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Ansari F, Ghasemi JB, Niazi A. Three Dimensional Quantitative Structure Activity Relationship and Pharmacophore Modeling of Tacrine Derivatives as Acetylcholinesterase Inhibitors in Alzheimer's Treatment. Med Chem 2020; 16:155-168. [DOI: 10.2174/1573406415666190513100646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 03/23/2019] [Accepted: 05/01/2019] [Indexed: 11/22/2022]
Abstract
Background:
Three dimensional quantitative structure activity relationship and pharmacophore
modeling are studied for tacrine derivatives as acetylcholinesterase inhibitors.
Methods:
The three dimensional quantitative structure–activity relationship and pharmacophore
methods were used to model the 68 derivatives of tacrine as human acetylcholinesterase inhibitors.
The effect of the docked conformer of each molecule in the enzyme cavity was investigated on the
predictive ability and statistical quality of the produced models.
Results:
The whole data set was divided into two training and test sets using hierarchical clustering
method. 3D-QSAR model, based on the comparative molecular field analysis has good statistical
parameters as indicated by q2 =0.613, r2 =0.876, and r2pred =0.75. In the case of comparative
molecular similarity index analysis, q2, r2 and r2pred values were 0.807, 0.96, and 0.865 respectively.
The statistical parameters of the models proved that the inhibition data are well fitted and
they have satisfactory predictive abilities.
Conclusion :
The results from this study illustrate the reliability of using techniques in exploring
the likely bonded conformations of the ligands in the active site of the protein target and improve
the understanding over the structural and chemical features of AChE.
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Affiliation(s)
- Fatemeh Ansari
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - Jahan B. Ghasemi
- Drug Design in Silico Lab, School of Sciences, Chemistry Faculty, University of Tehran, Tehran, Iran
| | - Ali Niazi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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Macalino SJY, Billones JB, Organo VG, Carrillo MCO. In Silico Strategies in Tuberculosis Drug Discovery. Molecules 2020; 25:E665. [PMID: 32033144 PMCID: PMC7037728 DOI: 10.3390/molecules25030665] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) remains a serious threat to global public health, responsible for an estimated 1.5 million mortalities in 2018. While there are available therapeutics for this infection, slow-acting drugs, poor patient compliance, drug toxicity, and drug resistance require the discovery of novel TB drugs. Discovering new and more potent antibiotics that target novel TB protein targets is an attractive strategy towards controlling the global TB epidemic. In silico strategies can be applied at multiple stages of the drug discovery paradigm to expedite the identification of novel anti-TB therapeutics. In this paper, we discuss the current TB treatment, emergence of drug resistance, and the effective application of computational tools to the different stages of TB drug discovery when combined with traditional biochemical methods. We will also highlight the strengths and points of improvement in in silico TB drug discovery research, as well as possible future perspectives in this field.
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Affiliation(s)
- Stephani Joy Y. Macalino
- Chemistry Department, De La Salle University, 2401 Taft Avenue, Manila 0992, Philippines;
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Junie B. Billones
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Voltaire G. Organo
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
| | - Maria Constancia O. Carrillo
- OVPAA-EIDR Program, “Computer-Aided Discovery of Compounds for the Treatment of Tuberculosis in the Philippines”, Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila 1000, Philippines; (V.G.O.); (M.C.O.C.)
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Teixeira C, Ventura C, Gomes JRB, Gomes P, Martins F. Cinnamic Derivatives as Antitubercular Agents: Characterization by Quantitative Structure-Activity Relationship Studies. Molecules 2020; 25:molecules25030456. [PMID: 31973244 PMCID: PMC7037561 DOI: 10.3390/molecules25030456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains one of the top ten causes of death worldwide and the main cause of mortality from a single infectious agent. The upsurge of multi- and extensively-drug resistant tuberculosis cases calls for an urgent need to develop new and more effective antitubercular drugs. As the cinnamoyl scaffold is a privileged and important pharmacophore in medicinal chemistry, some studies were conducted to find novel cinnamic acid derivatives (CAD) potentially active against tuberculosis. In this context, we have engaged in the setting up of a quantitative structure–activity relationships (QSAR) strategy to: (i) derive through multiple linear regression analysis a statistically significant model to describe the antitubercular activity of CAD towards wild-type Mtb; and (ii) identify the most relevant properties with an impact on the antitubercular behavior of those derivatives. The best-found model involved only geometrical and electronic CAD related properties and was successfully challenged through strict internal and external validation procedures. The physicochemical information encoded by the identified descriptors can be used to propose specific structural modifications to design better CAD antitubercular compounds.
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Affiliation(s)
- Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto, P-4169-007 Porto, Portugal
- Correspondence: (C.T.); (F.M.)
| | - Cristina Ventura
- Instituto Superior de Educação e Ciências, P-1750-142 Lisboa, Portugal
| | - José R. B. Gomes
- CICECO, Departamento de Química, Universidade de Aveiro, P-3810-193 Aveiro, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto, P-4169-007 Porto, Portugal
| | - Filomena Martins
- Centro de Química e Bioquímica (CQB), Centro de Química Estrutural (CQE), Faculdade de Ciências da Universidade de Lisboa, P-1749-016 Lisboa, Portugal
- Correspondence: (C.T.); (F.M.)
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Kausar S, Falcao AO. A visual approach for analysis and inference of molecular activity spaces. J Cheminform 2019; 11:63. [PMID: 33430986 PMCID: PMC6805449 DOI: 10.1186/s13321-019-0386-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/05/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Molecular space visualization can help to explore the diversity of large heterogeneous chemical data, which ultimately may increase the understanding of structure-activity relationships (SAR) in drug discovery projects. Visual SAR analysis can therefore be useful for library design, chemical classification for their biological evaluation and virtual screening for the selection of compounds for synthesis or in vitro testing. As such, computational approaches for molecular space visualization have become an important issue in cheminformatics research. The proposed approach uses molecular similarity as the sole input for computing a probabilistic surface of molecular activity (PSMA). This similarity matrix is transformed in 2D using different dimension reduction algorithms (Principal Coordinates Analysis ( PCooA), Kruskal multidimensional scaling, Sammon mapping and t-SNE). From this projection, a kernel density function is applied to compute the probability of activity for each coordinate in the new projected space. RESULTS This methodology was tested over four different quantitative structure-activity relationship (QSAR) binary classification data sets and the PSMAs were computed for each. The generated maps showed internal consistency with active molecules grouped together for all data sets and all dimensionality reduction algorithms. To validate the quality of the generated maps, the 2D coordinates of test molecules were computed into the new reference space using a data transformation matrix. In total sixteen PSMAs were built, and their performance was assessed using the Area Under Curve (AUC) and the Matthews Coefficient Correlation (MCC). For the best projections for each data set, AUC testing results ranged from 0.87 to 0.98 and the MCC scores ranged from 0.33 to 0.77, suggesting this methodology can validly capture the complexities of the molecular activity space. All four mapping functions provided generally good results yet the overall performance of PCooA and t-SNE was slightly better than Sammon mapping and Kruskal multidimensional scaling. CONCLUSIONS Our result showed that by using an appropriate combination of metric space representation and dimensionality reduction applied over metric spaces it is possible to produce a visual PSMA for which its consistency has been validated by using this map as a classification model. The produced maps can be used as prediction tools as it is simple to project any molecule into this new reference space as long as the similarities to the molecules used to compute the initial similarity matrix can be computed.
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Affiliation(s)
- Samina Kausar
- LaSIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Andre O. Falcao
- LaSIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Da C, Zhang D, Stashko M, Vasileiadi E, Parker R, Minson KA, Huey MG, Huelse JM, Hunter D, Gilbert TSK, Norris-Drouin J, Miley M, Herring LE, Graves LM, DeRyckere D, Earp HS, Graham D, Frye SV, Wang X, Kireev D. Data-Driven Construction of Antitumor Agents with Controlled Polypharmacology. J Am Chem Soc 2019; 141:15700-15709. [PMID: 31497954 PMCID: PMC6894422 DOI: 10.1021/jacs.9b08660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Controlling which particular members of a large protein family are targeted by a drug is key to achieving a desired therapeutic response. In this study, we report a rational data-driven strategy for achieving restricted polypharmacology in the design of antitumor agents selectively targeting the TYRO3, AXL, and MERTK (TAM) family tyrosine kinases. Our computational approach, based on the concept of fragments in structural environments (FRASE), distills relevant chemical information from structural and chemogenomic databases to assemble a three-dimensional inhibitor structure directly in the protein pocket. Target engagement by the inhibitors designed led to disruption of oncogenic phenotypes as demonstrated in enzymatic assays and in a panel of cancer cell lines, including acute lymphoblastic and myeloid leukemia (ALL/AML) and nonsmall cell lung cancer (NSCLC). Structural rationale underlying the approach was corroborated by X-ray crystallography. The lead compound demonstrated potent target inhibition in a pharmacodynamic study in leukemic mice.
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Affiliation(s)
- Chenxiao Da
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dehui Zhang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Stashko
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Eleana Vasileiadi
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Rebecca Parker
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Katherine A. Minson
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Madeline G. Huey
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Justus M. Huelse
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Debra Hunter
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas S. K. Gilbert
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Michael Miley
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Laura E. Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Lee M. Graves
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - H. Shelton Earp
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Douglas Graham
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, and Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
- Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599-7363
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Linking synthesis and structure descriptors from a large collection of synthetic records of zeolite materials. Nat Commun 2019; 10:4459. [PMID: 31575862 PMCID: PMC6773695 DOI: 10.1038/s41467-019-12394-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/08/2019] [Indexed: 11/23/2022] Open
Abstract
Correlating synthesis conditions and their consequences is a significant challenge, particularly for materials formed as metastable phases via kinetically controlled pathways, such as zeolites, owing to a lack of descriptors that effectively illustrate the synthesis protocols and their corresponding results. This study analyzes the synthetic records of zeolites compiled from the literature using machine learning techniques to rationalize physicochemical, structural, and heuristic insights to their chemistry. The synthesis descriptors extracted from the machine learning models are used to identify structure descriptors with the appropriate importance. A similarity network of crystal structures based on the structure descriptors shows the formation of communities populated by synthetically similar materials, including those outside the dataset. Crossover experiments based on previously overlooked structural similarities reveal the synthesis similarity of zeolites, confirming the synthesis–structure relationship. This approach is applicable to any system to rationalize empirical knowledge, populate synthesis records, and discover novel materials. Understanding zeolite synthesis-structure relationships remains challenging owing to the number of variables involved in their preparation. Here the authors analyze zeolite synthetic records from the literature via machine learning and find communities of synthetically related materials with previously overlooked similarities.
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Zhu C, Sawrey-Kubicek L, Beals E, Hughes RL, Rhodes CH, Sacchi R, Zivkovic AM. The HDL lipidome is widely remodeled by fast food versus Mediterranean diet in 4 days. Metabolomics 2019; 15:114. [PMID: 31422486 DOI: 10.1007/s11306-019-1579-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/12/2019] [Indexed: 11/24/2022]
Abstract
INTRODUCTION HDL is associated with increased longevity and protection from multiple chronic diseases. The major HDL protein ApoA-I has a half-life of about 4 days, however, the effects of diet on the composition of HDL particles at this time scale have not been studied. OBJECTIVES The objective of this study is to investigate the short term dietary effect on HDL lipidomic composition. METHODS In this randomized order cross-over study, ten healthy subjects consumed a Mediterranean (Med) and a fast food (FF) diet for 4 days, with a 4-day wash-out between treatments. Lipidomic composition was analyzed in isolated HDL fractions by an untargeted LC-MS method with 15 internal standards. RESULTS HDL phosphatidylethanolamine (PE) content was increased by FF diet, and 41 out of 170 lipid species were differentially affected by diet. Saturated fatty acids (FAs) and odd chain FA were enriched after FF diet, while very-long chain FA and unsaturated FA were enriched after Med diet. The composition of phosphatidylcholine (PC), triacylglycerol (TG) and cholesteryl ester (CE) were significantly altered to reflect the FA composition of the diet whereas the composition of sphingomyelin (SM) and ceramides were generally unaffected. CONCLUSION Results from this study indicate that the HDL lipidome is widely remodeled within 4 days of diet change and that certain lipid classes are more sensitive markers of diet whereas other lipid classes are better indicators of non-dietary factors.
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Affiliation(s)
- Chenghao Zhu
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Lisa Sawrey-Kubicek
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Elizabeth Beals
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Riley L Hughes
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Chris H Rhodes
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Romina Sacchi
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA
| | - Angela M Zivkovic
- Department of Nutrition, University of California, Davis, Davis, CA, 95616, USA.
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Anti-malarial, cytotoxicity and molecular docking studies of quinolinyl chalcones as potential anti-malarial agent. J Comput Aided Mol Des 2019; 33:677-688. [DOI: 10.1007/s10822-019-00210-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
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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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61
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Ebejer JP, Finn PW, Wong WK, Deane CM, Morris GM. Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening. J Chem Inf Model 2019; 59:2600-2616. [PMID: 31117509 PMCID: PMC7007185 DOI: 10.1021/acs.jcim.8b00779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present Ligity, a hybrid ligand-structure-based, non-superpositional method for virtual screening of large databases of small molecules. Ligity uses the relative spatial distribution of pharmacophoric interaction points (PIPs) derived from the conformations of small molecules. These are compared with the PIPs derived from key interaction features found in protein-ligand complexes and are used to prioritize likely binders. We investigated the effect of generating PIPs using the single lowest energy conformer versus an ensemble of conformers for each screened ligand, using different bin sizes for the distance between two features, utilizing triangular sets of pharmacophoric features (3-PIPs) versus chiral tetrahedral sets (4-PIPs), fusing data for targets with multiple protein-ligand complex structures, and applying different similarity measures. Ligity was benchmarked using the Directory of Useful Decoys-Enhanced (DUD-E). Optimal results were obtained using the tetrahedral PIPs derived from an ensemble of bound ligand conformers and a bin size of 1.5 Å, which are used as the default settings for Ligity. The high-throughput screening mode of Ligity, using only the lowest-energy conformer of each ligand, was used for benchmarking against the whole of the DUD-E, and a more resource-intensive, "information-rich" mode of Ligity, using a conformational ensemble of each ligand, were used for a representative subset of 10 targets. Against the full DUD-E database, mean area under the receiver operating characteristic curve (AUC) values ranged from 0.44 to 0.99, while for the representative subset they ranged from 0.61 to 0.86. Data fusion further improved Ligity's performance, with mean AUC values ranging from 0.64 to 0.95. Ligity is very efficient compared to a protein-ligand docking method such as AutoDock Vina: if the time taken for the precalculation of Ligity descriptors is included in the comparason, then Ligity is about 20 times faster than docking. A direct comparison of the virtual screening steps shows Ligity to be over 5000 times faster. Ligity highly ranks the lowest-energy conformers of DUD-E actives, in a statistically significant manner, behavior that is not observed for DUD-E decoys. Thus, our results suggest that active compounds tend to bind in relatively low-energy conformations compared to decoys. This may be because actives-and thus their lowest-energy conformations-have been optimized for conformational complementarity with their cognate binding sites.
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Affiliation(s)
- Jean-Paul Ebejer
- Centre for Molecular Medicine and Biobanking , University of Malta , Msida , MSD 2080 , Malta
| | - Paul W Finn
- Oxford Drug Design Limited, Oxford Centre for Innovation , New Road , Oxford OX1 1BY , U.K.,The School of Computing , University of Buckingham , Hunter Street , Buckingham , MK18 1EG , U.K
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
| | - Garrett M Morris
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
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Wang P, Li K, Tao Y, Li D, Zhang Y, Xu H, Yang H. TCM-ADMEpred: A novel strategy for poly-pharmacokinetics prediction of traditional Chinese medicine based on single constituent pharmacokinetics, structural similarity, and mathematical modeling. JOURNAL OF ETHNOPHARMACOLOGY 2019; 236:277-287. [PMID: 30826421 DOI: 10.1016/j.jep.2018.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/11/2018] [Accepted: 07/06/2018] [Indexed: 06/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Yuanhu Zhitong prescription (YZP) is a commonly used and relatively simple clinical herb preparation recorded in the China Pharmacopoeia. It contains Corydalis yanhusuo (Chinese name, Yanhusuo [YH]) and Angelica dahurica (Hoffm.) (Chinese name, Baizhi [BZ]), and has a long history of use in traditional Chinese medicine (TCM) for the treatment of stomach pain, hypochondriac pain, headache, and dysmenorrhea. AIM OF THE STUDY A TCM-ADMEpred method is developed for novel strategy for poly-pharmacokinetics prediction of TCM. To predict the pharmacokinetic characteristics of the main YZP constituents in rat plasma using in silico models, based on the theory that structurally similar constituents show similar pharmacokinetic properties. This approach may facilitate in silico prediction of the pharmacokinetics of TCM. MATERIALS AND METHODS A robust platform using ultra-performance liquid chromatography coupled with triple quadrupole electrospray tandem mass spectrometry (UPLC-ESI-MS/MS) was developed and validated for simultaneous determination of seven active YZP constituents in rat plasma. These seven compounds were divided into two structural classes, alkaloids and coumarins. The correlation between AUC profiles within a structural class was expressed as Γ+, and this variable was used to develop two novel in silico models to predict constituent AUC values. The pharmacokinetics of tetrahydropalmatine, tetrahydroberberine, and corydaline following YZP administration were predicted using the Γ+-values of α-allocryptopine observed following YH administration, while those of imperatorin and isoimperatorin following BZ administration were predicted using the Γ+-values of byakangelicin observed following YZP administration. RESULTS The UPLC-ESI-MS/MS method was successfully used to evaluate pharmacokinetic parameters after oral YZP, YH, or BZ administration. Our findings showed that co-administration of YH and BZ increased the AUC of four alkaloid constituents and reduced the AUC of three coumarin constituents, which might provide a scientific rationale for co-administering these herbs clinically as a YZP preparation, thus increasing their efficacy and reducing toxicity. The AUC values of imperatorin and isoimperatorin were predicted 3 h after oral BZ administration, with the bias ratios between the theoretical values and the observed experimental values ranging from 0.61% to 11.4%, and average bias ratios of 5.8% and 8.0%, respectively. The AUC values of tetrahydropalmatine, tetrahydroberberine, and corydaline were predicted 3 h after oral YZP administration, with bias ratios ranging from 3.7% to 46.4%, and average bias ratios of 23.8%, 15.4%, and 25.8%, respectively. CONCLUSION The UPLC-ESI-MS/MS method was successfully applied to pharmacokinetic evaluations after oral administration of YZP, YH, and BZ to rats. The Γ+ variable was used to express the correlation between the AUC profiles of structurally similar compounds. This facilitated the development of an in silico model that was used to predict the AUC of three alkaloids in YZP and of two coumarins in BZ. Calculation of the bias ratios between the predicted and experimental values suggested that this in silico model provided a viable approach for the prediction of TCM pharmacokinetics.
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Affiliation(s)
- Ping Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Ke Li
- Shandong Provincial Key Laboratory of Automotive Electronic Technology, Institute of Automation, Shandong Academy of Sciences, Jinan 250014, PR China
| | - Ye Tao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Defeng Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Yi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Haiyu Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China; Shaanxi Institute of International Trade & Commerce, Xianyang 712046, PR China.
| | - Hongjun Yang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
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63
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Kausar S, Falcao AO. Analysis and Comparison of Vector Space and Metric Space Representations in QSAR Modeling. Molecules 2019; 24:E1698. [PMID: 31052325 PMCID: PMC6539555 DOI: 10.3390/molecules24091698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 12/16/2022] Open
Abstract
The performance of quantitative structure-activity relationship (QSAR) models largely depends on the relevance of the selected molecular representation used as input data matrices. This work presents a thorough comparative analysis of two main categories of molecular representations (vector space and metric space) for fitting robust machine learning models in QSAR problems. For the assessment of these methods, seven different molecular representations that included RDKit descriptors, five different fingerprints types (MACCS, PubChem, FP2-based, Atom Pair, and ECFP4), and a graph matching approach (non-contiguous atom matching structure similarity; NAMS) in both vector space and metric space, were subjected to state-of-art machine learning methods that included different dimensionality reduction methods (feature selection and linear dimensionality reduction). Five distinct QSAR data sets were used for direct assessment and analysis. Results show that, in general, metric-space and vector-space representations are able to produce equivalent models, but there are significant differences between individual approaches. The NAMS-based similarity approach consistently outperformed most fingerprint representations in model quality, closely followed by Atom Pair fingerprints. To further verify these findings, the metric space-based models were fitted to the same data sets with the closest neighbors removed. These latter results further strengthened the above conclusions. The metric space graph-based approach appeared significantly superior to the other representations, albeit at a significant computational cost.
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Affiliation(s)
- Samina Kausar
- LASIGE, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
| | - Andre O Falcao
- LASIGE, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciencias, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
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64
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Garcia-Hernandez C, Fernández A, Serratosa F. Ligand-Based Virtual Screening Using Graph Edit Distance as Molecular Similarity Measure. J Chem Inf Model 2019; 59:1410-1421. [PMID: 30920214 PMCID: PMC6668628 DOI: 10.1021/acs.jcim.8b00820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Extended
reduced graphs provide summary representations of chemical
structures using pharmacophore-type node descriptions to encode the
relevant molecular properties. Commonly used similarity measures using
reduced graphs convert these graphs into 2D vectors like fingerprints,
before chemical comparisons are made. This study investigates the
effectiveness of a graph-only driven molecular comparison by using
extended reduced graphs along with graph edit distance methods for
molecular similarity calculation as a tool for ligand-based virtual
screening applications, which estimate the bioactivity of a chemical
on the basis of the bioactivity of similar compounds. The results
proved to be very stable and the graph editing distance method performed
better than other methods previously used on reduced graphs. This
is exemplified with six publicly available data sets: DUD-E, MUV,
GLL&GDD, CAPST, NRLiSt BDB, and ULS-UDS. The screening and statistical
tools available on the ligand-based virtual screening benchmarking
platform and the RDKit were also used. In the experiments, our method
performed better than other molecular similarity methods which use
array representations in most cases. Overall, it is shown that extended
reduced graphs along with graph edit distance is a combination of
methods that has numerous applications and can identify bioactivity
similarities in a structurally diverse group of molecules.
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Affiliation(s)
- Carlos Garcia-Hernandez
- Departament d'Enginyeria Química , Universitat Rovira i Virgili , Tarragona , Catalunya 43007 , Spain
| | - Alberto Fernández
- Departament d'Enginyeria Química , Universitat Rovira i Virgili , Tarragona , Catalunya 43007 , Spain
| | - Francesc Serratosa
- Departament d'Enginyeria Informàtica i Matemàtiques , Universitat Rovira i Virgili , Tarragona , Catalunya 43007 , Spain
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65
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Jaworska J, Nikolova-Jeliazkova N, Aldenberg T. QSAR Applicability Domain Estimation by Projection of the Training Set in Descriptor Space: A Review. Altern Lab Anim 2019; 33:445-59. [PMID: 16268757 DOI: 10.1177/026119290503300508] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
As the use of Quantitative Structure Activity Relationship (QSAR) models for chemical management increases, the reliability of the predictions from such models is a matter of growing concern. The OECD QSAR Validation Principles recommend that a model should be used within its applicability domain (AD). The Setubal Workshop report provided conceptual guidance on defining a (Q)SAR AD, but it is difficult to use directly. The practical application of the AD concept requires an operational definition that permits the design of an automatic (computerised), quantitative procedure to determine a model's AD. An attempt is made to address this need, and methods and criteria for estimating AD through training set interpolation in descriptor space are reviewed. It is proposed that response space should be included in the training set representation. Thus, training set chemicals are points in n-dimensional descriptor space and m-dimensional model response space. Four major approaches for estimating interpolation regions in a multivariate space are reviewed and compared: range, distance, geometrical, and probability density distribution.
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Affiliation(s)
- Joanna Jaworska
- Procter and Gamble, Eurocor, Central Product Safety, 100 Temselaan, 1853 Strombeek-Bever, Belgium.
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66
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Heine P, Witt G, Gilardi A, Gribbon P, Kummer L, Plückthun A. High-Throughput Fluorescence Polarization Assay to Identify Ligands Using Purified G Protein-Coupled Receptor. SLAS DISCOVERY 2019; 24:915-927. [PMID: 30925845 DOI: 10.1177/2472555219837344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of cell-free high-throughput (HT) methods to screen and select novel lead compounds remains one of the key challenges in G protein-coupled receptor (GPCR) drug discovery. Mutational approaches have allowed the stabilization of GPCRs in a purified and ligand-free state. The increased intramolecular stability overcomes two major drawbacks for usage in in vitro screening, the low receptor density on cells and the low stability in micelles. Here, an HT fluorescence polarization (FP) assay for the neurotensin receptor type 1 (NTS1) was developed. The assay operates in a 384-well format and is tolerant to DMSO. From a library screen of 1272 compounds, 12 (~1%) were identified as primary hits. These compounds were validated in orthogonal assay formats using surface plasmon resonance (SPR), which confirmed binding of seven compounds (0.6%). One of these compounds showed a clear preference for the orthosteric binding pocket with submicromolar affinity. A second compound revealed binding at a nonorthosteric binding region and showed specific biological activity on NTS1-expressing cells. A search of analogs led to further enhancement of affinity, but at the expense of activity. The identification of GPCR ligands in a cell-free assay should allow the expansion of GPCR pharmaceuticals with antagonistic or agonistic activity.
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Affiliation(s)
- P Heine
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - G Witt
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Hamburg, Germany
| | - A Gilardi
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Hamburg, Germany
| | - P Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Hamburg, Germany
| | - L Kummer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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67
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Zhou H, Cao H, Skolnick J. FINDSITE comb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. J Chem Inf Model 2018; 58:2343-2354. [PMID: 30278128 PMCID: PMC6437778 DOI: 10.1021/acs.jcim.8b00309] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Computational approaches for predicting protein-ligand interactions can facilitate drug lead discovery and drug target determination. We have previously developed a threading/structural-based approach, FINDSITEcomb, for the virtual ligand screening of proteins that has been extensively experimentally validated. Even when low resolution predicted protein structures are employed, FINDSITEcomb has the advantage of being faster and more accurate than traditional high-resolution structure-based docking methods. It also overcomes the limitations of traditional QSAR methods that require a known set of seed ligands that bind to the given protein target. Here, we further improve FINDSITEcomb by enhancing its template ligand selection from the PDB/DrugBank/ChEMBL libraries of known protein-ligand interactions by (1) parsing the template proteins and their corresponding binding ligands in the DrugBank and ChEMBL libraries into domains so that the ligands with falsely matched domains to the targets will not be selected as template ligands; (2) applying various thresholds to filter out falsely matched template structures in the structure comparison process and thus their corresponding ligands for template ligand selection. With a sequence identity cutoff of 30% of target to templates and modeled target structures, FINDSITEcomb2.0 is shown to significantly improve upon FINDSITEcomb on the DUD-E benchmark set by increasing the 1% enrichment factor from 16.7 to 22.1, with a p-value of 4.3 × 10-3 by the Student t-test. With an 80% sequence identity cutoff of target to templates for the DUD-E set and modeled target structures, FINDSITEcomb2.0, having a 1% ROC enrichment factor of 52.39, also outperforms state-of-the-art methods that employ machine learning such as a deep convolutional neural network, CNN, with an enrichment of 29.65. Thus, FINDSITEcomb2.0 represents a significant improvement in the state-of-the-art. The FINDSITEcomb2.0 web service is freely available for academic users at http://pwp.gatech.edu/cssb/FINDSITE-COMB-2 .
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Affiliation(s)
- Hongyi Zhou
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, GA 30332-2000
| | - Hongnan Cao
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, GA 30332-2000
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, GA 30332-2000
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68
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Peerless JS, Milliken NJB, Oweida TJ, Manning MD, Yingling YG. Soft Matter Informatics: Current Progress and Challenges. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800129] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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69
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Basu P, Maier C. Phytoestrogens and breast cancer: In vitro anticancer activities of isoflavones, lignans, coumestans, stilbenes and their analogs and derivatives. Biomed Pharmacother 2018; 107:1648-1666. [DOI: 10.1016/j.biopha.2018.08.100] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 01/11/2023] Open
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70
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Liu R, Glover KP, Feasel MG, Wallqvist A. General Approach to Estimate Error Bars for Quantitative Structure–Activity Relationship Predictions of Molecular Activity. J Chem Inf Model 2018; 58:1561-1575. [DOI: 10.1021/acs.jcim.8b00114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruifeng Liu
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States
| | - Kyle P. Glover
- Defense Threat Reduction Agency, Aberdeen Proving Ground, Maryland 21010, United States
| | - Michael G. Feasel
- U.S. Army—Edgewood Chemical Biological Center, Operational Toxicology, Aberdeen Proving Ground, Maryland 21010, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland 21702, United States
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71
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Yao Z, Jiang S, Zhang L, Gao B, He X, Zhang JZH, Wei D. Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes. Protein Sci 2018; 27:1526-1534. [PMID: 29722450 DOI: 10.1002/pro.3437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 11/07/2022]
Abstract
The study of enzyme substrate specificity is vital for developing potential applications of enzymes. However, the routine experimental procedures require lot of resources in the discovery of novel substrates. This article reports an in silico structure-based algorithm called Crius, which predicts substrates for enzyme. The results of this fragment-based algorithm show good agreements between the simulated and experimental substrate specificities, using a lipase from Candida antarctica (CALB), a nitrilase from Cyanobacterium syechocystis sp. PCC6803 (Nit6803), and an aldo-keto reductase from Gluconobacter oxydans (Gox0644). This opens new prospects of developing computer algorithms that can effectively predict substrates for an enzyme.
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Affiliation(s)
- Zhiqiang Yao
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Lujia Zhang
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
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72
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Pascoini AL, Federico LB, Arêas ALF, Verde BA, Freitas PG, Camps I. In silico development of new acetylcholinesterase inhibitors. J Biomol Struct Dyn 2018; 37:1007-1021. [DOI: 10.1080/07391102.2018.1447513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- A. L. Pascoini
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - L. B. Federico
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - A. L. F. Arêas
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - B. A. Verde
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - P. G. Freitas
- Laboratory of Molecular Modeling and Computer Simulations-MolMod-CS, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - I. Camps
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
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73
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Snell TW, Johnston RK, Matthews AB, Zhou H, Gao M, Skolnick J. Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers. Biogerontology 2018; 19:145-157. [PMID: 29340835 PMCID: PMC5834582 DOI: 10.1007/s10522-018-9745-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/09/2018] [Indexed: 12/29/2022]
Abstract
Pharmaceutical interventions can slow aging in animals, and have advantages because their dose can be tightly regulated and the timing of the intervention can be closely controlled. They also may complement environmental interventions like caloric restriction by acting additively. A fertile source for therapies slowing aging is FDA approved drugs whose safety has been investigated. Because drugs bind to several protein targets, they cause multiple effects, many of which have not been characterized. It is possible that some of the side effects of drugs prescribed for one therapy may have benefits in retarding aging. We used computationally guided drug screening for prioritizing drug targets to produce a short list of candidate compounds for in vivo testing. We applied the virtual ligand screening approach FINDSITEcomb for screening potential anti-aging protein targets against FDA approved drugs listed in DrugBank. A short list of 31 promising compounds was screened using a multi-tiered approach with rotifers as an animal model of aging. Primary and secondary survival screens and cohort life table experiments identified four drugs capable of extending rotifer lifespan by 8-42%. Exposures to 1 µM erythromycin, 5 µM carglumic acid, 3 µM capecitabine, and 1 µM ivermectin, extended rotifer lifespan without significant effect on reproduction. Some drugs also extended healthspan, as estimated by mitochondria activity and mobility (swimming speed). Our most promising result is that rotifer lifespan was extended by 7-8.9% even when treatment was started in middle age.
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Affiliation(s)
- Terry W Snell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA.
| | - Rachel K Johnston
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA
| | - Amelia B Matthews
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA
| | - Hongyi Zhou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA
| | - Mu Gao
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA
| | - Jeffrey Skolnick
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0230, USA
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74
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Poynton FE, Bright SA, Blasco S, Williams DC, Kelly JM, Gunnlaugsson T. The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications. Chem Soc Rev 2018; 46:7706-7756. [PMID: 29177281 DOI: 10.1039/c7cs00680b] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ruthenium(ii) [Ru(ii)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.
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Affiliation(s)
- Fergus E Poynton
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
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75
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76
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Miki T, Yokokawa T, Ke PJ, Hsieh IF, Hsieh CH, Kume T, Yoneya K, Matsui K. Statistical recipe for quantifying microbial functional diversity from EcoPlate metabolic profiling. Ecol Res 2017. [DOI: 10.1007/s11284-017-1554-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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77
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O'Hagan S, Kell DB. Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries. Biotechnol J 2017; 13. [PMID: 29168302 DOI: 10.1002/biot.201700503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/09/2017] [Indexed: 01/01/2023]
Abstract
Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates.
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Affiliation(s)
- Steve O'Hagan
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B Kell
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Prof. D. B. Kell, Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
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Chen R, Wan J, Song J, Qian Y, Liu Y, Gu S. Rational screening of peroxisome proliferator-activated receptor-γ agonists from natural products: potential therapeutics for heart failure. PHARMACEUTICAL BIOLOGY 2017; 55:503-509. [PMID: 27937122 PMCID: PMC6130577 DOI: 10.1080/13880209.2016.1255648] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 08/17/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
CONTEXT Peroxisome proliferator-activated receptor-γ (PPARγ) is a member of the nuclear hormone receptor superfamily of ligand-activated transcription factors. Activation of PPARγ pathway has been shown to enhance fatty acid oxidation, improve endothelial cell function, and decrease myocardial fibrosis in heart failure. Thus, the protein has been raised as an attractive target for heart failure therapy. OBJECTIVE This work attempted to discover new and potent PPARγ agonists from natural products using a synthetic strategy of computer virtual screening and transactivation reporter assay. MATERIALS AND METHODS A large library of structurally diverse, drug-like natural products was compiled, from which those with unsatisfactory pharmacokinetic profile and/or structurally redundant compounds were excluded. The binding mode of remaining candidates to PPARγ ligand-binding domain (LBD) was computationally modelled using molecular docking and their relative binding potency was ranked by an empirical scoring scheme. Consequently, eight commercially available hits with top scores were selected and their biological activity was determined using a cell-based reporter-gene assay. RESULTS Four natural product compounds, namely ZINC13408172, ZINC4292805, ZINC44179 and ZINC901461, were identified to have high or moderate agonistic potency against human PPARγ with EC50 values of 0.084, 2.1, 0.35 and 5.6 μM, respectively, which are comparable to or even better than that of the approved PPARγ full agonists pioglitazone (EC50 = 0.16 μM) and rosiglitazone (EC50 = 0.034 μM). Hydrophobic interactions and van der Waals contacts are the primary chemical forces to stabilize the complex architecture of PPARγ LBD domain with these agonist ligands, while few hydrogen bonds, salt bridges and/or π-π stacking at the complex interfaces confer selectivity and specificity for the domain-agonist recognition. DISCUSSION AND CONCLUSION The integrated in vitro-in silico screening strategy can be successfully applied to rational discovery of biologically active compounds. The newly identified natural products with PPARγ agonistic potency are considered as promising lead scaffolds to develop novel chemical therapeutics for heart failure.
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Affiliation(s)
- Rui Chen
- Department of Geriatric Medicine, Shanghai Eighth People's Hospital, Shanghai, China
| | - Jing Wan
- Department of Geriatric Medicine, Shanghai Eighth People's Hospital, Shanghai, China
| | - Jing Song
- Department of Geriatric Medicine, Shanghai Eighth People's Hospital, Shanghai, China
| | - Yan Qian
- Department of Geriatric Medicine, Shanghai Eighth People's Hospital, Shanghai, China
| | - Yong Liu
- Department of Geriatric Medicine, Shanghai Eighth People's Hospital, Shanghai, China
| | - Shuiming Gu
- Department of Cardiology, Shanghai Eighth People's Hospital, Shanghai, China
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79
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Taraji M, Haddad PR, Amos RIJ, Talebi M, Szucs R, Dolan JW, Pohl CA. Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review. Anal Chim Acta 2017; 1000:20-40. [PMID: 29289311 DOI: 10.1016/j.aca.2017.09.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/22/2017] [Accepted: 09/24/2017] [Indexed: 02/09/2023]
Abstract
With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.
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Affiliation(s)
- Maryam Taraji
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Paul R Haddad
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia.
| | - Ruth I J Amos
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Mohammad Talebi
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Roman Szucs
- Pfizer Global Research and Development, CT13 9NJ, Sandwich, UK
| | - John W Dolan
- LC Resources, 1795 NW Wallace Rd., McMinnville, OR 97128, USA
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80
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Tao Y, Zou W, Cremer D, Kraka E. Characterizing Chemical Similarity with Vibrational Spectroscopy: New Insights into the Substituent Effects in Monosubstituted Benzenes. J Phys Chem A 2017; 121:8086-8096. [PMID: 28960072 DOI: 10.1021/acs.jpca.7b08298] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A novel approach is presented to assess chemical similarity based the local vibrational mode analysis developed by Konkoli and Cremer. The local mode frequency shifts are introduced as similarity descriptors that are sensitive to any electronic structure change. In this work, 59 different monosubstituted benzenes are compared. For a subset of 43 compounds, for which experimental data was available, the ortho-/para- and meta-directing effect in electrophilic aromatic substitution reactions could be correctly reproduced, proving the robustness of the new similarity index. For the remaining 16 compounds, the directing effect was predicted. The new approach is broadly applicable to all compounds for which either experimental or calculated vibrational frequency information is available.
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Affiliation(s)
- Yunwen Tao
- Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Wenli Zou
- Institute of Modern Physics, Northwest University , Xi'an, Shaanxi 710069, People's Republic of China
| | - Dieter Cremer
- Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University , 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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81
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Yea SJ, Kim BY, Kim C, Yi MY. A framework for the targeted selection of herbs with similar efficacy by exploiting drug repositioning technique and curated biomedical knowledge. JOURNAL OF ETHNOPHARMACOLOGY 2017; 208:117-128. [PMID: 28687508 DOI: 10.1016/j.jep.2017.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
ETHNO PHARMACOLOGICAL RELEVANCE Plants have been the most important natural resources for traditional medicine and for the modern pharmaceutical industry. They have been in demand in regards to finding alternative medicinal herbs with similar efficacy. Due to the very low probability of discovering useful compounds by random screening, researchers have advocated for using targeted selection approaches. Furthermore, because drug repositioning can speed up the process of drug development, an integrated technique that exploits chemical, genetic, and disease information has been recently developed. Building upon these findings, in this paper, we propose a novel framework for the targeted selection of herbs with similar efficacy by exploiting drug repositioning technique and curated modern scientific biomedical knowledge, with the goal of improving the possibility of inferring the traditional empirical ethno-pharmacological knowledge. MATERIALS AND METHODS To rank candidate herbs on the basis of similarities against target herb, we proposed and evaluated a framework that is comprised of the following four layers: links, extract, similarity, and model. In the framework, multiple databases are linked to build an herb-compound-protein-disease network which was composed of one tripartite network and two bipartite networks allowing comprehensive and detailed information to be extracted. Further, various similarity scores between herbs are calculated, and then prediction models are trained and tested on the basis of theses similarity features. RESULTS The proposed framework has been found to be feasible in terms of link loss. Out of the 50 similarities, the best one enhanced the performance of ranking herbs with similar efficacy by about 120-320% compared with our previous study. Also, the prediction model showed improved performance by about 180-480%. While building the prediction model, we identified the compound information as being the most important knowledge source and structural similarity as the most useful measure. CONCLUSIONS In the proposed framework, we took the knowledge of herbal medicine, chemistry, biology, and medicine into consideration to rank herbs with similar efficacy in candidates. The experimental results demonstrated that the performances of framework outperformed the baselines and identified the important knowledge source and useful similarity measure.
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Affiliation(s)
- Sang-Jun Yea
- Graduate School of Knowledge Service Engineering, Korea Advanced Institute of Science and Technology, Republic of Korea; K-herb Research Center, Korea Institute of Oriental Medicine, Republic of Korea
| | - Bu-Yeo Kim
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Republic of Korea
| | - Chul Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Republic of Korea.
| | - Mun Yong Yi
- Graduate School of Knowledge Service Engineering, Korea Advanced Institute of Science and Technology, Republic of Korea.
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82
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Zhokhova NI, Baskin II. Energy‐based Neural Networks as a Tool for Harmony‐based Virtual Screening. Mol Inform 2017. [DOI: 10.1002/minf.201700054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nelly I. Zhokhova
- Faculty of PhysicsM.V. Lomonosov Moscow State University 119991 Moscow Russian Federation
| | - Igor I. Baskin
- Faculty of PhysicsM.V. Lomonosov Moscow State University 119991 Moscow Russian Federation
- A. M. Butlerov Institute of ChemistryKazan Federal University Kazan Russian Federation
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83
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First protein drug target’s appraisal of lead-likeness descriptors to unfold the intervening chemical space. J Mol Graph Model 2017; 72:272-282. [DOI: 10.1016/j.jmgm.2016.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/24/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
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84
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Affiliation(s)
- Arne Wagner
- Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hans-Jörg Himmel
- Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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85
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Abstract
Quantitative Structure-Activity Relationship (QSAR) models have manifold applications in drug discovery, environmental fate modeling, risk assessment, and property prediction of chemicals and pharmaceuticals. One of the principles recommended by the Organization of Economic Co-operation and Development (OECD) for model validation requires defining the Applicability Domain (AD) for QSAR models, which allows one to estimate the uncertainty in the prediction of a compound based on how similar it is to the training compounds, which are used in the model development. The AD is a significant tool to build a reliable QSAR model, which is generally limited in use to query chemicals structurally similar to the training compounds. Thus, characterization of interpolation space is significant in defining the AD. An attempt is made in this chapter to address the important concepts and methodology of the AD as well as criteria for estimating AD through training set interpolation in the descriptor space.
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86
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Basu A, Sohn YS, Alyan M, Nechushtai R, Domb AJ, Goldblum A. Discovering Novel and Diverse Iron-Chelators in Silico. J Chem Inf Model 2016; 56:2476-2485. [PMID: 28024407 DOI: 10.1021/acs.jcim.6b00450] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Specific iron chelation is a validated strategy in anticancer drug discovery. However, only a few chemical classes (4-5 categories) have been reported to date. We discovered in silico five new structurally diverse iron-chelators by screening through models based on previously known chelators. To encompass a larger chemical space and propose newer scaffolds, we used our iterative stochastic elimination (ISE) algorithm for model building and subsequent virtual screening (VS). The ISE models were developed by training a data set of 130 reported iron-chelators. The developed models are statistically significant with area under the receiver operating curve greater than 0.9. The models were used to screen the Enamine chemical database of ∼1.8 million molecules. The top ranked 650 molecules were reduced to 50 diverse structures, and a few others were eliminated due to the presence of reactive groups. Finally, 34 molecules were purchased and tested in vitro. Five compounds were identified with significant iron-chelation activity in Cal-G assay. Intracellular iron-chelation study revealed one compound as equivalent in potency to the iron chelating "gold standards" deferoxamine and deferiprone. The amount of discovered positives (5 out of 34) is expected by the realistic enrichment factor of the model.
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Affiliation(s)
- Arijit Basu
- School of Pharmacy, Institute for Drug Research, Hebrew University of Jerusalem , Jerusalem, 91120, Israel
| | - Yang-Sung Sohn
- Department of Plant and Environmental Sciences, the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem , Givat Ram, Jerusalem, 91904, Israel
| | - Mohamed Alyan
- School of Pharmacy, Institute for Drug Research, Hebrew University of Jerusalem , Jerusalem, 91120, Israel
| | - Rachel Nechushtai
- Department of Plant and Environmental Sciences, the Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem , Givat Ram, Jerusalem, 91904, Israel
| | - Abraham J Domb
- School of Pharmacy, Institute for Drug Research, Hebrew University of Jerusalem , Jerusalem, 91120, Israel
| | - Amiram Goldblum
- School of Pharmacy, Institute for Drug Research, Hebrew University of Jerusalem , Jerusalem, 91120, Israel
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87
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Abstract
Rapid determination of whether a candidate compound will bind to a particular target receptor remains a stumbling block in drug discovery. We use an approach inspired by random matrix theory to decompose the known ligand set of a target in terms of orthogonal "signals" of salient chemical features, and distinguish these from the much larger set of ligand chemical features that are not relevant for binding to that particular target receptor. After removing the noise caused by finite sampling, we show that the similarity of an unknown ligand to the remaining, cleaned chemical features is a robust predictor of ligand-target affinity, performing as well or better than any algorithm in the published literature. We interpret our algorithm as deriving a model for the binding energy between a target receptor and the set of known ligands, where the underlying binding energy model is related to the classic Ising model in statistical physics.
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88
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Abstract
The olfactory system removes correlations in natural odors using a network of inhibitory neurons in the olfactory bulb. It has been proposed that this network integrates the response from all olfactory receptors and inhibits them equally. However, how such global inhibition influences the neural representations of odors is unclear. Here, we study a simple statistical model of the processing in the olfactory bulb, which leads to concentration-invariant, sparse representations of the odor composition. We show that the inhibition strength can be tuned to obtain sparse representations that are still useful to discriminate odors that vary in relative concentration, size, and composition. The model reveals two generic consequences of global inhibition: (i) odors with many molecular species are more difficult to discriminate and (ii) receptor arrays with heterogeneous sensitivities perform badly. Comparing these predictions to experiments will help us to understand the role of global inhibition in shaping normalized odor representations in the olfactory bulb.
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Affiliation(s)
- David Zwicker
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, United States of America
- Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, MA 02138, United States of America
- * E-mail:
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89
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Ding X, Liu X, Song X, Yao J. Chemotherapy Drug Response to the L858R-induced Conformational Change of EGFR Activation Loop in Lung Cancer. Mol Inform 2016; 35:529-537. [PMID: 27643705 DOI: 10.1002/minf.201600088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/28/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Xi Ding
- Department of Pharmacy; The Affiliated Hospital of Nantong University; Dongtai 224200 China
| | - Xingcai Liu
- Department of Pharmacy; The Affiliated Hospital of Nantong University; Dongtai 224200 China
| | - Xiaoyun Song
- Department of Pharmacy; The Affiliated Hospital of Nantong University; Dongtai 224200 China
| | - Jun Yao
- Department of Pneumology; The Affiliated Hospital of Nantong University; Dongtai 224200 China
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90
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Yao H, Sun Q, Zhu J. Identification and Characterization of Small-Molecule Inhibitors to Selectively Target the DFG-in over the DFG-out Conformation of the B-Raf Kinase V600E Mutant in Colorectal Cancer. Arch Pharm (Weinheim) 2016; 349:808-815. [PMID: 27624806 DOI: 10.1002/ardp.201600184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Huixiang Yao
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
| | - Qun Sun
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
| | - Jinshui Zhu
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
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91
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Nix MA, Kaelin CB, Palomino R, Miller JL, Barsh GS, Millhauser GL. Electrostatic Similarity Analysis of Human β-Defensin Binding in the Melanocortin System. Biophys J 2016; 109:1946-58. [PMID: 26536271 DOI: 10.1016/j.bpj.2015.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
The β-defensins are a class of small cationic proteins that serve as components of numerous systems in vertebrate biology, including the immune and melanocortin systems. Human β-defensin 3 (HBD3), which is produced in the skin, has been found to bind to melanocortin receptors 1 and 4 through complementary electrostatics, a unique mechanism of ligand-receptor interaction. This finding indicates that electrostatics alone, and not specific amino acid contact points, could be sufficient for function in this ligand-receptor system, and further suggests that other small peptide ligands could interact with these receptors in a similar fashion. Here, we conducted molecular-similarity analyses and functional studies of additional members of the human β-defensin family, examining their potential as ligands of melanocortin-1 receptor, through selection based on their electrostatic similarity to HBD3. Using Poisson-Boltzmann electrostatic calculations and molecular-similarity analysis, we identified members of the human β-defensin family that are both similar and dissimilar to HBD3 in terms of electrostatic potential. Synthesis and functional testing of a subset of these β-defensins showed that peptides with an HBD3-like electrostatic character bound to melanocortin receptors with high affinity, whereas those that were anticorrelated to HBD3 showed no binding affinity. These findings expand on the central role of electrostatics in the control of this ligand-receptor system and further demonstrate the utility of employing molecular-similarity analysis. Additionally, we identified several new potential ligands of melanocortin-1 receptor, which may have implications for our understanding of the role defensins play in melanocortin physiology.
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Affiliation(s)
- Matthew A Nix
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California
| | - Rafael Palomino
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jillian L Miller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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92
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Dobchev D, Karelson M. Have artificial neural networks met expectations in drug discovery as implemented in QSAR framework? Expert Opin Drug Discov 2016; 11:627-39. [PMID: 27149299 DOI: 10.1080/17460441.2016.1186876] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Artificial neural networks (ANNs) are highly adaptive nonlinear optimization algorithms that have been applied in many diverse scientific endeavors, ranging from economics, engineering, physics, and chemistry to medical science. Notably, in the past two decades, ANNs have been used widely in the process of drug discovery. AREAS COVERED In this review, the authors discuss advantages and disadvantages of ANNs in drug discovery as incorporated into the quantitative structure-activity relationships (QSAR) framework. Furthermore, the authors examine the recent studies, which span over a broad area with various diseases in drug discovery. In addition, the authors attempt to answer the question about the expectations of the ANNs in drug discovery and discuss the trends in this field. EXPERT OPINION The old pitfalls of overtraining and interpretability are still present with ANNs. However, despite these pitfalls, the authors believe that ANNs have likely met many of the expectations of researchers and are still considered as excellent tools for nonlinear data modeling in QSAR. It is likely that ANNs will continue to be used in drug development in the future.
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Affiliation(s)
- Dimitar Dobchev
- a Department of Chemistry , Tallinn University of Technology , Tallinn , Estonia
| | - Mati Karelson
- b Institute of Chemistry , University of Tartu , Tartu , Estonia
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93
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Li YF, Tsai KJS, Harvey CJB, Li JJ, Ary BE, Berlew EE, Boehman BL, Findley DM, Friant AG, Gardner CA, Gould MP, Ha JH, Lilley BK, McKinstry EL, Nawal S, Parry RC, Rothchild KW, Silbert SD, Tentilucci MD, Thurston AM, Wai RB, Yoon Y, Aiyar RS, Medema MH, Hillenmeyer ME, Charkoudian LK. Comprehensive curation and analysis of fungal biosynthetic gene clusters of published natural products. Fungal Genet Biol 2016; 89:18-28. [PMID: 26808821 DOI: 10.1016/j.fgb.2016.01.012] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/11/2022]
Abstract
Microorganisms produce a wide range of natural products (NPs) with clinically and agriculturally relevant biological activities. In bacteria and fungi, genes encoding successive steps in a biosynthetic pathway tend to be clustered on the chromosome as biosynthetic gene clusters (BGCs). Historically, "activity-guided" approaches to NP discovery have focused on bioactivity screening of NPs produced by culturable microbes. In contrast, recent "genome mining" approaches first identify candidate BGCs, express these biosynthetic genes using synthetic biology methods, and finally test for the production of NPs. Fungal genome mining efforts and the exploration of novel sequence and NP space are limited, however, by the lack of a comprehensive catalog of BGCs encoding experimentally-validated products. In this study, we generated a comprehensive reference set of fungal NPs whose biosynthetic gene clusters are described in the published literature. To generate this dataset, we first identified NCBI records that included both a peer-reviewed article and an associated nucleotide record. We filtered these records by text and homology criteria to identify putative NP-related articles and BGCs. Next, we manually curated the resulting articles, chemical structures, and protein sequences. The resulting catalog contains 197 unique NP compounds covering several major classes of fungal NPs, including polyketides, non-ribosomal peptides, terpenoids, and alkaloids. The distribution of articles published per compound shows a bias toward the study of certain popular compounds, such as the aflatoxins. Phylogenetic analysis of biosynthetic genes suggests that much chemical and enzymatic diversity remains to be discovered in fungi. Our catalog was incorporated into the recently launched Minimum Information about Biosynthetic Gene cluster (MIBiG) repository to create the largest known set of fungal BGCs and associated NPs, a resource that we anticipate will guide future genome mining and synthetic biology efforts toward discovering novel fungal enzymes and metabolites.
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Affiliation(s)
- Yong Fuga Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States; Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Kathleen J S Tsai
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Colin J B Harvey
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - James Jian Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - Beatrice E Ary
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | - Erin E Berlew
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Brenna L Boehman
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - David M Findley
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Alexandra G Friant
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | | | - Michael P Gould
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Jae H Ha
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | - Brenna K Lilley
- Department of Biology, Haverford College, Haverford, PA, United States
| | - Emily L McKinstry
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Saadia Nawal
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Robert C Parry
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | | | - Samantha D Silbert
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States
| | | | - Alana M Thurston
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Rebecca B Wai
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Yongjin Yoon
- Department of Chemistry, Haverford College, Haverford, PA, United States
| | - Raeka S Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, The Netherlands
| | - Maureen E Hillenmeyer
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, United States.
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94
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Rivera-Borroto OM, García-de la Vega JM, Marrero-Ponce Y, Grau R. Relational Agreement Measures for Similarity Searching of Cheminformatic Data Sets. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:158-67. [PMID: 26886740 DOI: 10.1109/tcbb.2015.2424435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Research on similarity searching of cheminformatic data sets has been focused on similarity measures using fingerprints. However, nominal scales are the least informative of all metric scales, increasing the tied similarity scores, and decreasing the effectivity of the retrieval engines. Tanimoto's coefficient has been claimed to be the most prominent measure for this task. Nevertheless, this field is far from being exhausted since the computer science no free lunch theorem predicts that "no similarity measure has overall superiority over the population of data sets". We introduce 12 relational agreement (RA) coefficients for seven metric scales, which are integrated within a group fusion-based similarity searching algorithm. These similarity measures are compared to a reference panel of 21 proximity quantifiers over 17 benchmark data sets (MUV), by using informative descriptors, a feature selection stage, a suitable performance metric, and powerful comparison tests. In this stage, RA coefficients perform favourably with repect to the state-of-the-art proximity measures. Afterward, the RA-based method outperform another four nearest neighbor searching algorithms over the same data domains. In a third validation stage, RA measures are successfully applied to the virtual screening of the NCI data set. Finally, we discuss a possible molecular interpretation for these similarity variants.
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95
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Geidl S, Bouchal T, Raček T, Svobodová Vařeková R, Hejret V, Křenek A, Abagyan R, Koča J. High-quality and universal empirical atomic charges for chemoinformatics applications. J Cheminform 2015; 7:59. [PMID: 26633997 PMCID: PMC4667495 DOI: 10.1186/s13321-015-0107-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/16/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited. RESULTS We have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set ([Formula: see text]) and also on a test set ([Formula: see text]). They are applicable for at least 95 % of molecules in key drug databases (DrugBank, ChEMBL, Pubchem and ZINC) compared to less than 60 % of the molecules from these databases for which currently used EEM parameters are applicable. CONCLUSIONS We developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation (http://ncbr.muni.cz/eem_parameters). It enables the direct application of EEM in chemoinformatics.
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Affiliation(s)
- Stanislav Geidl
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Bouchal
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Raček
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
- />Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Václav Hejret
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aleš Křenek
- />Institute of Computer Science, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Ruben Abagyan
- />Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive, San Diego, MC 0657 USA
| | - Jaroslav Koča
- />National Centre for Biomolecular Research, Faculty of Science and CEITEC, Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
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96
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Capoferri L, Verkade-Vreeker MCA, Buitenhuis D, Commandeur JNM, Pastor M, Vermeulen NPE, Geerke DP. Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation. PLoS One 2015; 10:e0142232. [PMID: 26551865 PMCID: PMC4638363 DOI: 10.1371/journal.pone.0142232] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/18/2015] [Indexed: 11/22/2022] Open
Abstract
Prediction of human Cytochrome P450 (CYP) binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards different CYPs can provide an estimate of inhibitory activity or an indication of isoforms prone to interact with the substrate of inhibitors. However, the accuracy of global quantitative models for CYP substrate binding or inhibition based on traditional molecular descriptors can be limited, because of the lack of information on the structure and flexibility of the catalytic site of CYPs. Here we describe the application of a method that combines protein-ligand docking, Molecular Dynamics (MD) simulations and Linear Interaction Energy (LIE) theory, to allow for quantitative CYP affinity prediction. Using this combined approach, a LIE model for human CYP 1A2 was developed and evaluated, based on a structurally diverse dataset for which the estimated experimental uncertainty was 3.3 kJ mol-1. For the computed CYP 1A2 binding affinities, the model showed a root mean square error (RMSE) of 4.1 kJ mol-1 and a standard error in prediction (SDEP) in cross-validation of 4.3 kJ mol-1. A novel approach that includes information on both structural ligand description and protein-ligand interaction was developed for estimating the reliability of predictions, and was able to identify compounds from an external test set with a SDEP for the predicted affinities of 4.6 kJ mol-1 (corresponding to 0.8 pKi units).
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Affiliation(s)
- Luigi Capoferri
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Marlies C. A. Verkade-Vreeker
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Danny Buitenhuis
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader, 88, E-08003 Barcelona, Spain
| | - Nico P. E. Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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97
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Carrió P, Sanz F, Pastor M. Toward a unifying strategy for the structure-based prediction of toxicological endpoints. Arch Toxicol 2015; 90:2445-60. [PMID: 26553148 DOI: 10.1007/s00204-015-1618-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/19/2015] [Indexed: 01/13/2023]
Abstract
Most computational methods used for the prediction of toxicity endpoints are based on the assumption that similar compounds have similar biological properties. This principle can be exploited using computational methods like read across or quantitative structure-activity relationships. However, there is no general agreement about which method is the most appropriate for quantifying compound similarity neither for exploiting the similarity principle in order to obtain reliable estimations of the compound properties. Moreover, optimal similarity metrics and modeling methods might depend on the characteristics of the endpoints and training series used in each case. This study describes a comparative analysis of the predictive performance of diverse similarity metrics and modeling methods in toxicological applications. A collection of two quantitative (n = 660, n = 1114) and three qualitative (n = 447, n = 905, n = 1220) datasets representing very different endpoints of interest in drug safety evaluation and rigorous methods were used to estimate the external predictive ability in each case. The results confirm that no single approach produces the best results in all instances, and the best predictions were obtained using different tools in different situations. The trends observed in this study were exploited to propose a unifying strategy allowing the use of the most suitable method for every compound. A comparison of the quality of the predictions obtained by the unifying strategy with those obtained by standard prediction methods confirmed the usefulness of the proposed approach.
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Affiliation(s)
- Pau Carrió
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain.
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98
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Gligorijević V, Pržulj N. Methods for biological data integration: perspectives and challenges. J R Soc Interface 2015; 12:20150571. [PMID: 26490630 PMCID: PMC4685837 DOI: 10.1098/rsif.2015.0571] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/25/2015] [Indexed: 12/17/2022] Open
Abstract
Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development.
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Affiliation(s)
| | - Nataša Pržulj
- Department of Computing, Imperial College London, London SW7 2AZ, UK
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99
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Al-Dabbagh MM, Salim N, Himmat M, Ahmed A, Saeed F. A Quantum-Based Similarity Method in Virtual Screening. Molecules 2015; 20:18107-27. [PMID: 26445039 DOI: 10.3390/molecules201018107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 11/16/2022] Open
Abstract
One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB). The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR), maximum unbiased validation (MUV) and Directory of Useful Decoys (DUD) data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.
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Affiliation(s)
| | - Naomie Salim
- Faculty of Computing, Universiti Teknologi Malaysia, Skudia 81310, Malaysia.
| | - Mubarak Himmat
- Faculty of Computing, Universiti Teknologi Malaysia, Skudia 81310, Malaysia.
| | - Ali Ahmed
- Faculty of Computing, Universiti Teknologi Malaysia, Skudia 81310, Malaysia.
- Faculty of Engineering, Karary University, Khartoum 12304, Sudan.
| | - Faisal Saeed
- Faculty of Computing, Universiti Teknologi Malaysia, Skudia 81310, Malaysia.
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100
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Nicola G, Berthold MR, Hedrick MP, Gilson MK. Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav087. [PMID: 26384374 PMCID: PMC4572361 DOI: 10.1093/database/bav087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022]
Abstract
Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed. Database URL: www.bindingdb.org.
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Affiliation(s)
- George Nicola
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,
| | - Michael R Berthold
- Department of Computer and Information Science, Konstanz University, 78457 Konstanz, Germany, and
| | | | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA,
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