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Rath M, Wellnitz J, Martin HJ, Melo-Filho C, Hochuli JE, Silva GM, Beasley JM, Travis M, Sessions ZL, Popov KI, Zakharov AV, Cherkasov A, Alves V, Muratov EN, Tropsha A. Pharmacokinetics Profiler (PhaKinPro): Model Development, Validation, and Implementation as a Web Tool for Triaging Compounds with Undesired Pharmacokinetics Profiles. J Med Chem 2024; 67:6508-6518. [PMID: 38568752 DOI: 10.1021/acs.jmedchem.3c02446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Computational models that predict pharmacokinetic properties are critical to deprioritize drug candidates that emerge as hits in high-throughput screening campaigns. We collected, curated, and integrated a database of compounds tested in 12 major end points comprising over 10,000 unique molecules. We then employed these data to build and validate binary quantitative structure-activity relationship (QSAR) models. All trained models achieved a correct classification rate above 0.60 and a positive predictive value above 0.50. To illustrate their utility in drug discovery, we used these models to predict the pharmacokinetic properties for drugs in the NCATS Inxight Drugs database. In addition, we employed the developed models to predict the pharmacokinetic properties of all compounds in the DrugBank. All models described in this paper have been integrated and made publicly available via the PhaKinPro Web-portal that can be accessed at https://phakinpro.mml.unc.edu/.
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Affiliation(s)
- Marielle Rath
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - James Wellnitz
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Cleber Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Joshua E Hochuli
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Guilherme Martins Silva
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Jon-Michael Beasley
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Maxfield Travis
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Zoe L Sessions
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Konstantin I Popov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Vinicius Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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Jovanovic A, Xu B, Zhu C, Ren D, Wang H, Krause-Hauch M, Abel ED, Li J, Xiang YK. Characterizing Adrenergic Regulation of Glucose Transporter 4-Mediated Glucose Uptake and Metabolism in the Heart. JACC Basic Transl Sci 2023. [DOI: 10.1016/j.jacbts.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Li P, Jin C, Cui C, Cai P, Manohar SA, Jin L, Wei X, Pan S, Dixon RAF, Liu Q. Impact of family history of coronary artery disease on clinical outcomes in Takotsubo cardiomyopathy. J Investig Med 2022; 70:jim-2021-002186. [PMID: 35850971 DOI: 10.1136/jim-2021-002186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
Abstract
Family history of coronary artery disease (FHxCAD) is a critical risk factor for CAD, underscoring the contribution of genetic factors to disease pathogenesis and susceptibility. Takotsubo cardiomyopathy (TCM) simulates the clinical features of and frequently coexists with CAD. However, the association between FHxCAD and TCM is unclear. Here, we retrospectively examined the impact of FHxCAD on in-hospital outcomes of patients with TCM. Using the National Inpatient Sample database (2016-2018), we identified 4733 patients admitted to hospital with a primary diagnosis of TCM. We compared in-hospital outcomes and complications between TCM patients with (n=646, 13.7%) and without FHxCAD (n=646) in the unmatched and in a propensity-score matched cohort (1:1 ratio). TCM with FHxCAD patients had a reduced incidence of cardiogenic shock, acute kidney injury (AKI), and acute respiratory failure (ARF); lower mortality rates; shorter length of stay (LOS); and decreased total charge compared with TCM without FHxCAD patients (p<0.05). In the matched cohort, TCM with FHxCAD patients (vs TCM without FHxCAD patients) had a lower incidence of cardiogenic shock (2.2% vs 6.3%, p<0.001; OR 0.33, 95% CI 0.18 to 0.61), AKI (5.1% vs 8.7%, p=0.016; OR 0.57, 95% CI 0.36 to 0.88), and ARF (5.7% vs 12.7%, p<0.001; OR 0.42, 95% CI 0.28 to 0.63); decreased in-hospital mortality (<11% vs 3.1%, p=0.002; OR 0.2, 95% CI 0.07 to 0.57); shorter LOS (2.66±1.96 days vs 3.40±3.05 days, p<0.001); and a reduced total charge (p=0.001), respectively. FHxCAD was associated with favorable outcomes in both unmatched and propensity-matched cohorts.
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Affiliation(s)
- Pengyang Li
- Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Chengyue Jin
- Department of Medicine, Westchester Medical Center, Valhalla, New York, USA
| | - Can Cui
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Peng Cai
- Department of Mathematical Sciences, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Shamita Alisa Manohar
- Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Ling Jin
- Department of Medicine, Metrowest Medical Center, Framingham, Massachusetts, USA
| | - Xin Wei
- Division of Cardiology, Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Su Pan
- Wafic Said Molecular Cardiology Research Laboratory, Texas Heart Institute, Houston, Texas, USA
| | - Richard A F Dixon
- Wafic Said Molecular Cardiology Research Laboratory, Texas Heart Institute, Houston, Texas, USA
| | - Qi Liu
- Wafic Said Molecular Cardiology Research Laboratory, Texas Heart Institute, Houston, Texas, USA
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Genetic variability of five ADRB2 polymorphisms among Mexican Amerindian ethnicities and the Mestizo population. PLoS One 2019; 14:e0225030. [PMID: 31790415 PMCID: PMC6886845 DOI: 10.1371/journal.pone.0225030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
The Mexican population is characterized by high and particular admixture, and the picture of variants associated with disease remains unclear. Here we investigated the distribution of single nucleotide polymorphisms (SNPs) in the Mexican population. We focused on two non-synonymous and three synonymous SNPs in the beta-2 adrenergic receptor gene (ADRB2), which plays key roles in energy balance regulation. These SNPs were genotyped in 2,011 Mexican Amerindians (MAs) belonging to 62 ethnic groups and in 1,980 geographically matched Mexican Mestizos (MEZs). The frequency distribution of all five ADRB2 variants significantly differed between MAs, MEZs, and other continental populations (CPs) from the 1000 Genomes database. Allele frequencies of the three synonymous SNPs rs1042717A, rs1042718A, and rs1042719C were significantly higher in Mexican individuals, particularly among MAs, compared to in the other analyzed populations (P<0.05). The non-synonymous ADRB2 Glu27 allele (rs1042714G), which is associated with several common conditions, showed the lowest frequency in MAs (0.03) compared to other populations worldwide. Among MEZs, this allele showed a frequency of 0.15, intermediate between that in MAs and in Iberians (0.43). Moreover, Glu27 was the only SNP exhibiting a geographic gradient within the MEZ population (from 0.22 to 0.11), reflecting admixed mestizo ancestry across the country. Population differentiation analysis demonstrated that Glu27 had the highest FST value in MAs compared with Europeans (CEU) (0.71), and the lowest between MAs and Japanese (JPT) (0.01), even lower than that observed between MAs and MEZs (0.08). This analysis demonstrated the genetic diversity among Amerindian ethnicities, with the most extreme FST value (0.34) found between the Nahuatls from Morelos and the Seris. This is the first study of ADRB2 genetic variants among MA ethnicities. Our findings add to our understanding of the genetic contribution to variability in disease susceptibility in admixed populations.
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Xia K, Ding R, Zhang Z, Li W, Shang X, Yang X, Wang L, Zhang Q. The association of eight potentially functional polymorphisms in five adrenergic receptor-encoding genes with myocardial infarction risk in Han Chinese. Gene 2017; 624:43-49. [PMID: 28456594 DOI: 10.1016/j.gene.2017.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/20/2017] [Accepted: 04/25/2017] [Indexed: 12/26/2022]
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Zhao H, Wu X, Dong CL, Wang BY, Zhao J, Cao XE. Association Between ADRB2 Genetic Polymorphisms and the Risk of Chronic Obstructive Pulmonary Disease: A Case-Control Study in a Chinese Population. Genet Test Mol Biomarkers 2017; 21:491-496. [PMID: 28753063 DOI: 10.1089/gtmb.2017.0030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE This study was designed to investigate the association between single nucleotide polymorphisms (SNPs) of the β2-adrenergic receptor (ADRB2) gene and the risk of chronic obstructive pulmonary disease (COPD) in a Chinese population. METHODS From January 2010 to October 2014, 261 COPD patients were selected as the case group and 239 healthy subjects were selected as the control group. Pulmonary function tests were performed to detect forced vital capacity (FVC), 1-s forced expiratory volume (FEV1), and FEV1/FVC (%). rs1042711, rs1042714, and rs1042718 were selected as tagSNPs of the ADRB2 gene from the HapMap database in accordance with previous studies. The ADRB2 genotypes were established by real-time polymerase chain reaction assays using TaqMan-labeled probes. The relationships between the ADRB2 polymorphisms and COPD risk were estimated using logistic regression analyses. RESULTS The frequency of the genotypes and alleles of rs1042711 in ADRB2 showed a significant difference between the COPD and control groups (p < 0.05); compared with the CC genotype, the non-CC genotypes showed an increased COPD risk (p = 0.002). Compared with the CC haplotype, the TG haplotype increased COPD risk, while the CG haplotype reduced COPD risk for normal individuals. Compared with the CC genotype, the TT genotype showed significantly lower FEV1 and FEV1/FVC (p = 0.022, p = 0.0191, respectively). Both the TC and TG haplotypes showed lower FEV1 and FEV1/FVC in comparison with the CC haplotype (both p < 0.05). The results of logistic regression analysis showed that rs1042711 of ADRB2 and smoking history were associated with COPD risk (both p < 0.05). CONCLUSION It is indicated that the TT genotype of rs1042711 and smoking pack years are both risk factors for COPD.
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Affiliation(s)
- Hui Zhao
- 1 Department of Rheumatology, Linyi People's Hospital , Linyi, P.R. China
| | - Xuan Wu
- 2 Supply Room, Linyi People's Hospital , Linyi, P.R. China
| | - Chun-Ling Dong
- 3 Department of Nursing, Linyi People's Hospital , Linyi, P.R. China
| | - Bi-Ying Wang
- 4 Department of Geriatrics, Linyi People's Hospital , Linyi, P.R. China
| | - Jiao Zhao
- 4 Department of Geriatrics, Linyi People's Hospital , Linyi, P.R. China
| | - Xian-E Cao
- 4 Department of Geriatrics, Linyi People's Hospital , Linyi, P.R. China
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Eugene AR. A Clinical Trial Simulation Evaluating Epinephrine Pharmacokinetics at various Dosing Frequencies during Cardiopulmonary Resuscitation. MEDTUBE SCIENCE 2016; 4:8-15. [PMID: 28435854 PMCID: PMC5399886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE This article seeks to test the hypothesis that repeated 1mg intravenous epinephrine dosing intervals of 3-minutes and 5-minutes results in differences in the total drug exposure and the maximum epinephrine concentration using simulated cardiopulmonary resuscitation (CPR) dosing. METHODS Published population pharmacokinetic parameters were identified in the literature and pharmacokinetic dosing simulations were conducted according to the 2015 American Heart Association guidelines for CPR in adults. The stochastic pharmacokinetic simulations were conducted in MATLAB and R for statistical programming. RESULTS A total of 5000 simulations were conducted in MATLAB while 90,000 data points for the 3-minute dosing interval and 150,000 data points for the 5-minute epinephrine dosing interval resulted from pharmacokinetic simulations in R. The difference between the 3-minute and 5-minute dosing intervals for patients with a SAP score of 30, were found to be: Male ΔAUC=2416 and ΔCmax=71, Female ΔAUC=1422 and ΔCmax=41, and for a 70kg patient ΔAUC=2968 and ΔCmax=90. While in virtual healthy participants, the differences were calculated to be ΔAUC=2658 and ΔCmax=81 for 3-minute and 5-minute dosing frequencies. CONCLUSIONS Epinephrine plasma levels during a simulated CPR scenario in a virtual patient population are dependent upon intravenous dosing intervals of either 3-minutes or 5-minutes. Based on the results of this clinical trial simulation, implications may exist that may require clinical studies investigating the influence of the 1mg epinephrine dosing frequency on the return of spontaneous circulation.
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Affiliation(s)
- Andy R Eugene
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Gonda 19, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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