1
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Garzan A, Ahmed SK, Haese NN, Sulgey G, Medica S, Smith JL, Zhang S, Ahmad F, Karyakarte S, Rasmussen L, DeFilippis V, Tekwani B, Bostwick R, Suto MJ, Hirsch AJ, Morrison TE, Heise MT, Augelli-Szafran CE, Streblow DN, Pathak AK, Moukha-Chafiq O. 4-Substituted-2-Thiazole Amides as Viral Replication Inhibitors of Alphaviruses. J Med Chem 2024; 67:20858-20878. [PMID: 39621435 DOI: 10.1021/acs.jmedchem.4c01073] [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: 12/13/2024]
Abstract
2-(Methylthio)-N-(4-(naphthalen-2-yl)thiazol-2-yl)nicotinamide 1 was identified as an inhibitor against Chikungunya virus (CHIKV) with good antiviral activity [EC50 = 0.6 μM; EC90 = 0.93 μM and viral titer reduction (VTR) of 6.9 logs at 10 μM concentration] with no observed cytotoxicity (CC50 = 132 μM) in normal human dermal fibroblast (NHDF) cells. Structure-activity relationship (SAR) studies to further improve the potency, efficacy, and drug-like properties of 1 led to the discovery of a new potent inhibitor N-(4-(3-((4-cyanophenyl)amino)phenyl)thiazol-2-yl)-2-(methylthio)nicotinamide 26, which showed a VTR of 8.7 logs at 10 μM against CHIKV and an EC90 of 0.45 μM with considerably improved MLM stability (t1/2 = 74 min) as compared to 1. Mechanism of action studies show that 26 inhibits alphavirus replication by blocking subgenomic viral RNA translation and structural protein synthesis. The in vivo efficacy studies of compound 26 on CHIKV infection in mice are reported.
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Affiliation(s)
- Atefeh Garzan
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - S Kaleem Ahmed
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Nicole N Haese
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Gauthami Sulgey
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Samuel Medica
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Jessica L Smith
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Sixue Zhang
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Fahim Ahmad
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Shuklendu Karyakarte
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Lynn Rasmussen
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Victor DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Babu Tekwani
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert Bostwick
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Mark J Suto
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Alec J Hirsch
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Thomas E Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19th Avenue, Aurora, Colorado 80045, United States
| | - Mark T Heise
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Corinne E Augelli-Szafran
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Daniel N Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, Oregon 97006, United States
| | - Ashish K Pathak
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Omar Moukha-Chafiq
- Scientific Platforms Division, Southern Research, 2000 ninth Avenue South, Birmingham, Alabama 35205, United States
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2
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Ma Y, Chen X, Javeria H, Du Z. High-throughput screening of LogD by using a sample pooling approach based on the traditional shake flask method. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1227:123804. [PMID: 37393793 DOI: 10.1016/j.jchromb.2023.123804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023]
Abstract
A new approach for screening LogD is presented. The method is based on the shake flask method combined with rapid generic LC-MS/MS bioanalysis by using a sample pooling approach that enables high-throughput screening of LogD or LogP in the drug discovery stage. The method is evaluated by a comparison of measured LogD between single and pooled compounds for a test set of structurally diverse compounds with a wide range of LogD values (from -0.04 to 6.01). Test compounds include 10 commercially available drug standards along with 27 new chemical entities. A good correlation (RMSE = 0.21, R2 = 0.9879) of LogD between the single and pooled compounds was obtained, suggesting that at least 37 compounds can be simultaneously measured with acceptable accuracy. The sample pooling method significantly reduced the number of bioanalysis samples as compared to the single compound measurement by the conventional shake flask method. The impact of DMSO content on LogD measurement was also investigated and the result demonstrated that at least 0.5% DMSO was tolerated in this method. The current new development will facilitate the drug discovery process by more rapidly assessing the LogD or LogP of drug candidates.
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Affiliation(s)
- Yongfen Ma
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaowei Chen
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 117004, Liaoning, China
| | - Huma Javeria
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhenxia Du
- College of Chemistry, Beijing Key Laboratory of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing 100029, China.
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3
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Valli M, Souza JM, Chelucci RC, Biasetto CR, Araujo AR, Bolzani VDS, Andricopulo AD. Identification of natural cytochalasins as leads for neglected tropical diseases drug discovery. PLoS One 2022; 17:e0275002. [PMID: 36190979 PMCID: PMC9529094 DOI: 10.1371/journal.pone.0275002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Investigating the chemical diversity of natural products from tropical environments is an inspiring approach to developing new drug candidates for neglected tropical diseases (NTDs). In the present study, phenotypic screenings for antiprotozoal activity and a combination of computational and biological approaches enabled the identification and characterization of four cytochalasins, which are fungal metabolites from Brazilian biodiversity sources. Cytochalasins A-D exhibited IC50 values ranging from 2 to 20 μM against intracellular Trypanosoma cruzi and Leishmania infantum amastigotes, values comparable to those of the standard drugs benznidazole and miltefosine for Chagas disease and leishmaniasis, respectively. Furthermore, cytochalasins A-D reduced L. infantum infections by more than 80% in THP-1 cells, most likely due to the inhibition of phagocytosis by interactions with actin. Molecular modelling studies have provided useful insights into the mechanism of action of this class of compounds. Furthermore, cytochalasins A-D showed moderate cytotoxicity against normal cell lines (HFF-1, THP-1, and HepG2) and a good overall profile for oral bioavailability assessed in vitro. The results of this study support the use of natural products from Brazilian biodiversity sources to find potential drug candidates for two of the most important NTDs.
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Affiliation(s)
- Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
| | - Julia Medeiros Souza
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Rafael Consolin Chelucci
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
| | - Carolina Rabal Biasetto
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Angela Regina Araujo
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
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4
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Pauli I, Rezende CDO, Slafer BW, Dessoy MA, de Souza ML, Ferreira LLG, Adjanohun ALM, Ferreira RS, Magalhães LG, Krogh R, Michelan-Duarte S, Del Pintor RV, da Silva FBR, Cruz FC, Dias LC, Andricopulo AD. Multiparameter Optimization of Trypanocidal Cruzain Inhibitors With In Vivo Activity and Favorable Pharmacokinetics. Front Pharmacol 2022; 12:774069. [PMID: 35069198 PMCID: PMC8767159 DOI: 10.3389/fphar.2021.774069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cruzain, the main cysteine protease of Trypanosoma cruzi, plays key roles in all stages of the parasite's life cycle, including nutrition acquisition, differentiation, evasion of the host immune system, and invasion of host cells. Thus, inhibition of this validated target may lead to the development of novel drugs for the treatment of Chagas disease. In this study, a multiparameter optimization (MPO) approach, molecular modeling, and structure-activity relationships (SARs) were employed for the identification of new benzimidazole derivatives as potent competitive inhibitors of cruzain with trypanocidal activity and suitable pharmacokinetics. Extensive pharmacokinetic studies enabled the identification of metabolically stable and permeable compounds with high selectivity indices. CYP3A4 was found to be involved in the main metabolic pathway, and the identification of metabolic soft spots provided insights into molecular optimization. Compound 28, which showed a promising trade-off between pharmacodynamics and pharmacokinetics, caused no acute toxicity and reduced parasite burden both in vitro and in vivo.
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Affiliation(s)
- Ivani Pauli
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Celso de O Rezende
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Brian W Slafer
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marco A Dessoy
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Mariana L de Souza
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Leonardo L G Ferreira
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Abraham L M Adjanohun
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafaela S Ferreira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luma G Magalhães
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Renata Krogh
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Simone Michelan-Duarte
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | | | | | - Fabio C Cruz
- Departamento de Farmacologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Adriano D Andricopulo
- Laboratório de Química Medicinal e Computacional, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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5
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Ahmed SK, Haese NN, Cowan JT, Pathak V, Moukha-Chafiq O, Smith VJ, Rodzinak KJ, Ahmad F, Zhang S, Bonin KM, Streblow AD, Streblow CE, Kreklywich CN, Morrison C, Sarkar S, Moorman N, Sander W, Allen R, DeFilippis V, Tekwani BL, Wu M, Hirsch AJ, Smith JL, Tower NA, Rasmussen L, Bostwick R, Maddry JA, Ananthan S, Gerdes JM, Augelli-Szafran CE, Suto MJ, Morrison TE, Heise MT, Streblow DN, Pathak AK. Targeting Chikungunya Virus Replication by Benzoannulene Inhibitors. J Med Chem 2021; 64:4762-4786. [PMID: 33835811 PMCID: PMC9774970 DOI: 10.1021/acs.jmedchem.0c02183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A benzo[6]annulene, 4-(tert-butyl)-N-(3-methoxy-5,6,7,8-tetrahydronaphthalen-2-yl) benzamide (1a), was identified as an inhibitor against Chikungunya virus (CHIKV) with antiviral activity EC90 = 1.45 μM and viral titer reduction (VTR) of 2.5 log at 10 μM with no observed cytotoxicity (CC50 = 169 μM) in normal human dermal fibroblast cells. Chemistry efforts to improve potency, efficacy, and drug-like properties of 1a resulted in a novel lead compound 8q, which possessed excellent cellular antiviral activity (EC90 = 270 nM and VTR of 4.5 log at 10 μM) and improved liver microsomal stability. CHIKV resistance to an analog of 1a, compound 1c, tracked to a mutation in the nsP3 macrodomain. Further mechanism of action studies showed compounds working through inhibition of human dihydroorotate dehydrogenase in addition to CHIKV nsP3 macrodomain. Moderate efficacy was observed in an in vivo CHIKV challenge mouse model for compound 8q as viral replication was rescued from the pyrimidine salvage pathway.
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Affiliation(s)
| | | | - Jaden T. Cowan
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Vibha Pathak
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Omar Moukha-Chafiq
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Valerie J. Smith
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Kevin J. Rodzinak
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Fahim Ahmad
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Sixue Zhang
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Kiley M. Bonin
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Aaron D. Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Cassilyn E. Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Craig N. Kreklywich
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Clayton Morrison
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Sanjay Sarkar
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Nathaniel Moorman
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Wes Sander
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Robbie Allen
- Oregon Translational Research and Development Institute, Portland, Oregon 97239, United States
| | - Victor DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Babu L. Tekwani
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Mousheng Wu
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Alec J. Hirsch
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Jessica L. Smith
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Nichole A. Tower
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Lynn Rasmussen
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Robert Bostwick
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Joseph A. Maddry
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Subramaniam Ananthan
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - John M Gerdes
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | | | - Mark J. Suto
- Drug Discovery Division, Southern Research, Birmingham, Alabama 35205, United States
| | - Thomas E. Morrison
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Mark T. Heise
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Daniel N. Streblow
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon 97006, United States
| | - Ashish K. Pathak
- Drug Discovery Division, Southern, Research, Birmingham, Alabama 35205, United States
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6
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Artificial intelligence in the early stages of drug discovery. Arch Biochem Biophys 2020; 698:108730. [PMID: 33347838 DOI: 10.1016/j.abb.2020.108730] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Although the use of computational methods within the pharmaceutical industry is well established, there is an urgent need for new approaches that can improve and optimize the pipeline of drug discovery and development. In spite of the fact that there is no unique solution for this need for innovation, there has recently been a strong interest in the use of Artificial Intelligence for this purpose. As a matter of fact, not only there have been major contributions from the scientific community in this respect, but there has also been a growing partnership between the pharmaceutical industry and Artificial Intelligence companies. Beyond these contributions and efforts there is an underlying question, which we intend to discuss in this review: can the intrinsic difficulties within the drug discovery process be overcome with the implementation of Artificial Intelligence? While this is an open question, in this work we will focus on the advantages that these algorithms provide over the traditional methods in the context of early drug discovery.
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7
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Wang X, Liu M, Zhang L, Wang Y, Li Y, Lu T. Optimizing Pharmacokinetic Property Prediction Based on Integrated Datasets and a Deep Learning Approach. J Chem Inf Model 2020; 60:4603-4613. [PMID: 32804486 DOI: 10.1021/acs.jcim.0c00568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oral bioavailability (OBA)-related pharmacokinetic properties, such as aqueous solubility, lipophilicity, and intestinal membrane permeability, play a significant role in drug discovery. However, their measurement is usually costly and time-consuming. Therefore, prediction models based on diverse approaches have been established in recent decades. Computational prediction of molecular properties has become an important step in drug discovery, aiming to identify potential drug-like candidates and reduce costs. However, limitations related to dataset capacity and algorithm adaptation still place restrictions on the applicability of the related models. In this study, we considered both dataset and algorithm optimization to address the challenge of predicting OBA-related molecular properties. Benchmark datasets of aqueous solubility (log S), lipophilicity (log D), and membrane permeability measured using the Caco-2 cell line (log Papp) were constructed by merging and calibrating experimental data from diverse articles and databases. Then, a novel molecular property prediction model, called a multiembedding-based synthetic network (MESN), was generated by applying a deep learning algorithm based on the synthesis of multiple types of molecular embeddings. MESN achieves performance improvements over other state-of-the-art methods for the prediction of aqueous solubility, lipophilicity, and membrane permeability. Results were also obtained using several other algorithms and independent validation datasets as a control study. Moreover, a dimension reduction analysis (based on t-distributed stochastic neighbor embedding, t-SNE) and an atomic feature similarity analysis showed that the molecular embeddings extracted from the MESN model exhibit good clustering and diversity. Overall, considering the fundamental role of the data and the superior prediction performance of the model, we highlight the applicability of MESN on benchmark datasets for further utility in drug discovery-related molecular property prediction.
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Affiliation(s)
- Xiting Wang
- Life Science School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Meng Liu
- Chinese Medicine School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lan Zhang
- Chinese Medicine School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yun Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yu Li
- Chinese Medicine School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Tao Lu
- Life Science School, Beijing University of Chinese Medicine, Beijing 100029, China
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8
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Fu L, Liu L, Yang ZJ, Li P, Ding JJ, Yun YH, Lu AP, Hou TJ, Cao DS. Systematic Modeling of log D7.4 Based on Ensemble Machine Learning, Group Contribution, and Matched Molecular Pair Analysis. J Chem Inf Model 2019; 60:63-76. [DOI: 10.1021/acs.jcim.9b00718] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Li Fu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Lu Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Pan Li
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, P. R. China
| | - Jun-Jie Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing 102205, P. R. China
| | - Yong-Huan Yun
- College of Food Science and Engineering, Hainan University, Haikou 570228, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R. China
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9
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Miniaturized shake-flask HPLC method for determination of distribution coefficient of drugs used in inflammatory bowel diseases. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2019; 69:649-660. [PMID: 31639082 DOI: 10.2478/acph-2019-0046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/09/2019] [Indexed: 01/19/2023]
Abstract
A new method for determination of distribution coefficient of drugs azathioprine, 6-mercaptopurine and 6-thioguanine and nutrient folic acid used in the treatment of inflammatory bowel disease based on a miniaturized shake-flask and HPLC/DAD was developed. Special attention was made to the most commonly reported problems in the measurement of distribution coefficients using a shake-flask method such as mixing technique, speed and time, the temperature of experiment, type of buffer and its pH as well as n-octanol/buffer phase ratio. The concentration of compounds in the buffer is determined by HPLC directly from shake flasks or conventional 2-mL vials. The developed method was fully validated according to ICH guidelines. Furthermore, experimental data were successfully compared with lipophilicity and human intestinal absorption calculated by the use of four different theoretical approaches. The method shows potential for high-throughput measurements of a large number of compounds.
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10
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Degorce SL, Bodnarchuk MS, Scott JS. Lowering Lipophilicity by Adding Carbon: AzaSpiroHeptanes, a log D Lowering Twist. ACS Med Chem Lett 2019; 10:1198-1204. [PMID: 31417667 DOI: 10.1021/acsmedchemlett.9b00248] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022] Open
Abstract
We have conducted an analysis of azaspiro[3.3]heptanes used as replacements for morpholines, piperidines, and piperazines in a medicinal chemistry context. In most cases, introducing a spirocyclic center lowered the measured logD 7.4 of the corresponding molecules by as much as -1.0 relative to the more usual heterocycle. This may seem counterintuitive, as the net change in the molecule is the addition of a single carbon atom, but it may be rationalized in terms of increased basicity. An exception to this was found with N-linked 2-azaspiro[3.3]heptane, where logD 7.4 increased by as much as +0.5, consistent with the addition of carbon. During our investigation, we also concluded that azaspiro[3.3]heptanes are most likely not suitable bioisosteres for morpholines, piperidines, and piperazines, when not used as terminal groups, due to significant changes in their geometry.
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Affiliation(s)
- Sébastien L. Degorce
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - Michael S. Bodnarchuk
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
| | - James S. Scott
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge Science Park, Unit 310 Darwin Building, Cambridge CB4 0WG, United Kingdom
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11
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di Cagno MP, Stein PC. Studying the effect of solubilizing agents on drug diffusion through the unstirred water layer (UWL) by localized spectroscopy. Eur J Pharm Biopharm 2019; 139:205-212. [DOI: 10.1016/j.ejpb.2019.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 01/17/2023]
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12
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Kempińska D, Chmiel T, Kot-Wasik A, Mróz A, Mazerska Z, Namieśnik J. State of the art and prospects of methods for determination of lipophilicity of chemical compounds. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.01.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Monolith weak affinity chromatography for μg-protein-ligand interaction study. J Pharm Biomed Anal 2019; 166:164-173. [DOI: 10.1016/j.jpba.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/17/2022]
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14
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(Pyrrolo-pyridin-5-yl)benzamides: BBB permeable monoamine oxidase B inhibitors with neuroprotective effect on cortical neurons. Eur J Med Chem 2019; 162:793-809. [DOI: 10.1016/j.ejmech.2018.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/06/2023]
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15
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PSMA-Oriented Target Delivery of Novel Anticancer Prodrugs: Design, Synthesis, and Biological Evaluations of Oligopeptide-Camptothecin Conjugates. Int J Mol Sci 2018; 19:ijms19103251. [PMID: 30347770 PMCID: PMC6214026 DOI: 10.3390/ijms19103251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/09/2018] [Accepted: 10/14/2018] [Indexed: 01/18/2023] Open
Abstract
Clinical applications of camptothecin (CPT) have been heavily hindered due to its non-targeted toxicity, active lactone ring instability, and poor water solubility. Targeted drug delivery systems may offer the possibility to overcome the above issues as reported. In this research, a series of prostate-specific membrane antigen (PSMA)-activated CPT prodrugs were designed and synthesized by coupling water-soluble pentapeptide, a PSMA hydrolyzing substrate, to CPT through an appropriate linker. The cytotoxicity of CPT prodrugs was masked temporarily until they were hydrolyzed by the PSMA present within the tumor sites, which restored cytotoxicity. The in vitro selective cytotoxic activities of the prodrugs were evaluated against PSMA-expressing human prostate cancer cells LNCaP-FGC and non-PSMA-expressing cancer cells HepG2, Hela, MCF-7, DU145, PC-3 and normal cells MDCK, LO2 by standard methylthiazol tetrazolium (MTT) assay. Most of the newly synthesized CPT prodrugs showed excellent selective toxicity to PSMA-producing prostate cancer cells LNCaP-FGC with improved water solubility. From among the library, CPT-HT-J-ZL12 showed the best cytotoxic selectivity between the PSMA-expressing and the non-PSMA-expressing cancer cells. For example, the cytotoxicity of CPT-HT-J-ZL12 (IC50 = 1.00 ± 0.20 µM) against LNCaP-FGC (PSMA+) was 40-fold, 40-fold, 21-fold, 5-fold and 40-fold, respectively, higher than that against the non-PSMA-expressing cells HepG2 (IC50 > 40.00 µM), Hela (IC50 > 40.00 µM), MCF-7 (IC50 = 21.68 ± 4.96 µM), DU145 (IC50 = 5.40 ± 1.22 µM), PC-3 (IC50 = 42.96 ± 3.69 µM) cells. Moreover, CPT-HT-J-ZL12 exhibited low cytotoxicity (IC50 > 40 μM) towards MDCK and LO2 cells. The cellular uptake experiment demonstrated the superior PSMA-targeting ability of the CPT-HT-J-ZL12, which was significantly accumulated in LNCaP-FGC (PSMA+), while it was minimized in HepG2 (PSMA−) cells. Further cell apoptosis analyses indicated that it showed a dramatically higher apoptosis-inducing activity in LNCaP-FGC (PSMA+) cells than in HepG2 (PSMA−) cells. Cell cycle analysis indicated that CPT-HT-J-ZL12 could induce cell cycle arrest at the S phase.
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16
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Mora MJ, Onnainty R, Granero GE. Comparative Oral Drug Classification Systems: Acetazolamide, Azithromycin, Clopidogrel, and Efavirenz Case Studies. Mol Pharm 2018; 15:3187-3196. [DOI: 10.1021/acs.molpharmaceut.8b00274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Maria Julia Mora
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000-HUA Córdoba, Argentina
| | - Renée Onnainty
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000-HUA Córdoba, Argentina
| | - Gladys Ester Granero
- Unidad de Investigación y Desarrollo en Tecnología Farmacéutica (UNITEFA), CONICET and Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000-HUA Córdoba, Argentina
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17
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Lapins M, Arvidsson S, Lampa S, Berg A, Schaal W, Alvarsson J, Spjuth O. A confidence predictor for logD using conformal regression and a support-vector machine. J Cheminform 2018; 10:17. [PMID: 29616425 PMCID: PMC5882484 DOI: 10.1186/s13321-018-0271-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/25/2018] [Indexed: 02/03/2023] Open
Abstract
Lipophilicity is a major determinant of ADMET properties and overall suitability of drug candidates. We have developed large-scale models to predict water–octanol distribution coefficient (logD) for chemical compounds, aiding drug discovery projects. Using ACD/logD data for 1.6 million compounds from the ChEMBL database, models are created and evaluated by a support-vector machine with a linear kernel using conformal prediction methodology, outputting prediction intervals at a specified confidence level. The resulting model shows a predictive ability of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {Q}^{2}=0.973$$\end{document}Q2=0.973 and with the best performing nonconformity measure having median prediction interval of \documentclass[12pt]{minimal}
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\begin{document}$$\pm ~0.39$$\end{document}±0.39 log units at 80% confidence and \documentclass[12pt]{minimal}
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\begin{document}$$\pm ~0.60$$\end{document}±0.60 log units at 90% confidence. The model is available as an online service via an OpenAPI interface, a web page with a molecular editor, and we also publish predictive values at 90% confidence level for 91 M PubChem structures in RDF format for download and as an URI resolver service.![]()
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Affiliation(s)
- Maris Lapins
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Staffan Arvidsson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Arvid Berg
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Wesley Schaal
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Jonathan Alvarsson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden.
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18
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Lipophilicity Studies on Thiosemicarbazide Derivatives. Molecules 2017; 22:molecules22060952. [PMID: 28594381 PMCID: PMC6152747 DOI: 10.3390/molecules22060952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/01/2017] [Indexed: 12/21/2022] Open
Abstract
The lipophilicity of two series of thiosemicarbazide derivatives was assessed by the RP-HPLC method with the RP-18 chromatographic column and the methanol–water mixture as the mobile phase. Distribution coefficients logPHPLC were compared to calculated values generated by commonly used AClogP software and quantum chemical calculations. The reliability of the predictions was evaluated using the correlation matrix and PCA. For 4-benzoylthiosemicarbazides, a high correlation between theoretical and experimental logP parameters was obtained using the XlogP3 algorithm, while for 4-aryl/(cyclohexyl)thiosemicarbazides, the XlogP2 parameter was strongly correlated with the experimentally obtained logP.
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19
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Bowles S, Joubert E, de Beer D, Louw J, Brunschwig C, Njoroge M, Lawrence N, Wiesner L, Chibale K, Muller C. Intestinal Transport Characteristics and Metabolism of C-Glucosyl Dihydrochalcone, Aspalathin. Molecules 2017; 22:molecules22040554. [PMID: 28358310 PMCID: PMC6154319 DOI: 10.3390/molecules22040554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022] Open
Abstract
Insight into the mechanisms of intestinal transport and metabolism of aspalathin will provide important information for dose optimisation, in particular for studies using mouse models. Aspalathin transportation across the intestinal barrier (Caco-2 monolayer) tested at 1–150 µM had an apparent rate of permeability (Papp) typical of poorly absorbed compounds (1.73 × 10−6 cm/s). Major glucose transporters, sodium glucose linked transporter 1 (SGLT1) and glucose transporter 2 (GLUT2), and efflux protein (P-glycoprotein, PgP) (1.84 × 10−6 cm/s; efflux ratio: 1.1) were excluded as primary transporters, since the Papp of aspalathin was not affected by the presence of specific inhibitors. The Papp of aspalathin was also not affected by constituents of aspalathin-enriched rooibos extracts, but was affected by high glucose concentration (20.5 mM), which decreased the Papp value to 2.9 × 10−7 cm/s. Aspalathin metabolites (sulphated, glucuronidated and methylated) were found in mouse urine, but not in blood, following an oral dose of 50 mg/kg body weight of the pure compound. Sulphates were the predominant metabolites. These findings suggest that aspalathin is absorbed and metabolised in mice to mostly sulphate conjugates detected in urine. Mechanistically, we showed that aspalathin is not actively transported by the glucose transporters, but presumably passes the monolayer paracellularly.
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Affiliation(s)
- Sandra Bowles
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7130, South Africa.
| | - Elizabeth Joubert
- Plant Bioactives Group, Post-Harvest and Wine Technology Division, Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch 7600, South Africa.
- Department of Food Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Dalene de Beer
- Plant Bioactives Group, Post-Harvest and Wine Technology Division, Agricultural Research Council, Infruitec-Nietvoorbij, Stellenbosch 7600, South Africa.
- Department of Food Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7130, South Africa.
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa 3886, South Africa.
| | - Christel Brunschwig
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa.
- Division of Clinical Pharmacology, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Mathew Njoroge
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa.
- Division of Clinical Pharmacology, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Nina Lawrence
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa.
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa.
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa.
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
- South African Medical Research Council Drug, Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa.
| | - Christo Muller
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, Cape Town 7130, South Africa.
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa 3886, South Africa.
- Department of Medical Physiology, Stellenbosch University, Tygerberg 7507, South Africa.
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20
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Optimised method to estimate octanol water distribution coefficient (logD) in a high throughput format. Eur J Pharm Sci 2016; 92:110-6. [DOI: 10.1016/j.ejps.2016.06.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/10/2016] [Accepted: 06/28/2016] [Indexed: 11/22/2022]
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21
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Brown DG. A Medicinal Chemistry Perspective on the Hit‐to‐Lead Phase in the Current Era of Drug Discovery. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/9783527677047.ch12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Engesland A, Škalko-Basnet N, Flaten GE. In vitro models to estimate drug penetration through the compromised stratum corneum barrier. Drug Dev Ind Pharm 2016; 42:1742-51. [PMID: 27019078 DOI: 10.3109/03639045.2016.1171334] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The phospholipid vesicle-based permeation assay (PVPA) is a recently established in vitro stratum corneum model to estimate the permeability of intact and healthy skin. The aim here was to further evolve this model to mimic the stratum corneum in a compromised skin barrier by reducing the barrier functions in a controlled manner. METHODS To mimic compromised skin barriers, PVPA barriers were prepared with explicitly defined reduced barrier function and compared with literature data from both human and animal skin with compromised barrier properties. Caffeine, diclofenac sodium, chloramphenicol and the hydrophilic marker calcein were tested to compare the PVPA models with established models. RESULTS AND DISCUSSIONS The established PVPA models mimicking the stratum corneum in healthy skin showed good correlation with biological barriers by ranking drugs similar to those ranked by the pig ear skin model and were comparable to literature data on permeation through healthy human skin. The PVPA models provided reproducible and consistent results with a distinction between the barriers mimicking compromised and healthy skin. The trends in increasing drug permeation with an increasing degree of compromised barriers for the model drugs were similar to the literature data from other in vivo and in vitro models. CONCLUSIONS The PVPA models have the potential to provide permeation predictions when investigating drugs or cosmeceuticals intended for various compromised skin conditions and can thus possibly reduce the time and cost of testing as well as the use of animal testing in the early development of drug candidates, drugs and cosmeceuticals.
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Affiliation(s)
- André Engesland
- a Department of Pharmacy, Drug Transport and Delivery Research Group , University of Tromsø The Arctic University of Norway , Tromsø , N-9037 , Norway
| | - Nataša Škalko-Basnet
- a Department of Pharmacy, Drug Transport and Delivery Research Group , University of Tromsø The Arctic University of Norway , Tromsø , N-9037 , Norway
| | - Gøril Eide Flaten
- a Department of Pharmacy, Drug Transport and Delivery Research Group , University of Tromsø The Arctic University of Norway , Tromsø , N-9037 , Norway
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23
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The microscale flocculation test (MFT)—A high-throughput technique for optimizing separation performance. Chem Eng Res Des 2016. [DOI: 10.1016/j.cherd.2015.10.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Xu B, Chu F, Zhang Y, Wang X, Li Q, Liu W, Xu X, Xing Y, Chen J, Wang P, Lei H. A Series of New Ligustrazine-Triterpenes Derivatives as Anti-Tumor Agents: Design, Synthesis, and Biological Evaluation. Int J Mol Sci 2015; 16:21035-55. [PMID: 26404253 PMCID: PMC4613240 DOI: 10.3390/ijms160921035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/11/2023] Open
Abstract
A series of novel ligustrazine-triterpenes derivatives was designed, synthesized and screened for their cytotoxicity against five cancer cell lines (Bel-7402, HepG2, HT-29, Hela, and MCF-7) and Madin-Darby canine kidney (MDCK). Current study suggested that most of the ligustrazine-triterpenes conjunctions showed better cytotoxicity than the starting materials. In particular, compound 4a exhibited better cytotoxic activity (IC50 < 5.23 μM) against Bel-7402, HT-29, MCF-7, Hela, and HepG2 than the standard anticancer drug cisplatin (DDP). The cytotoxicity selectivity detection revealed that 4a exhibited low cytotoxicity (IC50 > 20 μM) towards MDCK cells. A combination of fluorescence staining observation and flow cytometric analysis indicated that 4a could induce HepG2 cell apoptosis. Further studies suggested that 4a-induced apoptosis is mediated through depolarization of the mitochondrial membrane potential and increase of intracellular free Ca2+ concentration. In addition, the structure-activity relationships of these derivatives were briefly discussed.
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Affiliation(s)
- Bing Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Fuhao Chu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yuzhong Zhang
- Department of Pathology, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xiaobo Wang
- Center of Scientific Experiment, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Qiang Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Wei Liu
- School of Management, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Xin Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Yanyi Xing
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Jing Chen
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Penglong Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
| | - Haimin Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 100102, China.
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25
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Colclough N, Wenlock MC. Interpreting physicochemical experimental data sets. J Comput Aided Mol Des 2015; 29:779-94. [PMID: 26054297 DOI: 10.1007/s10822-015-9850-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/29/2015] [Indexed: 12/01/2022]
Abstract
With the wealth of experimental physicochemical data available to chemoinformaticians from the literature, commercial, and company databases an increasing challenge is the interpretation of such datasets. Subtle differences in experimental methodology used to generate these datasets can give rise to variations in physicochemical property values. Such methodology nuances will be apparent to an expert experimentalist but not necessarily to the data analyst and modeller. This paper describes the differences between common methodologies for measuring the four most important physicochemical properties namely aqueous solubility, octan-1-ol/water distribution coefficient, pK(a) and plasma protein binding highlighting key factors that can lead to systematic differences. Insight is given into how to identify datasets suitable for combining.
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Affiliation(s)
- Nicola Colclough
- Oncology and Drug Safety and Metabolism, Innovative Medicines, Mereside, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
| | - Mark C Wenlock
- Oncology and Drug Safety and Metabolism, Innovative Medicines, Mereside, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
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26
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Abay ET, van der Westuizen JH, Swart KJ, Gibhard L, Lawrence N, Dambuza N, Wilhelm A, Pravin K, Wiesner L. Efficacy and pharmacokinetic evaluation of a novel anti-malarial compound (NP046) in a mouse model. Malar J 2015; 14:8. [PMID: 25563929 PMCID: PMC4326489 DOI: 10.1186/1475-2875-14-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/17/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Even though malaria is a completely preventable and treatable disease, it remains a threat to human life and a burden to the global economy due to the emergence of multiple-drug resistant malaria parasites. According to the World Malaria Report 2013, in 2012 there were an estimated 207 million malaria cases and 627,000 deaths. Thus, the discovery and development of new, effective anti-malarial drugs are required. To achieve this goal, the Department of Chemistry at the University of the Free State has synthesized a number of novel amino-alkylated chalcones and analogues, which showed in vitro anti-malarial activity against both chloroquine-sensitive and chloroquine-resistant Plasmodium falciparum strains. The lead compound (NP046) was selected for a comprehensive pharmacokinetic (PK) and in vivo efficacy evaluation in a mouse model. METHODS In vivo efficacy: Water solutions of NP046 were administered orally at 50 and 10 mg/kg using oral gavage and IV at 5 and 1 mg/kg via the dorsal penile vein to Plasmodium berghei (ANKA strain) infected male C57BL/6 mice (n = 5), once a day for four days. Blood samples were collected via tail bleeding in tubes containing phosphate buffer saline (PBS) on day five to determine the % parasitaemia by flow cytometry.In vivo PK: NP046 solutions in water were administered orally (50 and 10 mg/kg) and IV (5 mg/kg) to male C57BL/6 mice (n = 5). Blood samples were collected via tail bleeding into heparinized tubes and analysed using a validated LC-MS/MS assay. Data obtained from the concentration-time profile was evaluated using Summit PK software to determine the PK parameters of NP046. RESULTS NP046 inhibited parasite growth for the oral and IV groups. Better parasite growth inhibition was observed for the IV group. The PK evaluation of NP046 showed low oral bioavailability (3.2% and 6% at 50 mg/kg and 10 mg/kg dose, respectively and a moderate mean half-life ranging from 3.1 to 4.4 hours. CONCLUSION Even though the oral bioavailability of NP046 is low, its percentage parasite growth inhibition is promising, but in order to improve the oral bioavailability, structure-activity-relationship (SAR) optimization studies are currently being conducted.
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Affiliation(s)
- Efrem T Abay
- />Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
- />PAREXEL® International Clinical Research Organization, Private Bag X09, Brandhof, 9324 Bloemfontein, South Africa
| | - Jan H van der Westuizen
- />Research Development, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Kenneth J Swart
- />PAREXEL® International Clinical Research Organization, Private Bag X09, Brandhof, 9324 Bloemfontein, South Africa
- />Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Liezl Gibhard
- />Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Nina Lawrence
- />Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Ntokozo Dambuza
- />Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Anke Wilhelm
- />Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Kendrekar Pravin
- />Research Development, University of the Free State, PO Box 339, Bloemfontein, 9300 South Africa
| | - Lubbe Wiesner
- />Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
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27
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Wagner B, Fischer H, Kansy M, Seelig A, Assmus F. Carrier Mediated Distribution System (CAMDIS): a new approach for the measurement of octanol/water distribution coefficients. Eur J Pharm Sci 2014; 68:68-77. [PMID: 25513709 DOI: 10.1016/j.ejps.2014.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 12/01/2022]
Abstract
Here we present a miniaturized assay, referred to as Carrier-Mediated Distribution System (CAMDIS) for fast and reliable measurement of octanol/water distribution coefficients, log D(oct). By introducing a filter support for octanol, phase separation from water is facilitated and the tendency of emulsion formation (emulsification) at the interface is reduced. A guideline for the best practice of CAMDIS is given, describing a strategy to manage drug adsorption at the filter-supported octanol/buffer interface. We validated the assay on a set of 52 structurally diverse drugs with known shake flask log D(oct) values. Excellent agreement with literature data (r(2) = 0.996, standard error of estimate, SEE = 0.111), high reproducibility (standard deviation, SD < 0.1 log D(oct) units), minimal sample consumption (10 μL of 100 μM DMSO stock solution) and a broad analytical range (log D(oct) range = -0.5 to 4.2) make CAMDIS a valuable tool for the high-throughput assessment of log D(oc)t.
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Affiliation(s)
- Bjoern Wagner
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research and Early Development, Pharmaceutical Research, Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Holger Fischer
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research and Early Development, Pharmaceutical Research, Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Manfred Kansy
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research and Early Development, Pharmaceutical Research, Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Anna Seelig
- Biozentrum, University of Basel, Div. of Biophysical Chemistry, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Frauke Assmus
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research and Early Development, Pharmaceutical Research, Innovation Center Basel, CH-4070 Basel, Switzerland; Biozentrum, University of Basel, Div. of Biophysical Chemistry, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.
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Hendrickx R, Johansson JG, Lohmann C, Jenvert RM, Blomgren A, Börjesson L, Gustavsson L. Identification of novel substrates and structure-activity relationship of cellular uptake mediated by human organic cation transporters 1 and 2. J Med Chem 2013; 56:7232-42. [PMID: 23984907 DOI: 10.1021/jm400966v] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Recently the clinical importance of human organic cation transporters 1 (hOCT1/SLC22A1) and 2 (hOCT2/SLC22A2) in drug disposition, for example, clearance, toxicity, and drug-drug interactions, have been highlighted [Annu. Rev. Pharmacol. Toxicol. 2012, 52, 249-273; Nat. Rev. Drug Discovery 2010, 9 (3), 215-236]. Consequently, there is an extensive need for experimental assessment of structure-transport relationships as well as tools to predict drug uptake by these transporters in ADMET (absorption, distribution, metabolism, excretion, toxicity) investigations. In the present study, we developed a robust assay for screening unlabeled compound uptake by hOCT1 and hOCT2 using transfected HEK293 cells. For the first time, an extensive data set comprising uptake of 354 compounds is presented. As expected, there was a large overlap in substrate specificity between the two organic cation transporters. However, several compounds selectively taken up by either hOCT1 or hOCT2 were identified. In particular, a chemical series of phenylthiophenecarboxamide ureas was identified as selective hOCT1 substrates. Moreover, the drivers for transport differed: molecular volume was the most important determinant of hOCT1 substrates, whereas H-bonding parameters like polar surface area (PSA) dominated for hOCT2.
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Affiliation(s)
- Ramon Hendrickx
- Respiratory, Inflammation and Autoimmunity Innovative Medicines Unit, AstraZeneca R&D Mölndal , SE-431 83 Mölndal, Sweden
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Shalaeva M, Caron G, Abramov YA, O’Connell TN, Plummer MS, Yalamanchi G, Farley KA, Goetz GH, Philippe L, Shapiro MJ. Integrating Intramolecular Hydrogen Bonding (IMHB) Considerations in Drug Discovery Using ΔlogP As a Tool. J Med Chem 2013; 56:4870-9. [DOI: 10.1021/jm301850m] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marina Shalaeva
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Giulia Caron
- Molecular Biotechnology and
Health Sciences Department, University of Torino, via Quarello 15, 10135 Torino, Italy
| | - Yuriy A. Abramov
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Thomas N. O’Connell
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Mark S. Plummer
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Geeta Yalamanchi
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Kathleen A. Farley
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Gilles H. Goetz
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Laurence Philippe
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
| | - Michael J. Shapiro
- Worldwide Medicinal Chemistry, Pfizer Global Research & Development, Pfizer, Inc., Groton, Connecticut 06340, United States
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30
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Engesland A, Skar M, Hansen T, Škalko-basnet N, Flaten GE. New Applications of Phospholipid Vesicle-Based Permeation Assay: Permeation Model Mimicking Skin Barrier. J Pharm Sci 2013; 102:1588-600. [DOI: 10.1002/jps.23509] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/28/2013] [Accepted: 02/27/2013] [Indexed: 12/30/2022]
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31
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Sirajuddin P, Das S, Ringer L, Rodriguez OC, Sivakumar A, Lee YC, Üren A, Fricke ST, Rood B, Ozcan A, Wang SS, Karam S, Yenugonda V, Salinas P, Petricoin E, Pishvaian M, Lisanti MP, Wang Y, Schlegel R, Moasser B, Albanese C. Quantifying the CDK inhibitor VMY-1-103's activity and tissue levels in an in vivo tumor model by LC-MS/MS and by MRI. Cell Cycle 2012; 11:3801-9. [PMID: 22983062 PMCID: PMC3495823 DOI: 10.4161/cc.21988] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The development of new small molecule-based therapeutic drugs requires accurate quantification of drug bioavailability, biological activity and treatment efficacy. Rapidly measuring these endpoints is often hampered by the lack of efficient assay platforms with high sensitivity and specificity. Using an in vivo model system, we report a simple and sensitive liquid chromatography-tandem mass spectrometry assay to quantify the bioavailability of a recently developed novel cyclin-dependent kinase inhibitor VMY-1-103, a purvalanol B-based analog whose biological activity is enhanced via dansylation. We developed a rapid organic phase extraction technique and validated wide and functional VMY-1-103 distribution in various mouse tissues, consistent with its enhanced potency previously observed in a variety of human cancer cell lines. More importantly, in vivo MRI and single voxel proton MR-Spectroscopy further established that VMY-1-103 inhibited disease progression and affected key metabolites in a mouse model of hedgehog-driven medulloblastoma.
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Affiliation(s)
- Paul Sirajuddin
- Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
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32
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Wang X, Barber WE, Long WJ. Applications of superficially porous particles: High speed, high efficiency or both? J Chromatogr A 2012; 1228:72-88. [DOI: 10.1016/j.chroma.2011.07.083] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 02/07/2023]
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33
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Yamashita T, Yamamoto E, Kushida I. Frozen water phase method for logD measurement using a 96-well plate. Talanta 2011; 84:809-13. [DOI: 10.1016/j.talanta.2011.02.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 11/15/2022]
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