón , Marcapaso Artificial , Complicaciones Posoperatorias/cirugía , Stents , Síndrome de la Vena Cava Superior/cirugía , Vena Cava Superior/cirugía , Adulto , Angioplastia de Balón/métodos , Humanos , Masculino , Complicaciones Posoperatorias/etiología , Radiografía Intervencional , Síndrome de la Vena Cava Superior/etiología , Cirugía Asistida por Computador , Resultado del Tratamiento
13.
J Chem Theory Comput ; 2024 Jul 10.
Artículo en Inglés | MEDLINE | ID: mdl-38984825

RESUMEN

Computing free energy differences between metastable states characterized by nonoverlapping Boltzmann distributions is often a computationally intensive endeavor, usually requiring chains of intermediate states to connect them. Targeted free energy perturbation (TFEP) can significantly lower the computational cost of FEP calculations by choosing a set of invertible maps used to directly connect the distributions of interest, achieving the necessary statistically significant overlaps without sampling any intermediate states. Probabilistic generative models (PGMs) based on normalizing flow architectures can make it much easier via machine learning to train invertible maps needed for TFEP. However, the accuracy and applicability of approaches based on empirically learned maps depend crucially on the choice of reweighting method adopted to estimate the free energy differences. In this work, we assess the accuracy, rate of convergence, and data efficiency of different free energy estimators, including exponential averaging, Bennett acceptance ratio (BAR), and multistate Bennett acceptance ratio (MBAR), in reweighting PGMs trained by maximum likelihood on limited amounts of molecular dynamics data sampled only from end-states of interest. We carry out the comparisons on a set of simple but representative case studies, including conformational ensembles of alanine dipeptide and ibuprofen. Our results indicate that BAR and MBAR are both data efficient and robust, even in the presence of significant model overfitting in the generation of invertible maps. This analysis can serve as a stepping stone for the deployment of efficient and quantitatively accurate ML-based free energy calculation methods in complex systems.

14.
J Pharm Sci ; 2024 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-38936475

RESUMEN

For a pair of hydrated and anhydrous crystals, the hydrate is more stable than the anhydrate when the water activity is above the critical water activity (awc). Conventional methods to determine awc are based on either hydrate-anhydrate competitive slurries at different aw or solubilities measured at different temperatures. However, these methods are typically resource-intensive and time-consuming. Here, we present simple and complementary solution- and solid-based methods and illustrate them using carbamazepine and theophylline. In the solution-based method, awc can be predicted using intrinsic dissolution rate (IDR) ratio or solubility ratio of the hydrate-anhydrate pair measured at a known water activity. In the solid-based method, awc is predicted as a function of temperature from the dehydration temperature and enthalpy obtained by differential scanning calorimetry (DSC) near a water activity of unity. For carbamazepine and theophylline, the methods yielded awc values in good agreement with those from the conventional methods. By incorporating awc as an additional variable, the hydrate-anhydrate relationship is categorized into four classes based on their dehydration temperature (Td) and enthalpy (ΔHd) in analogy with the monotropy/enantiotropy classification for crystal polymorphs. In Class 1 (ΔHd< 0 and Td ≥ 373 K), no awc exists. In Class 2 (ΔHd>0andTd≥373K), awc always exists under conventional crystallization conditions. In Class 3 (ΔHd<0andTd<373K), awc exists when T>Td. In Class 4 (ΔHd>0andTd<373K), awc exists only when T

15.
Arterioscler Thromb Vasc Biol ; 32(1): 92-102, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-22034515

RESUMEN

OBJECTIVE: Clinical trials of bone marrow-derived stem cell therapy for the heart have yielded variable results. The basic mechanism(s) that underlies their potential efficacy remains unknown. In the present study, we evaluated the survival kinetics, transcriptional response, and functional outcome of intramyocardial bone marrow mononuclear cell (BMMC) transplantation for cardiac repair in a murine myocardial infarction model. METHODS AND RESULTS: We used bioluminescence imaging and high-throughput transcriptional profiling to evaluate the in vivo survival kinetics and gene expression changes of transplanted BMMCs after their engraftment into ischemic myocardium. Our results demonstrate short-lived survival of cells following transplant, with less than 1% of cells surviving by 6 weeks posttransplantation. Moreover, transcriptomic analysis of BMMCs revealed nonspecific upregulation of various cell regulatory genes, with a marked downregulation of cell differentiation and maturation pathways. BMMC therapy caused limited improvement of heart function as assessed by echocardiography, invasive hemodynamics, and positron emission tomography. Histological evaluation of cell fate further confirmed findings of the in vivo cell tracking and transcriptomic analysis. CONCLUSIONS: Collectively, these data suggest that BMMC therapy, in its present iteration, may be less efficacious than once thought. Additional refinement of existing cell delivery protocols should be considered to induce better therapeutic efficacy.


Asunto(s)
Trasplante de Células Madre Hematopoyéticas , Isquemia Miocárdica/terapia , Animales , Supervivencia Celular , Ecocardiografía , Femenino , Perfilación de la Expresión Génica , Genes Reporteros , Células Madre Hematopoyéticas/metabolismo , Células Madre Hematopoyéticas/patología , Humanos , Masculino , Ratones , Ratones Transgénicos , Isquemia Miocárdica/genética , Isquemia Miocárdica/patología , Isquemia Miocárdica/fisiopatología , Tomografía de Emisión de Positrones , Factores de Tiempo
16.
J Med Chem ; 66(23): 15883-15893, 2023 12 14.
Artículo en Inglés | MEDLINE | ID: mdl-38016916

RESUMEN

Early assessment of crystalline thermodynamic solubility continues to be elusive for drug discovery and development despite its critical importance, especially for the ever-increasing fraction of poorly soluble drug candidates. Here we present a detailed evaluation of a physics-based free energy perturbation (FEP+) approach for computing the thermodynamic aqueous solubility. The predictive power of this approach is assessed across diverse chemical spaces, spanning pharmaceutically relevant literature compounds and more complex AbbVie compounds. Our approach achieves predictive (RMSE = 0.86) and differentiating power (R2 = 0.69) and therefore provides notably improved correlations to experimental solubility compared to state-of-the-art machine learning approaches that utilize quantum mechanics-based descriptors. The importance of explicit considerations of crystalline packing in predicting solubility by the FEP+ approach is also highlighted in this study. Finally, we show how computed energetics, including hydration and sublimation free energies, can provide further insights into molecule design to feed the medicinal chemistry DMTA cycle.


Asunto(s)
Descubrimiento de Drogas , Agua , Solubilidad , Entropía , Termodinámica , Agua/química
17.
J Chem Theory Comput ; 18(9): 5725-5738, 2022 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-35930763

RESUMEN

Crystal structure prediction (CSP) is generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.


Asunto(s)
Algoritmos , Electricidad Estática
18.
JAMA Cardiol ; 7(11): 1160-1169, 2022 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-36197675

RESUMEN

Importance: The risk of adverse events from ascending thoracic aorta aneurysm (TAA) is poorly understood but drives clinical decision-making. Objective: To evaluate the association of TAA size with outcomes in nonsyndromic patients in a large non-referral-based health care delivery system. Design, Setting, and Participants: The Kaiser Permanente Thoracic Aortic Aneurysm (KP-TAA) cohort study was a retrospective cohort study at Kaiser Permanente Northern California, a fully integrated health care delivery system insuring and providing care for more than 4.5 million persons. Nonsyndromic patients from a regional TAA safety net tracking system were included. Imaging data including maximum TAA size were merged with electronic health record (EHR) and comprehensive death data to obtain demographic characteristics, comorbidities, medications, laboratory values, vital signs, and subsequent outcomes. Unadjusted rates were calculated and the association of TAA size with outcomes was evaluated in multivariable competing risk models that categorized TAA size as a baseline and time-updated variable and accounted for potential confounders. Data were analyzed from January 2018 to August 2021. Exposures: TAA size. Main Outcomes and Measures: Aortic dissection (AD), all-cause death, and elective aortic surgery. Results: Of 6372 patients with TAA identified between 2000 and 2016 (mean [SD] age, 68.6 [13.0] years; 2050 female individuals [32.2%] and 4322 male individuals [67.8%]), mean (SD) initial TAA size was 4.4 (0.5) cm (828 individuals [13.0% of cohort] had initial TAA size 5.0 cm or larger and 280 [4.4%] 5.5 cm or larger). Rates of AD were low across a mean (SD) 3.7 (2.5) years of follow-up (44 individuals [0.7% of cohort]; incidence 0.22 events per 100 person-years). Larger initial aortic size was associated with higher risk of AD and all-cause death in multivariable models, with an inflection point in risk at 6.0 cm. Estimated adjusted risks of AD within 5 years were 0.3% (95% CI, 0.3-0.7), 0.6% (95% CI, 0.4-1.3), 1.5% (95% CI, 1.2-3.9), 3.6% (95% CI, 1.8-12.8), and 10.5% (95% CI, 2.7-44.3) in patients with TAA size of 4.0 to 4.4 cm, 4.5 to 4.9 cm, 5.0 to 5.4 cm, 5.5 to 5.9 cm, and 6.0 cm or larger, respectively, in time-updated models. Rates of the composite outcome of AD and all-cause death were higher than for AD alone, but a similar inflection point for increased risk was observed at 6.0 cm. Conclusions and Relevance: In a large sociodemographically diverse cohort of patients with TAA, absolute risk of aortic dissection was low but increased with larger aortic sizes after adjustment for potential confounders and competing risks. Our data support current consensus guidelines recommending prophylactic surgery in nonsyndromic individuals with TAA at a 5.5-cm threshold.


Asunto(s)
Aneurisma de la Aorta Torácica , Disección Aórtica , Humanos , Masculino , Femenino , Anciano , Aneurisma de la Aorta Torácica/epidemiología , Aneurisma de la Aorta Torácica/cirugía , Estudios Retrospectivos , Estudios de Cohortes , Disección Aórtica/diagnóstico , Incidencia
19.
J Clin Invest ; 118(10): 3343-54, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18769630

RESUMEN

Apelin and its cognate G protein-coupled receptor APJ constitute a signaling pathway with a positive inotropic effect on cardiac function and a vasodepressor function in the systemic circulation. The apelin-APJ pathway appears to have opposing physiological roles to the renin-angiotensin system. Here we investigated whether the apelin-APJ pathway can directly antagonize vascular disease-related Ang II actions. In ApoE-KO mice, exogenous Ang II induced atherosclerosis and abdominal aortic aneurysm formation; we found that coinfusion of apelin abrogated these effects. Similarly, apelin treatment rescued Ang II-mediated increases in neointimal formation and vascular remodeling in a vein graft model. NO has previously been implicated in the vasodepressor function of apelin; we found that apelin treatment increased NO bioavailability in ApoE-KO mice. Furthermore, infusion of an NO synthase inhibitor blocked the apelin-mediated decrease in atherosclerosis and aneurysm formation. In rat primary aortic smooth muscle cells, apelin inhibited Ang II-mediated transcriptional regulation of multiple targets as measured by reporter assays. In addition, we demonstrated by coimmunoprecipitation and fluorescence resonance energy transfer analysis that the Ang II and apelin receptors interacted physically. Taken together, these findings indicate that apelin signaling can block Ang II actions in vascular disease by increasing NO production and inhibiting Ang II cellular signaling.


Asunto(s)
Angiotensina II/antagonistas & inhibidores , Aterosclerosis/fisiopatología , Proteínas Portadoras/metabolismo , Modelos Animales de Enfermedad , Transducción de Señal , Vasoconstrictores/antagonistas & inhibidores , Adipoquinas , Angiotensina II/farmacología , Antagonistas de Receptores de Angiotensina , Animales , Aneurisma de la Aorta Abdominal/mortalidad , Aneurisma de la Aorta Abdominal/fisiopatología , Apelina , Receptores de Apelina , Aterosclerosis/inducido químicamente , Aterosclerosis/metabolismo , Vasos Sanguíneos/metabolismo , Núcleo Celular/metabolismo , Dieta , Péptidos y Proteínas de Señalización Intercelular , Masculino , Ratones , Ratones Noqueados , Óxido Nítrico/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Receptores de Angiotensina/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Vasoconstrictores/farmacología
20.
Proc Natl Acad Sci U S A ; 105(35): 12991-6, 2008 Sep 02.
Artículo en Inglés | MEDLINE | ID: mdl-18728188

RESUMEN

Given their self-renewing and pluripotent capabilities, human embryonic stem cells (hESCs) are well poised as a cellular source for tissue regeneration therapy. However, the host immune response against transplanted hESCs is not well characterized. In fact, controversy remains as to whether hESCs have immune-privileged properties. To address this issue, we used in vivo bioluminescent imaging to track the fate of transplanted hESCs stably transduced with a double-fusion reporter gene consisting of firefly luciferase and enhanced GFP. We show that survival after transplant is significantly limited in immunocompetent as opposed to immunodeficient mice. Repeated transplantation of hESCs into immunocompetent hosts results in accelerated hESC death, suggesting an adaptive donor-specific immune response. Our data demonstrate that transplanted hESCs trigger robust cellular and humoral immune responses, resulting in intragraft infiltration of inflammatory cells and subsequent hESC rejection. Moreover, we have found CD4(+) T cells to be an important modulator of hESC immune-mediated rejection. Finally, we show that immunosuppressive drug regimens can mitigate the anti-hESC immune response and that a regimen of combined tacrolimus and sirolimus therapies significantly prolongs survival of hESCs for up to 28 days. Taken together, these data suggest that hESCs are immunogenic, trigger both cellular and humoral-mediated pathways, and, as a result, are rapidly rejected in xenogeneic hosts. This process can be mitigated by a combined immunosuppressive regimen as assessed by molecular imaging approaches.


Asunto(s)
Células Madre Embrionarias/inmunología , Rechazo de Injerto/inmunología , Rechazo de Injerto/terapia , Terapia de Inmunosupresión , Inmunoterapia , Trasplante de Células Madre , Trasplante Heterólogo , Animales , Formación de Anticuerpos/efectos de los fármacos , Linfocitos T CD4-Positivos/efectos de los fármacos , Linfocitos T CD4-Positivos/inmunología , Línea Celular , Supervivencia Celular/efectos de los fármacos , Células Madre Embrionarias/efectos de los fármacos , Genes Reporteros , Supervivencia de Injerto/efectos de los fármacos , Proteínas Fluorescentes Verdes/metabolismo , Humanos , Inmunidad Celular/efectos de los fármacos , Inmunocompetencia/efectos de los fármacos , Huésped Inmunocomprometido , Inmunosupresores/farmacología , Ratones , Transducción Genética
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