1
|
Chen T, Sun T, Bian Y, Pei Y, Feng F, Chi H, Li Y, Tang X, Sang S, Du C, Chen Y, Chen Y, Sun H. The Design and Optimization of Monomeric Multitarget Peptides for the Treatment of Multifactorial Diseases. J Med Chem 2022; 65:3685-3705. [DOI: 10.1021/acs.jmedchem.1c01456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Tianyu Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yaoyao Bian
- College of Acupuncture and Massage, College of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Feng Feng
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Heng Chi
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Yuan Li
- Department of Pharmaceutical Engineering, Jiangsu Food and Pharmaceuticals Science College, Huaian 223005, People’s Republic of China
| | - Xu Tang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Shenghu Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Chenxi Du
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Ying Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| |
Collapse
|
2
|
Dragunow M. Human Brain Neuropharmacology: A Platform for Translational Neuroscience. Trends Pharmacol Sci 2020; 41:777-792. [PMID: 32994050 DOI: 10.1016/j.tips.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/10/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022]
Abstract
Central nervous system (CNS) drug development has been plagued by a failure to translate effective therapies from the lab to the clinic. There are many potential reasons for this, including poor understanding of brain pharmacokinetic (PK) and pharmacodynamic (PD) factors, preclinical study flaws, clinical trial design issues, the complexity and variability of human brain diseases, as well as species differences. To address some of these problems, we have developed a platform for CNS drug discovery comprising: drug screening of primary adult human brain cells; human brain tissue microarray analysis of drug targets; and high-content phenotypic screening methods. In this opinion, I summarise the theoretical basis and the practical development and use of this platform in CNS drug discovery.
Collapse
Affiliation(s)
- Mike Dragunow
- Department of Pharmacology and Hugh Green Biobank, Centre for Brain Research, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| |
Collapse
|
3
|
Stępnicki P, Kondej M, Koszła O, Żuk J, Kaczor AA. Multi-targeted drug design strategies for the treatment of schizophrenia. Expert Opin Drug Discov 2020; 16:101-114. [PMID: 32915109 DOI: 10.1080/17460441.2020.1816962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Schizophrenia is a complex psychiatric disease (or a conglomeration of disorders) manifesting with positive, negative and cognitive symptoms. The pathophysiology of schizophrenia is not completely known; however, it involves many neurotransmitters and their receptors. In order to treat schizophrenia, drugs need to be multi-target drugs. Indeed, the action of second and third generation antipsychotics involves interactions with many receptors, belonging mainly to aminergic GPCRs. AREAS COVERED In this review, the authors summarize current concepts of schizophrenia with the emphasis on the modern dopaminergic, serotoninergic, and glutamatergic hypotheses. Next, they discuss treatments of the disease, stressing multi-target antipsychotics. They cover different aspects of design of multi-target ligands, including the application of molecular modeling approaches for the design and benefits and limitations of multifunctional compounds. Finally, they present successful case studies of multi-target drug design against schizophrenia. EXPERT OPINION Treatment of schizophrenia requires the application of multi-target drugs. While designing single target drugs is relatively easy, designing multifunctional compounds is a challenge due to the necessity to balance the affinity to many targets, while avoiding promiscuity and the problems with drug-likeness. Multi-target drugs bring many benefits: better efficiency, fewer adverse effects, and drug-drug interactions and better patient compliance to drug regime.
Collapse
Affiliation(s)
- Piotr Stępnicki
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin , Lublin, Poland
| | - Magda Kondej
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin , Lublin, Poland
| | - Oliwia Koszła
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin , Lublin, Poland
| | - Justyna Żuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin , Lublin, Poland
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin , Lublin, Poland.,School of Pharmacy, University of Eastern Finland , Kuopio, Finland
| |
Collapse
|
4
|
Profiling the Protein Targets of Unmodified Bio‐Active Molecules with Drug Affinity Responsive Target Stability and Liquid Chromatography/Tandem Mass Spectrometry. Proteomics 2020; 20:e1900325. [DOI: 10.1002/pmic.201900325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/28/2019] [Indexed: 12/17/2022]
|
5
|
Long K, Kostman SJ, Fernandez C, Burnett JC, Huryn DM. Do Zebrafish Obey Lipinski Rules? ACS Med Chem Lett 2019; 10:1002-1006. [PMID: 31223462 PMCID: PMC6580538 DOI: 10.1021/acsmedchemlett.9b00063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/24/2019] [Indexed: 12/26/2022] Open
Abstract
The use of zebrafish in whole organism phenotypic assays has become a valuable strategy throughout the drug discovery process. Zebrafish assays can be used not only to screen libraries of compounds at the earliest stages but also to evaluate advanced leads for their effects on specific biological pathways or for toxicity. However, when confronted with inactivity of a compound in a zebrafish assay, there are little data that can be used to judge if the compound is truly biologically inert or inactive due to a lack of permeability into the model organism. While medicinal chemistry principles suggest parameters that are predictive of human oral bioavailability, cellular permeability, and even bacterial permeability, there have been no such parameters developed for zebrafish absorption. To address this question, we compiled a set of 700 compounds reported in the literature to be active in zebrafish assays, evaluated their properties, and compared them to properties derived from a set of historical drugs and a set of recently approved oral drugs. While some properties overlap, the averages and 10th and 90th percentiles of molecular weight, octanol-water partition coefficient (logP), H-bond counts, and polar surface area for zebrafish-active compounds are statistically different from those of known drugs. This analysis should be useful to scientists interpreting structure-activity relationships based on data from zebrafish assays and help to inform the translation from fish to mammals.
Collapse
Affiliation(s)
- Keith Long
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | - Christian Fernandez
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James C. Burnett
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Donna M. Huryn
- Department
of Pharmaceutical Sciences, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
6
|
Zhou J, Jiang X, He S, Jiang H, Feng F, Liu W, Qu W, Sun H. Rational Design of Multitarget-Directed Ligands: Strategies and Emerging Paradigms. J Med Chem 2019; 62:8881-8914. [PMID: 31082225 DOI: 10.1021/acs.jmedchem.9b00017] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to the complexity of multifactorial diseases, single-target drugs do not always exhibit satisfactory efficacy. Recently, increasing evidence indicates that simultaneous modulation of multiple targets may improve both therapeutic safety and efficacy, compared with single-target drugs. However, few multitarget drugs are on market or in clinical trials, despite the best efforts of medicinal chemists. This article discusses the systematic establishment of target combination, lead generation, and optimization of multitarget-directed ligands (MTDLs). Moreover, we analyze some MTDLs research cases for several complex diseases in recent years and the physicochemical properties of 117 clinical multitarget drugs, with the aim to reveal the trends and insights of the potential use of MTDLs.
Collapse
Affiliation(s)
- Junting Zhou
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Xueyang Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Siyu He
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
| | - Hongli Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China.,Jiangsu Food and Pharmaceutical Science College , Huaian 223003 , People's Republic of China
| | - Wenyuan Liu
- Department of Analytical Chemistry , China Pharmaceutical University , Nanjing 210009 , People's Republic of China
| | - Wei Qu
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Haopeng Sun
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
| |
Collapse
|
7
|
Singh VK, Seed TM, Olabisi AO. Drug discovery strategies for acute radiation syndrome. Expert Opin Drug Discov 2019; 14:701-715. [PMID: 31008662 DOI: 10.1080/17460441.2019.1604674] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: There are at the minimum two major, quite different approaches to advance drug discovery. The first being the target-based drug discovery (TBDD) approach that is commonly referred to as the molecular approach. The second approach is the phenotype-based drug discovery (PBDD), also known as physiology-based drug discovery or empirical approach. Area covered: The authors discuss, herein, the need for developing radiation countermeasure agents for various sub-syndromes of acute radiation syndromes (ARS) following TBDD and PBDD approaches. With time and continuous advances in radiation countermeasure drug development research, the expectation is to have multiple radiation countermeasure agents for each sub-syndrome made available to radiation exposed victims. Expert opinion: The majority of the countermeasures currently being developed for ARS employ the PBDD approach, while the TBDD approach is clearly under-utilized. In the future, an improved drug development strategy might be a 'hybrid' strategy that is more reliant on TBDD for the initial drug discovery via large-scale screening of potential candidate agents, while utilizing PBDD for secondary screening of those candidates, followed by tertiary analytics phase in order to pinpoint efficacious candidates that target the specific sub-syndromes of ARS.
Collapse
Affiliation(s)
- Vijay K Singh
- a Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine , Uniformed Services University of the Health Sciences , Bethesda , MD , USA.,b Scientific Research Department , Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences , Bethesda , MD , USA
| | | | - Ayodele O Olabisi
- b Scientific Research Department , Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences , Bethesda , MD , USA
| |
Collapse
|
8
|
Possible Role of the Ca 2+/Mn 2+ P-Type ATPase Pmr1p on Artemisinin Toxicity through an Induction of Intracellular Oxidative Stress. Molecules 2019; 24:molecules24071233. [PMID: 30934859 PMCID: PMC6480206 DOI: 10.3390/molecules24071233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/24/2019] [Accepted: 03/27/2019] [Indexed: 02/04/2023] Open
Abstract
Artemisinins are widely used to treat Plasmodium infections due to their high clinical efficacy; however, the antimalarial mechanism of artemisinin remains unresolved. Mutations in P. falciparum ATPase6 (PfATP6), a sarcoplasmic endoplasmic reticulum Ca2+-transporting ATPase, are associated with increased tolerance to artemisinin. We utilized Saccharomyces cerevisiae as a model to examine the involvement of Pmr1p, a functional homolog of PfATP6, on the toxicity of artemisinin. Our analysis demonstrated that cells lacking Pmr1p are less susceptible to growth inhibition from artemisinin and its derivatives. No association between sensitivity to artemisinin and altered trafficking of the drug efflux pump Pdr5p, calcium homeostasis, or protein glycosylation was found in pmr1∆ yeast. Basal ROS levels are elevated in pmr1∆ yeast and artemisinin exposure does not enhance ROS accumulation. This is in contrast to WT cells that exhibit a significant increase in ROS production following treatment with artemisinin. Yeast deleted for PMR1 are known to accumulate excess manganese ions that can function as ROS-scavenging molecules, but no correlation between manganese content and artemisinin resistance was observed. We propose that loss of function mutations in Pmr1p in yeast cells and PfATP6 in P. falciparum are protective against artemisinin toxicity due to reduced intracellular oxidative damage.
Collapse
|
9
|
de Lange ECM, van den Brink W, Yamamoto Y, de Witte WEA, Wong YC. Novel CNS drug discovery and development approach: model-based integration to predict neuro-pharmacokinetics and pharmacodynamics. Expert Opin Drug Discov 2017; 12:1207-1218. [PMID: 28933618 DOI: 10.1080/17460441.2017.1380623] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION CNS drug development has been hampered by inadequate consideration of CNS pharmacokinetic (PK), pharmacodynamics (PD) and disease complexity (reductionist approach). Improvement is required via integrative model-based approaches. Areas covered: The authors summarize factors that have played a role in the high attrition rate of CNS compounds. Recent advances in CNS research and drug discovery are presented, especially with regard to assessment of relevant neuro-PK parameters. Suggestions for further improvements are also discussed. Expert opinion: Understanding time- and condition dependent interrelationships between neuro-PK and neuro-PD processes is key to predictions in different conditions. As a first screen, it is suggested to use in silico/in vitro derived molecular properties of candidate compounds and predict concentration-time profiles of compounds in multiple compartments of the human CNS, using time-course based physiology-based (PB) PK models. Then, for selected compounds, one can include in vitro drug-target binding kinetics to predict target occupancy (TO)-time profiles in humans. This will improve neuro-PD prediction. Furthermore, a pharmaco-omics approach is suggested, providing multilevel and paralleled data on systems processes from individuals in a systems-wide manner. Thus, clinical trials will be better informed, using fewer animals, while also, needing fewer individuals and samples per individual for proof of concept in humans.
Collapse
Affiliation(s)
- Elizabeth C M de Lange
- a Leiden Academic Center of Drug Research, Translational Pharmacology , Leiden University , Leiden , The Netherlands
| | - Willem van den Brink
- a Leiden Academic Center of Drug Research, Translational Pharmacology , Leiden University , Leiden , The Netherlands
| | - Yumi Yamamoto
- a Leiden Academic Center of Drug Research, Translational Pharmacology , Leiden University , Leiden , The Netherlands
| | - Wilhelmus E A de Witte
- a Leiden Academic Center of Drug Research, Translational Pharmacology , Leiden University , Leiden , The Netherlands
| | - Yin Cheong Wong
- a Leiden Academic Center of Drug Research, Translational Pharmacology , Leiden University , Leiden , The Netherlands
| |
Collapse
|
10
|
Lee H, Lee JW. Target identification for biologically active small molecules using chemical biology approaches. Arch Pharm Res 2016; 39:1193-201. [DOI: 10.1007/s12272-016-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
|
11
|
Kutilek VD, Andrews CL, Richards MP, Xu Z, Sun T, Chen Y, Hashke A, Smotrov N, Fernandez R, Nickbarg EB, Chamberlin C, Sauvagnat B, Curran PJ, Boinay R, Saradjian P, Allen SJ, Byrne N, Elsen NL, Ford RE, Hall DL, Kornienko M, Rickert KW, Sharma S, Shipman JM, Lumb KJ, Coleman K, Dandliker PJ, Kariv I, Beutel B. Integration of Affinity Selection-Mass Spectrometry and Functional Cell-Based Assays to Rapidly Triage Druggable Target Space within the NF-κB Pathway. ACTA ACUST UNITED AC 2016; 21:608-19. [PMID: 26969322 DOI: 10.1177/1087057116637353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/15/2016] [Indexed: 11/15/2022]
Abstract
The primary objective of early drug discovery is to associate druggable target space with a desired phenotype. The inability to efficiently associate these often leads to failure early in the drug discovery process. In this proof-of-concept study, the most tractable starting points for drug discovery within the NF-κB pathway model system were identified by integrating affinity selection-mass spectrometry (AS-MS) with functional cellular assays. The AS-MS platform Automated Ligand Identification System (ALIS) was used to rapidly screen 15 NF-κB proteins in parallel against large-compound libraries. ALIS identified 382 target-selective compounds binding to 14 of the 15 proteins. Without any chemical optimization, 22 of the 382 target-selective compounds exhibited a cellular phenotype consistent with the respective target associated in ALIS. Further studies on structurally related compounds distinguished two chemical series that exhibited a preliminary structure-activity relationship and confirmed target-driven cellular activity to NF-κB1/p105 and TRAF5, respectively. These two series represent new drug discovery opportunities for chemical optimization. The results described herein demonstrate the power of combining ALIS with cell functional assays in a high-throughput, target-based approach to determine the most tractable drug discovery opportunities within a pathway.
Collapse
Affiliation(s)
- Victoria D Kutilek
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Christine L Andrews
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Matthew P Richards
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Zangwei Xu
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Tianxiao Sun
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Yiping Chen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Andrew Hashke
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nadya Smotrov
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Rafael Fernandez
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Elliott B Nickbarg
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Chad Chamberlin
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Berengere Sauvagnat
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Patrick J Curran
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ryan Boinay
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Peter Saradjian
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Samantha J Allen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Noel Byrne
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nathaniel L Elsen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: AbbVie, North Chicago, IL USA
| | - Rachael E Ford
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Dawn L Hall
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Maria Kornienko
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Keith W Rickert
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Medimmune, Gaithersburg, MD, USA
| | - Sujata Sharma
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Jennifer M Shipman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin J Lumb
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin Coleman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Arvinas, New Haven, CT, USA
| | - Peter J Dandliker
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ilona Kariv
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Bruce Beutel
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| |
Collapse
|
12
|
Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
|
13
|
Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery. Arch Pharm Res 2015; 38:1627-41. [DOI: 10.1007/s12272-015-0618-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/19/2015] [Indexed: 01/01/2023]
|
14
|
Caldwell GW. In silico tools used for compound selection during target-based drug discovery and development. Expert Opin Drug Discov 2015; 10:901-23. [DOI: 10.1517/17460441.2015.1043885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gary W Caldwell
- Janssen Research & Development LLC, Discovery Sciences, Spring House, PA, USA
| |
Collapse
|
15
|
Deosarkar SP, Bhatt P, Gillespie J, Goetz DJ, McCall KD. Inhibition of LPS-Induced TLR4 Signaling Products in Murine Macrophages by Phenylmethimazole: An Assay Methodology for Screening Potential Phenylmethimazole Analogs. Drug Dev Res 2014; 75:497-509. [DOI: 10.1002/ddr.21231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/05/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Pooja Bhatt
- Department of Biological Sciences; Molecular and Cellular Biology Program; College or Arts and Sciences; Ohio University; Athens Ohio 45701 United States
| | | | - Douglas J. Goetz
- Department of Chemical and Biomolecular Engineering; Biomedical Engineering Program; Ohio University; Athens Ohio 45701 United States
| | - Kelly D. McCall
- Department of Biological Sciences; Molecular and Cellular Biology Program; College or Arts and Sciences; Ohio University; Athens Ohio 45701 United States
- Department of Specialty Medicine; Heritage College of Osteopathic Medicine; Ohio University; Athens Ohio 45701 United States
- Department of Biomedical Sciences; Heritage College of Osteopathic Medicine; Ohio University; Athens Ohio 45701 United States
- The Diabetes Institute at Ohio University; Heritage College of Osteopathic Medicine; Ohio University; Athens Ohio 45701 United States
- Biomedical Engineering Program; Russ College of Engineering and Technology; Ohio University; Athens Ohio 45701 United States
| |
Collapse
|
16
|
Pandey RP, Kwon HJ, Ahn JS, Osada H, Sohng JK. The 7th Japan-Korea chemical biology symposium: chemical biology of natural bioactive molecules. ACS Chem Biol 2014; 9:1070-4. [PMID: 24831667 DOI: 10.1021/cb5002558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural bioactive molecules possess supreme chemical diversity and drug-like properties and are an important source for drug lead compounds. At the seventh Japan-Korea Chemical Biology Symposium at Jeju Island, Korea, chemical biologists from Korea and Japan highlighted the remarkable features of natural products and their significance.
Collapse
Affiliation(s)
- Ramesh Prasad Pandey
- Institute
of Biomolecule Reconstruction, Sun Moon University, Asansi, Chungnam 336-708, Korea
| | - Ho Jeong Kwon
- Chemical
Genomics National Research Laboratory, Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul 120-749, Korea
| | - Jong Seog Ahn
- Chemical
Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Ochangeup,
Cheongwongun, Chungcheongbukdo 363-883, Korea
| | - Hiroyuki Osada
- Chemical Biology
Research Group, RIKEN Center
for Sustainable Resource Science, and Antibiotics Laboratory, 2-1 Hirosawa, Wako-shi 351-0198, Japan
| | - Jae Kyung Sohng
- Institute
of Biomolecule Reconstruction, Sun Moon University, Asansi, Chungnam 336-708, Korea
| |
Collapse
|
17
|
Jung HJ, Kwon HJ. Exploring the role of mitochondrial UQCRB in angiogenesis using small molecules. MOLECULAR BIOSYSTEMS 2013; 9:930-9. [PMID: 23475074 DOI: 10.1039/c3mb25426g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bioactive small molecules are powerful tools used to evaluate protein function under physiological and pathological conditions. Over recent decades, utilization of a variety of biologically active small molecules in basic research and clinical applications has provided tremendous benefits in understanding the molecular mechanisms of biology and accelerating drug development. This review focuses on recent advances in the identification of new small molecules and their target proteins for exploring angiogenesis at the molecular level. In particular, we focus on the oxygen-sensing role of ubiquinol-cytochrome c reductase binding protein (UQCRB) of mitochondrial Complex III through identification of the protein target and the mode of action of a natural small molecule, terpestacin. The positive feedback approach of chemistry and biology provides a new way to explore functional roles of proteins and to translate this information into practical applications.
Collapse
Affiliation(s)
- Hye Jin Jung
- Chemical Genomics National Research Laboratory, Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749, Korea
| | | |
Collapse
|
18
|
Secrier M, Schneider R. PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. PLoS One 2013; 8:e72361. [PMID: 23951317 PMCID: PMC3741141 DOI: 10.1371/journal.pone.0072361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/13/2013] [Indexed: 01/04/2023] Open
Abstract
Timing common and specific modulators of disease progression is crucial for treatment, but the understanding of the underlying complex system of interactions is limited. While attempts at elucidating this experimentally have produced enormous amounts of phenotypic data, tools that are able to visualize and analyze them are scarce and the insight obtained from the data is often unsatisfactory. Linking and visualizing processes from genes to phenotypes and back, in a temporal context, remains a challenge in systems biology. We introduce PhenoTimer, a 2D/3D visualization tool for the mapping of time-resolved phenotypic links in a genetic context. It uses a novel visualization approach for relations between morphological defects, pathways or diseases, to enable fast pattern discovery and hypothesis generation. We illustrate its capabilities of tracing dynamic motifs on cell cycle datasets that explore the phenotypic order of events upon perturbations of the system, transcriptional activity programs and their connection to disease. By using this tool we are able to fine-grain regulatory programs for individual time points of the cell cycle and better understand which patterns arise when these programs fail. We also illustrate a way to identify common mechanisms of misregulation in diseases and drug abuse.
Collapse
Affiliation(s)
- Maria Secrier
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
| | | |
Collapse
|
19
|
Evaluation of impedance-based label-free technology as a tool for pharmacology and toxicology investigations. BIOSENSORS-BASEL 2013; 3:132-56. [PMID: 25587404 PMCID: PMC4263586 DOI: 10.3390/bios3010132] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/15/2013] [Accepted: 02/27/2013] [Indexed: 12/23/2022]
Abstract
The use of label-free technologies based on electrical impedance is becoming more and more popular in drug discovery. Indeed, such a methodology allows the continuous monitoring of diverse cellular processes, including proliferation, migration, cytotoxicity and receptor-mediated signaling. The objective of the present study was to further assess the usefulness of the real-time cell analyzer (RTCA) and, in particular, the xCELLigence platform, in the context of early drug development for pharmacology and toxicology investigations. In the present manuscript, four cellular models were exposed to 50 compounds to compare the cell index generated by RTCA and cell viability measured with a traditional viability assay. The data revealed an acceptable correlation (ca. 80%) for both cell lines (i.e., HepG2 and HepaRG), but a lack of correlation (ca. 55%) for the primary human and rat hepatocytes. In addition, specific RTCA profiles (signatures) were generated when HepG2 and HepaRG cells were exposed to calcium modulators, antimitotics, DNA damaging and nuclear receptor agents, with a percentage of prediction close to 80% for both cellular models. In a subsequent experiment, HepG2 cells were exposed to 81 proprietary UCB compounds known to be genotoxic or not. Based on the DNA damaging signatures, the RTCA technology allowed the detection of ca. 50% of the genotoxic compounds (n = 29) and nearly 100% of the non-genotoxic compounds (n = 52). Overall, despite some limitations, the xCELLigence platform is a powerful and reliable tool that can be used in drug discovery for toxicity and pharmacology studies.
Collapse
|