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Zeng W, Wang Y, Gao R, Wen H, Yu M. Unlocking the Reverse Targeting Mechanisms of Cannabidiol: Unveiling New Therapeutic Avenues. J Med Chem 2024; 67:14574-14585. [PMID: 39092992 DOI: 10.1021/acs.jmedchem.4c01353] [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: 08/04/2024]
Abstract
Cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC), the main components of Cannabis sativa plants, have attracted a significant amount of attention due to their biological activities. This study identified GPR18 as the target of partial agonist CBD activating the p42/p44 MAPK pathway leading to migration of endometrial epithelial cells. Induced fit docking (IFD) showed that the affinity of THC for GPR18 is higher than that of CBD, and molecular dynamics (MD) simulations showed that CBD-GPR18 complexes at 130/200 ns might have stable conformations, potentially activating GPR18 by changing the distances of key residues in its active pocket. In contrast, THC maintains "metastable" conformations, generating a "shrinking space" leading to full agonism of THC by adding mechanical constraints in GPR18's active pocket. Steered molecular dynamics (SMD) revealed GPR18's active pocket was influenced more by CBD's partial agonism compared with THC. This combined IFD-MD-SMD method may be used to explain the mechanism of activation of partial or full agonists of GPR18.
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Affiliation(s)
- Wen Zeng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China
| | - Yifei Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Rui Gao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Hongliang Wen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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Fischer MA, Mustafa AHM, Hausmann K, Ashry R, Kansy AG, Liebl MC, Brachetti C, Piée-Staffa A, Zessin M, Ibrahim HS, Hofmann TG, Schutkowski M, Sippl W, Krämer OH. Novel hydroxamic acid derivative induces apoptosis and constrains autophagy in leukemic cells. J Adv Res 2024; 60:201-214. [PMID: 37467961 PMCID: PMC11156613 DOI: 10.1016/j.jare.2023.07.005] [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: 04/10/2023] [Revised: 06/18/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023] Open
Abstract
INTRODUCTION Posttranslational modification of proteins by reversible acetylation regulates key biological processes. Histone deacetylases (HDACs) catalyze protein deacetylation and are frequently dysregulated in tumors. This has spurred the development of HDAC inhibitors (HDACi). Such epigenetic drugs modulate protein acetylation, eliminate tumor cells, and are approved for the treatment of blood cancers. OBJECTIVES We aimed to identify novel, nanomolar HDACi with increased potency over existing agents and selectivity for the cancer-relevant class I HDACs (HDAC1,-2,-3,-8). Moreover, we wanted to define how such drugs control the apoptosis-autophagy interplay. As test systems, we used human leukemic cells and embryonic kidney-derived cells. METHODS We synthesized novel pyrimidine-hydroxamic acid HDACi (KH9/KH16/KH29) and performed in vitro activity assays and molecular modeling of their direct binding to HDACs. We analyzed how these HDACi affect leukemic cell fate, acetylation, and protein expression with flow cytometry and immunoblot. The publicly available DepMap database of CRISPR-Cas9 screenings was used to determine sensitivity factors across human leukemic cells. RESULTS Novel HDACi show nanomolar activity against class I HDACs. These agents are superior to the clinically used hydroxamic acid HDACi SAHA (vorinostat). Within the KH-series of compounds, KH16 (yanostat) is the most effective inhibitor of HDAC3 (IC50 = 6 nM) and the most potent inducer of apoptosis (IC50 = 110 nM; p < 0.0001) in leukemic cells. KH16 though spares embryonic kidney-derived cells. Global data analyses of knockout screenings verify that HDAC3 is a dependency factor in 115 human blood cancer cells of different lineages, independent of mutations in the tumor suppressor p53. KH16 alters pro- and anti-apoptotic protein expression, stalls cell cycle progression, and induces caspase-dependent processing of the autophagy proteins ULK1 and p62. CONCLUSION These data reveal that HDACs are required to stabilize autophagy proteins through suppression of apoptosis in leukemic cells. HDAC3 appears as a valid anti-cancer target for pharmacological intervention.
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Affiliation(s)
- Marten A Fischer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
| | - Al-Hassan M Mustafa
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; Department of Zoology, Faculty of Science, Aswan University, Aswan, Egypt.
| | - Kristin Hausmann
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
| | - Ramy Ashry
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany; Department of Oral Pathology, Faculty of Dentistry, Mansoura University, Egypt.
| | - Anita G Kansy
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
| | - Magdalena C Liebl
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
| | | | - Andrea Piée-Staffa
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
| | - Matthes Zessin
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
| | - Hany S Ibrahim
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt.
| | - Thomas G Hofmann
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
| | - Oliver H Krämer
- Department of Toxicology, University Medical Center, 55131 Mainz, Germany.
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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Salerno L, Vanella L, Sorrenti V, Consoli V, Ciaffaglione V, Fallica AN, Canale V, Zajdel P, Pignatello R, Intagliata S. Novel mutual prodrug of 5-fluorouracil and heme oxygenase-1 inhibitor (5-FU/HO-1 hybrid): design and preliminary in vitro evaluation. J Enzyme Inhib Med Chem 2021; 36:1378-1386. [PMID: 34167427 PMCID: PMC8231349 DOI: 10.1080/14756366.2021.1928111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In this work, the first mutual prodrug of 5-fluorouracil and heme oxygenase1 inhibitor (5-FU/HO-1 hybrid) has been designed, synthesised, and evaluated for its in vitro chemical and enzymatic hydrolysis stability. Predicted in silico physicochemical properties of the newly synthesised hybrid (3) demonstrated a drug-like profile with suitable Absorption, Distribution, Metabolism, and Excretion (ADME) properties and low toxic liabilities. Preliminary cytotoxicity evaluation towards human prostate (DU145) and lung (A549) cancer cell lines demonstrated that 3 exerted a similar effect on cell viability to that produced by the reference drug 5-FU. Among the two tested cancer cell lines, the A549 cells were more susceptible for 3. Of note, hybrid 3 also had a significantly lower cytotoxic effect on healthy human lung epithelial cells (BEAS-2B) than 5-FU. Altogether our results served as an initial proof-of-concept to develop 5-FU/HO-1 mutual prodrugs as potential novel anticancer agents.
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Affiliation(s)
- Loredana Salerno
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Luca Vanella
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Valeria Sorrenti
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Valeria Consoli
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | | | - Antonino N Fallica
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Vittorio Canale
- Department of Organic Chemistry, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Zajdel
- Department of Organic Chemistry, Jagiellonian University Medical College, Kraków, Poland
| | - Rosario Pignatello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
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Abstract
PURPOSE OF REVIEW Drug development has evolved over the years from being one-at-a-time to be massive screens in an industrial manner. Bringing a new therapeutic agent from concept to bedside can take a decade and cost billions of dollars-with most concepts failing along the way. Of the few compounds that make it to clinical testing, less than one out of eight make it to approval. This traditional drug development pipeline is challenging for prevalent diseases and makes the development of new therapeutics for rare diseases financially intractable. RECENT FINDINGS Repurposing of drugs is an alternative to identify new applications for the thousands of compounds that have already been approved for clinical use. There is now a range of strategies for such efforts that leverage clinical data, pharmacologic data, and/or genomic or transcriptomic data. These strategies, together with examples, are detailed in this review. Drug repurposing bypasses the pre-clinical work and thereby opens up the opportunity to provide targeted treatment at a fraction of the cost that is accompanied with the development from ideation to full approval. Such an approach makes drug discovery for any disease process more efficient but holds particular promise for rare diseases for which there is little to no other viable drug development channel.
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Affiliation(s)
- Eric Kort
- DeVos Cardiovascular Research Program, Van Andel Institute/Spectrum Health, Grand Rapids, MI, USA.,Dept of Pediatrics & Human Development, Michigan State University, Grand Rapids, MI, USA.,Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Stefan Jovinge
- DeVos Cardiovascular Research Program, Van Andel Institute/Spectrum Health, Grand Rapids, MI, USA. .,Frederik Meijer Heart and Vascular Institute, Spectrum Health, Grand Rapids, MI, USA. .,Cardiovascular Institute, Stanford University, Palo Alto, CA, USA.
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Kullappan M, Mallavarapu Ambrose J, Surapaneni KM. Understanding the binding conformation of ceftolozane/tazobactam with Metallo-β-lactamases VIM-5 and IMP-7 of Pseudomonas aeruginosa: A molecular docking and virtual screening process. J Mol Recognit 2021; 34:e2898. [PMID: 33780080 DOI: 10.1002/jmr.2898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/11/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is one of the community-acquired and healthcare-associated infections causing organisms. It has become resistant to most of the available antibiotics and is termed multi-drug resistance (MDR). There are a limited number of antibiotics are available to treat such MDR organism causing infections. The ceftolozane/tazobactam is one among the combination drug therapy (CDT) prescribed for the treatment of MDR causing infections. The resistance for the same CDT was observed in the MDR P. aeruginosa harboring VIM-5 and IMP-7 Metallo beta (β)-lactamases (MBLs). To explore the resistance mechanism at the molecular level, docking studies were carried out for antibiotics against VIM-5 and IMP-7 MBLs. The Zn2 metal ions carry out the nucleophile attack on the carbonyl carbon of the β-lactam ring along with conserved water molecules. To find lead compounds against the MBLs, a virtual screening process was carried out. We have employed MODELLER for structure modeling, AutoDock for molecular docking and AutoDock Vina, Molinspiration, PASS prediction & admetSAR in virtual screening. The search of low binding energy ceftolozane analogs against VIM-5 and IMP-7 MBLs has resulted in the ZINC000029060075 and ZINC000009163636 analogs. Similarly, the screening of high binding energy inhibitors against VIM-5 and IMP-7 MBLs has resulted in ZINC000003831503 and ZINC000000897247 tazobactam analogs respectively. The ADMET prediction results in the non-toxicity of the lead compounds. Our study may provide new insights for the scientist who are designing novel drugs against MDR P. aeruginosa causing infections.
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Affiliation(s)
- Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
| | - Jenifer Mallavarapu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Clinical Skills & Simulation and Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
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Skaugen JM, Scoccimarro A, Pizon AF, Rymer JA, Giannoutsos S, Ekins S, Krasowski MD, Tamama K. Novel ketamine analogues cause a false positive phencyclidine immunoassay. Ann Clin Biochem 2019; 56:598-607. [DOI: 10.1177/0004563219858125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Background Immunoassays are commonly used to test for drugs of abuse in patients in a variety of settings. The increasing prevalence of ‘designer’ drugs causes difficulties for the toxicology laboratory and may result in unexpected false positives and identification of unfamiliar compounds. Within the past decade, there have been a variety of ketamine and phencyclidine analogues identified, particularly as drugs of abuse. Method We present a case of intoxication with a novel ketamine analogue, deschloro-N-ethyl-ketamine, causing a false positive phencyclidine immunoassay. Additionally, we performed spiking studies and 2D molecular similarity calculations for deschloro-N-ethyl-ketamine, ketamine and three other analogues on the Siemens Viva-E EMIT-II phencyclidine assay to assess their cross-reactivity. Results Four of the tested compounds (deschloro-N-ethyl-ketamine, 3-methoxy-phencyclidine, 3-methoxy-eticyclidine and methoxetamine) cause false positive phencyclidine immunoassay results, while ketamine gives a negative result. The cross-reactivity data are in accord with the similarity calculations of these molecules, further validating the ability of 2D molecular similarity analysis to predict the molecular cross-reactivity in immunoassays. Conclusions The cross-reactivity data of phencyclidine and ketamine analogues presented in this study could help toxicology laboratories and clinicians in evaluating unexpected results, particularly when novel PCP and ketamine analogues are being considered.
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Affiliation(s)
- John M Skaugen
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Clinical Laboratories, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
| | - Anthony Scoccimarro
- Division of Medical Toxicology, Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anthony F Pizon
- Division of Medical Toxicology, Department of Emergency Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jacqueline A Rymer
- Clinical Laboratories, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
| | - Spiros Giannoutsos
- Clinical Laboratories, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
| | - Matthew D Krasowski
- Department of Pathology, University of Iowa Hospital and Clinics, Iowa City, IA, USA
| | - Kenichi Tamama
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Clinical Laboratories, University of Pittsburgh Medical Center Presbyterian Hospital, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical Laboratory, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
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Abstract
Pharmacological science is trying to establish the link between chemicals, targets, and disease-related phenotypes. A plethora of chemical proteomics and structural data have been generated, thanks to the target-based approach that has dominated drug discovery at the turn of the century. There is an invaluable source of information for in silico target profiling. Prediction is based on the principle of chemical similarity (similar drugs bind similar targets) or on first principles from the biophysics of molecular interactions. In the first case, compound comparison is made through ligand-based chemical similarity search or through classifier-based machine learning approach. The 3D techniques are based on 3D structural descriptors or energy-based scoring scheme to infer a binding affinity of a compound with its putative target. More recently, a new approach based on compound set metric has been proposed in which a query compound is compared with a whole of compounds associated with a target or a family of targets. This chapter reviews the different techniques of in silico target profiling and their main applications such as inference of unwanted targets, drug repurposing, or compound prioritization after phenotypic-based screening campaigns.
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Novel selective, potent naphthyl TRPM8 antagonists identified through a combined ligand- and structure-based virtual screening approach. Sci Rep 2017; 7:10999. [PMID: 28887460 PMCID: PMC5591244 DOI: 10.1038/s41598-017-11194-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 07/21/2017] [Indexed: 02/03/2023] Open
Abstract
Transient receptor potential melastatin 8 (TRPM8), a nonselective cation channel, is the predominant mammalian cold temperature thermosensor and it is activated by cold temperatures and cooling compounds, such as menthol and icilin. Because of its role in cold allodynia, cold hyperalgesia and painful syndromes TRPM8 antagonists are currently being pursued as potential therapeutic agents for the treatment of pain hypersensitivity. Recently TRPM8 has been found in subsets of bladder sensory nerve fibres, providing an opportunity to understand and treat chronic hypersensitivity. However, most of the known TRPM8 inhibitors lack selectivity, and only three selective compounds have reached clinical trials to date. Here, we applied two virtual screening strategies to find new, clinics suitable, TRPM8 inhibitors. This strategy enabled us to identify naphthyl derivatives as a novel class of potent and selective TRPM8 inhibitors. Further characterization of the pharmacologic properties of the most potent compound identified, compound 1, confirmed that it is a selective, competitive antagonist inhibitor of TRPM8. Compound 1 also proved itself active in a overreactive bladder model in vivo. Thus, the novel naphthyl derivative compound identified here could be optimized for clinical treatment of pain hypersensitivity in bladder disorders but also in different other pathologies.
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Zheng C, Qiu M, Xu X, Ye H, Zhang Q, Li Y, Liu X, Chen J. Understanding the diverse functions of Huatan Tongluo Fang on rheumatoid arthritis from a pharmacological perspective. Exp Ther Med 2016; 12:87-94. [PMID: 27347021 PMCID: PMC4906768 DOI: 10.3892/etm.2016.3329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/03/2016] [Indexed: 11/25/2022] Open
Abstract
Huatan Tongluo Fang (HTTLF) is a traditional herbal formula that can resolve phlegm and dredge collaterals. HTTLF has also been used to treat rheumatoid arthritis (RA); however, the mechanism underlying the therapeutic effects of HTTLF on RA has not been clearly elucidated at the molecular level. In the present study, an integrated model of system pharmacology containing chemical space analysis, potential active compound prediction and compound-target-disease network was constructed to investigate the molecular mechanisms of HTTLF. The compounds from HTTLF dispersed well in the chemical space. Most of the compounds from HTTLF had similar chemical spaces to drug/drug-like compounds associated with RA, according to the MDL Drug Data Report. A total of 127 potentially active compounds and 17 targets of RA were identified. Among them, 50 compounds interacted with ≥2 targets, while 77 compounds interacted with only one target. In addition, 17 targets were associated with 82 diseases that belonged to 26 categories. These results indicate that HTTLF has diverse chemical spaces and polypharmacology with regards to the treatment of RA. In addition, HTTLF demonstrated therapeutic potential against diverse diseases other than RA, including osteoarthritis, atherosclerosis and brain cancer. This study provides a novel platform for understanding how HTTLF treats RA; this is beneficial for explaining the diverse functions of HTTLF with regards to RA, and may help develop novel compounds with desirable therapeutic targets to treat RA.
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Affiliation(s)
- Chunsong Zheng
- Institute of Bone Disease, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Mingshan Qiu
- Department of Rheumatism and Immunology, Affiliated Xiamen Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Xiamen, Fujian 361009, P.R. China
| | - Xiaojie Xu
- Institute of Bone Disease, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Hongzhi Ye
- Institute of Bone Disease, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Qian Zhang
- Department of Rheumatism and Immunology, Affiliated Xiamen Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Xiamen, Fujian 361009, P.R. China
| | - Yihan Li
- Department of Rheumatism and Immunology, Affiliated Xiamen Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Xiamen, Fujian 361009, P.R. China
| | - Xianxiang Liu
- Institute of Bone Disease, Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, P.R. China
| | - Jinchun Chen
- Department of Rheumatism and Immunology, Affiliated Xiamen Hospital of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Xiamen, Fujian 361009, P.R. China
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Tang J, Aittokallio T. Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. Curr Pharm Des 2014; 20:23-36. [PMID: 23530504 PMCID: PMC3894695 DOI: 10.2174/13816128113199990470] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/18/2013] [Indexed: 12/12/2022]
Abstract
Polypharmacology has emerged as novel means in drug discovery for improving treatment response in clinical use. However, to really capitalize on the polypharmacological effects of drugs, there is a critical need to better model and understand how the complex interactions between drugs and their cellular targets contribute to drug efficacy and possible side effects. Network graphs provide a convenient modeling framework for dealing with the fact that most drugs act on cellular systems through targeting multiple proteins both through on-target and off-target binding. Network pharmacology models aim at addressing questions such as how and where in the disease network should one target to inhibit disease phenotypes, such as cancer growth, ideally leading to therapies that are less vulnerable to drug resistance and side effects by means of attacking the disease network at the systems level through synergistic and synthetic lethal interactions. Since the exponentially increasing number of potential drug target combinations makes pure experimental approach quickly unfeasible, this review depicts a number of computational models and algorithms that can effectively reduce the search space for determining the most promising combinations for experimental evaluation. Such computational-experimental strategies are geared toward realizing the full potential of multi-target treatments in different disease phenotypes. Our specific focus is on system-level network approaches to polypharmacology designs in anticancer drug discovery, where we give representative examples of how network-centric modeling may offer systematic strategies toward better understanding and even predicting the phenotypic responses to multi-target therapies.
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Williams AJ, Ekins S, Tkachenko V. Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation. Drug Discov Today 2012; 17:685-701. [PMID: 22426180 DOI: 10.1016/j.drudis.2012.02.013] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/17/2012] [Accepted: 02/28/2012] [Indexed: 01/25/2023]
Abstract
In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure that the data are high quality to ensure that time is not wasted in erroneous searches, that models are underpinned by accurate data and that improved discoverability of online resources is not marred by incorrect data. In this article we provide an overview of some of the experiences of the authors using online chemical compound databases, critique the approaches taken to assemble data and we suggest approaches to deliver definitive reference data sources.
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Affiliation(s)
- Antony J Williams
- Royal Society of Chemistry, US Office, 904 Tamaras Circle, Wake Forest, NC 27587, USA.
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Abstract
This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein–ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.
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Briansó F, Carrascosa MC, Oprea TI, Mestres J. Cross-pharmacology analysis of G protein-coupled receptors. Curr Top Med Chem 2011; 11:1956-63. [PMID: 21851335 PMCID: PMC3717414 DOI: 10.2174/156802611796391285] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/24/2011] [Indexed: 11/22/2022]
Abstract
The degree of applicability of chemogenomic approaches to protein families depends on the accuracy and completeness of pharmacological data and the corresponding level of pharmacological similarity observed among their protein members. The recent public domain availability of pharmacological data for thousands of small molecules on 204 G protein-coupled receptors (GPCRs) provides a firm basis for an in-depth cross-pharmacology analysis of this superfamily. The number of protein targets included in the cross-pharmacology profile of the different GPCRs changes significantly upon varying the ligand similarity and binding affinity criteria. However, with the exception of muscarinic receptors, aminergic GPCRs distinguish themselves from the rest of the members in the family by their remarkably high levels of pharmacological similarity among them. Clusters of non-GPCR targets related by cross-pharmacology with particular GPCRs are identified and the implications for unwanted side-effects, as well as for repurposing opportunities, discussed.
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Affiliation(s)
- Ferran Briansó
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Maria C. Carrascosa
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Tudor I. Oprea
- Division of Biocomputing, Department of Biochemistry & Molecular Biology and UNM Center for Molecular Discovery, University of New Mexico School of Medicine, MSC11 6145, Albuquerque NM 87131, USA
| | - Jordi Mestres
- Chemogenomics Laboratory, Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica and Universitat Pompeu Fabra, Pare de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Yang JO, Oh S, Ko G, Park SJ, Kim WY, Lee B, Lee S. VnD: a structure-centric database of disease-related SNPs and drugs. Nucleic Acids Res 2011; 39:D939-44. [PMID: 21051351 PMCID: PMC3013797 DOI: 10.1093/nar/gkq957] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 09/30/2010] [Indexed: 11/13/2022] Open
Abstract
Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.
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Affiliation(s)
- Jin Ok Yang
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Sangho Oh
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Gunhwan Ko
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Seong-Jin Park
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Woo-Yeon Kim
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Byungwook Lee
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
| | - Sanghyuk Lee
- Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305–806 and Ewha Research Center for Systems Biology, Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seoul 120–750, Korea
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Kalinski C, Umkehrer M, Weber L, Kolb J, Burdack C, Ross G. On the industrial applications of MCRs: molecular diversity in drug discovery and generic drug synthesis. Mol Divers 2010; 14:513-22. [PMID: 20229364 DOI: 10.1007/s11030-010-9225-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 01/19/2010] [Indexed: 10/19/2022]
Abstract
During the last decades, multicomponent chemistry has gained much attention in pharmaceutical research, especially in the context of lead finding and optimization. Here, in particular, the main advantages of multicomponent reactions (MCRs) like ease of automation and high diversity generation were utilized. In consequence of these beneficial properties, a plethora of new MCRs combined with appropriate classical reaction sequences have been published, the accessible chemical space was extended steadily. In the meantime, the desired high diversity became a challenge itself, because by now the systematic use of this huge and unmanageable space for drug discovery was limited by the lack of suitable computational tools. Therefore, this article provides an insight for the rational use of this enormous chemical space in drug discovery and generic drug synthesis. In this context, a short overview of the applied chemo informatics, necessary for the virtual screening of the biggest available chemical space, is given. Furthermore, some examples for recently developed multicomponent sequences are presented.
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Yan BB, Xue MZ, Xiong B, Liu K, Hu DY, Shen JK. ScafBank: a public comprehensive Scaffold database to support molecular hopping. Acta Pharmacol Sin 2009; 30:251-8. [PMID: 19151741 PMCID: PMC4002465 DOI: 10.1038/aps.2008.22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 12/08/2008] [Indexed: 11/08/2022] Open
Abstract
AIM The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years. Our goal is to provide a publically searchable database of scaffolds out from a large collection of existing chemical molecules. RESULTS Although a number of in silico methods have emerged to facilitate this process, which has become known as "scaffold hopping" or "molecular hopping", there is an urgent need for a database system to provide such valuable data in the drug design field. Here we have systematically analyzed a collection of commercially available small molecule databases and a bioactive compound database to identify unique scaffolds and we have built a publically searchable database. The analysis of approximately 4,800,000 of these compounds identified 241,824 unique scaffolds, which are stored in a relational database (http://202.127.30.184:8080/db.html). Each entry in the database is associated with a molecular occurrence and includes its distribution of molecular properties, such as molecular weight, logP, hydrogen bond acceptor number, hydrogen bond donor number, rotatable bond number and ring number. More importantly, for scaffolds derived from the bioactive compounds database, it also contains the original compounds and their target information. CONCLUSION This Web-based database system could help researchers in the fields of medicinal and organic chemistry to design novel molecules with properties similar to the original compounds, but built on novel scaffolds.
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Affiliation(s)
- Bi-bo Yan
- Electronics and Information College, Yangtze University, Jingzhou 434023, China
| | - Meng-zhu Xue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bing Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ke Liu
- Electronics and Information College, Yangtze University, Jingzhou 434023, China
| | - Ding-yu Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing-kang Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
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Rothweiler U, Czarna A, Krajewski M, Ciombor J, Kalinski C, Khazak V, Ross G, Skobeleva N, Weber L, Holak TA. Isoquinolin-1-one inhibitors of the MDM2-p53 interaction. ChemMedChem 2008; 3:1118-28. [PMID: 18428185 DOI: 10.1002/cmdc.200800025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
p53 has been at the centre of attention for drug design since the discovery of its growth-suppressive and pro-apoptotic activity. Herein we report the design and characterisation of a new class of isoquinolinone inhibitors of the MDM2-p53 interaction. Our identification of druglike and selective inhibitors of this protein-protein interaction included a straightforward in silico compound-selection process, a recently reported NMR spectroscopic approach for studying the MDM2-p53 interaction, and selectivity screening assays using cells with the same genetic background. The selected inhibitors were all able to induce apoptosis and the expression of p53-related genes, but only the isoquinolin-1-one-based inhibitors stabilised p53. Our NMR experiments give a persuading explanation for these results, showing that isoquinolin-1-one derivates are able to dissociate the preformed MDM2-p53 complex in vitro, releasing a folded and soluble p53. The joint application of these methods provides a framework for the discovery of protein interaction inhibitors as a promising starting point for further drug design.
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Affiliation(s)
- Ulli Rothweiler
- Max Planck Institute for Biochemistry, 82152 Martinsried, Germany
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Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK. Quantifying the relationships among drug classes. J Chem Inf Model 2008; 48:755-65. [PMID: 18335977 PMCID: PMC2722950 DOI: 10.1021/ci8000259] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The similarity of drug targets is typically measured using sequence or structural information. Here, we consider chemo-centric approaches that measure target similarity on the basis of their ligands, asking how chemoinformatics similarities differ from those derived bioinformatically, how stable the ligand networks are to changes in chemoinformatics metrics, and which network is the most reliable for prediction of pharmacology. We calculated the similarities between hundreds of drug targets and their ligands and mapped the relationship between them in a formal network. Bioinformatics networks were based on the BLAST similarity between sequences, while chemoinformatics networks were based on the ligand-set similarities calculated with either the Similarity Ensemble Approach (SEA) or a method derived from Bayesian statistics. By multiple criteria, bioinformatics and chemoinformatics networks differed substantially, and only occasionally did a high sequence similarity correspond to a high ligand-set similarity. In contrast, the chemoinformatics networks were stable to the method used to calculate the ligand-set similarities and to the chemical representation of the ligands. Also, the chemoinformatics networks were more natural and more organized, by network theory, than their bioinformatics counterparts: ligand-based networks were found to be small-world and broad-scale.
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Affiliation(s)
- Jérôme Hert
- Department of Pharmaceutical Chemistry, University of California—San Francisco, 1700 4th St., San Francisco, California 94143-2550
| | - Michael J. Keiser
- Department of Pharmaceutical Chemistry, University of California—San Francisco, 1700 4th St., San Francisco, California 94143-2550
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California—San Francisco, 1700 4th St., San Francisco, California 94143-2550
| | - Tudor I. Oprea
- Division of Biocomputing, MSC11 6145, University of New Mexico School of Medicine, 2703 Frontier NE, Albuquerque, New Mexico 87131
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California—San Francisco, 1700 4th St., San Francisco, California 94143-2550
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Zhang M, Sheng C, Xu H, Song Y, Zhang W. Constructing virtual combinatorial fragment libraries based upon MDL Drug Data Report database. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11426-007-0056-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Glen R, Adams S. Similarity Metrics and Descriptor Spaces – Which Combinations to Choose? ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200610097] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hassan M, Brown RD, Varma-O'brien S, Rogers D. Cheminformatics analysis and learning in a data pipelining environment. Mol Divers 2006; 10:283-99. [PMID: 17031533 DOI: 10.1007/s11030-006-9041-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 02/23/2006] [Indexed: 10/24/2022]
Abstract
Workflow technology is being increasingly applied in discovery information to organize and analyze data. SciTegic's Pipeline Pilot is a chemically intelligent implementation of a workflow technology known as data pipelining. It allows scientists to construct and execute workflows using components that encapsulate many cheminformatics based algorithms. In this paper we review SciTegic's methodology for molecular fingerprints, molecular similarity, molecular clustering, maximal common subgraph search and Bayesian learning. Case studies are described showing the application of these methods to the analysis of discovery data such as chemical series and high throughput screening results. The paper demonstrates that the methods are well suited to a wide variety of tasks such as building and applying predictive models of screening data, identifying molecules for lead optimization and the organization of molecules into families with structural commonality.
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Affiliation(s)
- Moises Hassan
- SciTegic, Inc., 10188 Telesis Court, Suite 100, San Diego, CA, 92121, USA,
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Davies JW, Glick M, Jenkins JL. Streamlining lead discovery by aligning in silico and high-throughput screening. Curr Opin Chem Biol 2006; 10:343-51. [PMID: 16822701 DOI: 10.1016/j.cbpa.2006.06.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2006] [Accepted: 06/21/2006] [Indexed: 12/01/2022]
Abstract
Lead discovery in the pharmaceutical environment is largely an industrial-scale process in which it is typical to screen 1-5 million compounds in a matter of weeks using High Throughput Screening (HTS). This process is a very costly endeavor. Typically a HTS campaign of 1 million compounds will cost anywhere from $500000 to $1000000. There is consequently a great deal of pressure to maximize the return on investment by finding fast and more effective ways to screen. A panacea that has emerged over the past few years to help address this issue is in silico screening. In silico screening is now incorporated in all areas of lead discovery; from target identification and library design, to hit analysis and compound profiling. However, as lead discovery has evolved over the past few years, so has the role of in silico screening.
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Affiliation(s)
- John W Davies
- Lead Discovery Center, Novartis Institutes for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Hoppe C, Steinbeck C, Wohlfahrt G. Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials. J Mol Graph Model 2006; 24:328-40. [PMID: 16260161 DOI: 10.1016/j.jmgm.2005.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 08/29/2005] [Accepted: 09/29/2005] [Indexed: 11/23/2022]
Abstract
We describe the application of knowledge-based potentials implemented in the MOE program to compare the ligand-binding sites of several proteins. The binding probabilities for a polar and a hydrophobic probe are calculated on a grid to allow easy comparison of binding sites of superimposed related proteins. The method is fast and simple enough to simultaneously use structural information of multiple proteins of a target family. The method can be used to rapidly cluster proteins into subfamilies according to the similarity of hydrophobic and polar fields of their ligand-binding sites. Regions of the binding site which are common within a protein family can be identified and analysed for the design of family-targeted libraries or those which differ for improvement of ligand selectivity. The field-based hierarchical clustering is demonstrated for three protein families: the ligand-binding domains of nuclear receptors, the ATP-binding sites of protein kinases and the substrate binding sites of proteases. More detailed comparisons are presented for serine proteases of the chymotrypsin family, for the peroxisome proliferator-activated receptor subfamily of nuclear receptors and for progesterone and androgen receptor. The results are in good accordance with structure-based analysis and highlight important differences of the binding sites, which have been also described in the literature.
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Affiliation(s)
- Christian Hoppe
- Orion Pharma, Medicinal Chemistry, P.O. Box 65, FIN-02101 Espoo, Finland
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25
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Abstract
Ligand flexibility is an important problem in molecular docking and virtual screening. To address this challenge, we investigate a hierarchical pre-organization of multiple conformations of small molecules. Such organization of pre-calculated conformations removes the exploration of ligand conformational space from the docking calculation and allows for concise representation of what can be thousands of conformations. The hierarchy also recognizes and prunes incompatible conformations early in the calculation, eliminating redundant calculations of fit. We investigate the method by docking the MDL Drug Data Report (MDDR), an annotated database of 100,000 molecules, into apo and holo forms of seven unrelated targets. This annotated database allows us to track the ranking of tens to hundreds of annotated ligands in each of the docking systems. The binding sites and database are prepared in an automated fashion in an attempt to remove some human bias from the calculations. Many thousands of explicit and implicit ligand conformations may be docked in calculations not much longer than required for single conformer docking. As long as internal energies are not considered, recombination with the hierarchy is additive as the number of degrees of freedom is increased. Molecules with even millions of conformations can be docked in a few minutes on a single desktop computer.
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Affiliation(s)
| | - Brian K. Shoichet
- *Address correspondence to this author at the University of California San Francisco, Dept. of Pharmaceutical Chemistry, 1700 4 Street, QB3 Building Room 508D, San Francisco, CA 94143-2550; Tel: 415-514-4126; Fax: 415-514-4260; E-mail:
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Cluzeau J, Lubell WD. Design, synthesis, and application of azabicyclo[X.Y.0]alkanone amino acids as constrained dipeptide surrogates and peptide mimics. Biopolymers 2005; 80:98-150. [PMID: 15795926 DOI: 10.1002/bip.20213] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Azabicyclo[X.Y.0]alkanone amino acids are challenging synthetic targets and useful tools for studying structure-activity relationships of native peptide ligands. They have been employed to increase potency and stability in conformationally rigid enzyme inhibitors and receptor ligands. Since last reviewed in 1997, activity in their synthesis and application has increased significantly and access is now available to a wider diversity of these peptide mimics. This review focuses on recent syntheses of these heterocyclic amino acids and their application in the investigation of biologically active peptides and peptide mimics.
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Affiliation(s)
- Jérôme Cluzeau
- Département de Chimie, Université de Montréal, Montréal H3C 3J7, Québec, Canada
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