51
|
Assirey E, Alsaggaf A, Naqvi A, Moussa Z, Okasha RM, Afifi TH, Abd-El-Aziz AS. Synthesis, Biological Assessment, and Structure Activity Relationship Studies of New Flavanones Embodying Chromene Moieties. Molecules 2020; 25:molecules25030544. [PMID: 32012737 PMCID: PMC7037824 DOI: 10.3390/molecules25030544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 02/04/2023] Open
Abstract
Novel flavanones that incorporate chromene motifs are synthesized via a one-step multicomponent reaction. The structures of the new chromenes are elucidated by using IR, 1H-NMR, 13C-NMR, 1H-1H COSY, HSQC, HMBC, and elemental analysis. The new compounds are screened for their in vitro antimicrobial and cytotoxic activities. The antimicrobial properties are investigated and established against seven human pathogens, employing the agar well diffusion method and the minimum inhibitory concentrations. A majority of the assessed derivatives are found to exhibit significant antimicrobial activities against most bacterial strains, in comparison to standard reference drugs. Moreover, their cytotoxicity is appraised against four different human carcinoma cell lines: human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), human breast adenocarcinoma (MCF-7), and adenocarcinoma human alveolar basal epithelial cell (A-549). All the desired compounds are subjected to in-silico studies, forecasting their drug likeness, bioactivity, and the absorption, distribution, metabolism, and excretion (ADME) properties prior to their synthetic assembly. The in-silico molecular docking evaluation of all the targeted derivatives is undertaken on gyrase B and the cyclin-dependent kinase. The in-silico predicted outcomes were endorsed by the in vitro studies.
Collapse
Affiliation(s)
- Eman Assirey
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Azhaar Alsaggaf
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Arshi Naqvi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE;
| | - Rawda M. Okasha
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Tarek H. Afifi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Alaa S. Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
- Correspondence: ; Tel.: +1-(902)-566-0400
| |
Collapse
|
52
|
Bagherian M, Sabeti E, Wang K, Sartor MA, Nikolovska-Coleska Z, Najarian K. Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. Brief Bioinform 2020; 22:247-269. [PMID: 31950972 PMCID: PMC7820849 DOI: 10.1093/bib/bbz157] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022] Open
Abstract
The task of predicting the interactions between drugs and targets plays a key role in the process of drug discovery. There is a need to develop novel and efficient prediction approaches in order to avoid costly and laborious yet not-always-deterministic experiments to determine drug–target interactions (DTIs) by experiments alone. These approaches should be capable of identifying the potential DTIs in a timely manner. In this article, we describe the data required for the task of DTI prediction followed by a comprehensive catalog consisting of machine learning methods and databases, which have been proposed and utilized to predict DTIs. The advantages and disadvantages of each set of methods are also briefly discussed. Lastly, the challenges one may face in prediction of DTI using machine learning approaches are highlighted and we conclude by shedding some lights on important future research directions.
Collapse
Affiliation(s)
- Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Elyas Sabeti
- Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kai Wang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maureen A Sartor
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Kayvan Najarian
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| |
Collapse
|
53
|
Shehzadi N, Hussain K, Bukhari NI, Islam M, Salman M, Khan MT. Speeding up the Development of 5-[(4-Chlorophenoxy)-Methyl]-1,3,4-Oxadiazole-2-Thiol as Successful Oral Drug Candidate Based on Physicochemical Characteristics. Pharm Chem J 2020. [DOI: 10.1007/s11094-020-02101-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
54
|
Molecular mechanism of action of Liuwei Dihuang pill for the treatment of osteoporosis based on network pharmacology and molecular docking. Eur J Integr Med 2020. [DOI: 10.1016/j.eujim.2019.101009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
55
|
Mehta P, Malik R. Discovery and identification of putative adenosine kinase inhibitors as potential anti-epileptic agents from structural insights. J Biomol Struct Dyn 2019; 38:5320-5337. [DOI: 10.1080/07391102.2019.1699447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Pakhuri Mehta
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, Ajmer, Rajasthan, India
| |
Collapse
|
56
|
A Bayesian machine learning approach for drug target identification using diverse data types. Nat Commun 2019; 10:5221. [PMID: 31745082 PMCID: PMC6863850 DOI: 10.1038/s41467-019-12928-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/10/2019] [Indexed: 11/18/2022] Open
Abstract
Drug target identification is a crucial step in development, yet is also among the most complex. To address this, we develop BANDIT, a Bayesian machine-learning approach that integrates multiple data types to predict drug binding targets. Integrating public data, BANDIT benchmarked a ~90% accuracy on 2000+ small molecules. Applied to 14,000+ compounds without known targets, BANDIT generated ~4,000 previously unknown molecule-target predictions. From this set we validate 14 novel microtubule inhibitors, including 3 with activity on resistant cancer cells. We applied BANDIT to ONC201—an anti-cancer compound in clinical development whose target had remained elusive. We identified and validated DRD2 as ONC201’s target, and this information is now being used for precise clinical trial design. Finally, BANDIT identifies connections between different drug classes, elucidating previously unexplained clinical observations and suggesting new drug repositioning opportunities. Overall, BANDIT represents an efficient and accurate platform to accelerate drug discovery and direct clinical application. Drug target identification is a crucial step in drug development. Here, the authors introduce a Bayesian machine learning framework that integrates multiple data types to predict the targets of small molecules, enabling identification of a new set of microtubule inhibitors and the target of the anti-cancer molecule ONC201.
Collapse
|
57
|
Rosado-Solano DN, Barón-Rodríguez MA, Sanabria Florez PL, Luna-Parada LK, Puerto-Galvis CE, Zorro-González AF, Kouznetsov VV, Vargas-Méndez LY. Synthesis, Biological Evaluation and In Silico Computational Studies of 7-Chloro-4-(1 H-1,2,3-triazol-1-yl)quinoline Derivatives: Search for New Controlling Agents against Spodoptera frugiperda (Lepidoptera: Noctuidae) Larvae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9210-9219. [PMID: 31390203 DOI: 10.1021/acs.jafc.9b01067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The insecticidal and antifeedant activities of five 7-chloro-4-(1H-1,2,3-triazol-1-yl)quinoline derivatives were evaluated against the maize armyworm, Spodoptera frugiperda (J.E. Smith). These hybrids were prepared through a copper-catalyzed azide alkyne cycloaddition (CuAAC, known as a click reaction) and displayed larvicidal properties with LD50 values below 3 mg/g insect, and triazolyl-quinoline hybrid 6 showed an LD50 of 0.65 mg/g insect, making it 2-fold less potent than methomyl, which was used as a reference insecticide (LD50 = 0.34 mg/g insect). Compound 4 was the most active antifeedant derivative (CE50 = 162.1 μg/mL) with a good antifeedant index (56-79%) at concentrations of 250-1000 μg/mL. Additionally, triazolyl-quinoline hybrids 4-8 exhibited weak inhibitory activity against commercial acetylcholinesterase from Electrophorus electricus (electric-eel AChE) (IC50 = 27.7 μg/mL) as well as low anti-ChE activity on S. frugiperda larvae homogenate (IC50 = 68.4 μg/mL). Finally, molecular docking simulations suggested that hybrid 7 binds to the catalytic active site (CAS) of this enzyme and around the rim of the enzyme cavity, acting as a mixed (competitive and noncompetitive) inhibitor like methomyl. Triazolyl-quinolines 4-6 and 8 inhibit AChE by binding over the perimeter of the enzyme cavity, functioning as noncompetitive inhibitors. The results described in this work can help to identify lead triazole structures from click chemistry for the development of insecticide and deterrent products against S. frugiperda and related insect pests.
Collapse
Affiliation(s)
- Doris Natalia Rosado-Solano
- Grupo de Investigaciones Ambientales para el Desarrollo Sostenible, Facultad de Química Ambiental , Universidad Santo Tomás , Bucaramanga A.A. 1076 , Colombia
| | - Mario Alberto Barón-Rodríguez
- Grupo de Investigaciones Ambientales para el Desarrollo Sostenible, Facultad de Química Ambiental , Universidad Santo Tomás , Bucaramanga A.A. 1076 , Colombia
| | - Pedro Luis Sanabria Florez
- Grupo de Investigaciones Ambientales para el Desarrollo Sostenible, Facultad de Química Ambiental , Universidad Santo Tomás , Bucaramanga A.A. 1076 , Colombia
| | - Luz Karime Luna-Parada
- Laboratorio de Química Orgánica y Biomolecular, CMN, Parque Tecnológico Guatiguará , Universidad Industrial de Santander , Km 2 vía Refugio , Piedecuesta , A.A. 681011 , Colombia
| | - Carlos Eduardo Puerto-Galvis
- Laboratorio de Química Orgánica y Biomolecular, CMN, Parque Tecnológico Guatiguará , Universidad Industrial de Santander , Km 2 vía Refugio , Piedecuesta , A.A. 681011 , Colombia
- Laboratorio de Química Orgánica Aplicada , Universidad Manuela Beltrán , Cl. 33 # 26-34 , Bucaramanga , A.A. 680002 , Colombia
| | - Andrés Felipe Zorro-González
- Grupo de Investigaciones Ambientales para el Desarrollo Sostenible, Facultad de Química Ambiental , Universidad Santo Tomás , Bucaramanga A.A. 1076 , Colombia
| | - Vladimir V Kouznetsov
- Laboratorio de Química Orgánica y Biomolecular, CMN, Parque Tecnológico Guatiguará , Universidad Industrial de Santander , Km 2 vía Refugio , Piedecuesta , A.A. 681011 , Colombia
| | - Leonor Yamile Vargas-Méndez
- Grupo de Investigaciones Ambientales para el Desarrollo Sostenible, Facultad de Química Ambiental , Universidad Santo Tomás , Bucaramanga A.A. 1076 , Colombia
| |
Collapse
|
58
|
Raunio H, Taavitsainen P, Honkakoski P, Juvonen R, Pelkonen O. In Vitro Methods in the Prediction of Kinetics of Drugs: Focus on Drug Metabolism. Altern Lab Anim 2019; 32:425-30. [PMID: 15651928 DOI: 10.1177/026119290403200415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of a candidate drug influence its final clinical success. These properties have traditionally been evaluated by using various in vivo animal approaches, but recently, a number of in vitro and in silico methods have been introduced to determine key ADMET features. Basic events, such as absorption through the gut wall, binding to plasma proteins, active and passive transfer through the blood-brain barrier, and various metabolic parameters, can now be screened with rapid in vitro and computer modelling methods. The focus in this short review is on the basic in vitro and in silico methods that are used for studying the metabolism properties of new drug molecules.
Collapse
Affiliation(s)
- Hannu Raunio
- Department of Pharmacology and Toxicology, University of Kuopio, Kuopio, Finland.
| | | | | | | | | |
Collapse
|
59
|
Sachdev K, Gupta MK. A comprehensive review of feature based methods for drug target interaction prediction. J Biomed Inform 2019; 93:103159. [PMID: 30926470 DOI: 10.1016/j.jbi.2019.103159] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
Abstract
Drug target interaction is a prominent research area in the field of drug discovery. It refers to the recognition of interactions between chemical compounds and the protein targets in the human body. Wet lab experiments to identify these interactions are expensive as well as time consuming. The computational methods of interaction prediction help limit the search space for these experiments. These computational methods can be divided into ligand based approaches, docking approaches and chemogenomic approaches. In this review, we aim to describe the various feature based chemogenomic methods for drug target interaction prediction. It provides a comprehensive overview of the various techniques, datasets, tools and metrics. The feature based methods have been categorized, explained and compared. A novel framework for drug target interaction prediction has also been proposed that aims to improve the performance of existing methods. To the best of our knowledge, this is the first comprehensive review focusing only on feature based methods of drug target interaction.
Collapse
Affiliation(s)
- Kanica Sachdev
- Computer Science and Engineering Department, SMVDU, J&K, India.
| | | |
Collapse
|
60
|
Abstract
Fulfilling the promises of precision medicine will depend on our ability to create patient-specific treatment regimens. Therefore, being able to translate genomic sequencing into predicting how a patient will respond to a given drug is critical. In this chapter, we review common bioinformatics approaches that aim to use sequencing data to predict sample-specific drug susceptibility. First, we explain the importance of customized drug regimens to the future of medical care. Second, we discuss the different public databases and community efforts that can be leveraged to develop new methods for identifying new predictive biomarkers. Third, we cover the basic methods that are currently used to identify markers or signatures of drug response, without any prior knowledge of the drug's mechanism of action. We further discuss how one can integrate knowledge about drug targets, mechanisms, and predictive markers to better estimate drug response in a diverse set of samples. We begin this section with a primer on popular methods to identify targets and mechanism of action for new small molecules. This discussion also includes a set of computational methods that incorporate other drug features, which do not relate to drug-induced genetic changes or sequencing data such as drug structures, side-effects, and efficacy profiles. Those additional drug properties can aid in gaining higher accuracy for the identification of drug target and mechanism of action. We then progress to discuss using these targets in combination with disease-specific expression patterns, known pathways, and genetic interaction networks to aid drug choice. Finally, we conclude this chapter with a general overview of machine learning methods that can integrate multiple pieces of sequencing data along with prior drug or biological knowledge to drastically improve response prediction.
Collapse
|
61
|
Patel RD, Prasanth Kumar S, Pandya HA, Solanki HA. MDCKpred: a web-tool to calculate MDCK permeability coefficient of small molecule using membrane-interaction chemical features. Toxicol Mech Methods 2018; 28:685-698. [PMID: 29998769 DOI: 10.1080/15376516.2018.1499840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Structure-based models to understand the transport of small molecules through biological membrane can be developed by enumerating intermolecular interactions of the small molecule with a biological membrane, usually a dimyristoylphosphatidylcholine (DMPC) monolayer. This ADME (absorption, distribution, metabolism, and excretion) property based on Madin-Darby Canine Kidney (MDCK) cell line demonstrates intestinal drug absorption of small molecules and correlated to human intestinal absorption which acts as a determining factor to forecast small-molecule prioritization in drug-discovery projects. We present here the development of MDCKpred web-tool which calculates MDCK permeability coefficient of small molecule based on the regression model, developed using membrane-interaction chemical features. The web-tool allows users to calculate the MDCK permeability coefficient (nm/s) instantly by providing simple descriptor inputs. The chemical-interaction features are derived from different parts of the DMPC molecule viz. head, middle, and tail regions and accounts overall intermolecular contacts of the small molecule when passively diffused through the phospholipid-rich biological membrane. The MDCKpred model is both internally (R2 = .76; [Formula: see text]= .68; Rtrain = .87; Rtest = .69) and externally (Rext = .55) validated. Furthermore, we used natural molecules as application examples to demonstrate its utility in lead exploration and optimization projects. The MDCKpred web-tool can be accessed freely at http://www.mdckpred.in . This web-tool is designed to offer an intuitive way of prioritizing small molecules based on calculated MDCK permeabilities.
Collapse
Affiliation(s)
- Rikin D Patel
- a Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences , Gujarat University , Ahmedabad , India
| | | | - Himanshu A Pandya
- a Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences , Gujarat University , Ahmedabad , India
| | - Hitesh A Solanki
- a Department of Bioinformatics, Applied Botany Centre (ABC), University School of Sciences , Gujarat University , Ahmedabad , India
| |
Collapse
|
62
|
Mehta P, Srivastava S, Sharma M, Singh I, Malik R. Identification of chemically diverse GABA A agonists as potential anti-epileptic agents using structure-guided virtual screening, ADMET, quantum mechanics and clinical validation through off-target analysis. Int J Biol Macromol 2018; 119:1113-1128. [PMID: 30098361 DOI: 10.1016/j.ijbiomac.2018.08.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/19/2022]
Abstract
Development of resistance against existing anti-epileptic drugs has alarmed the scientific innovators to find novel potential chemical starting points for the treatment of epilepsy and GABAA inhibition is a promising drug target strategy against epilepsy. The crystal structure of a subtype-selective β3-homopentameric ligand-gated ion channel of GABAA receptor has been used for the first time for screening the Asinex library for discovery of GABAA agonists as potential anti-epileptic agents. Co-crystallized ligand established the involvement of part of the β7-β8 loop (Glu155 and Tyr157) and β9-β10 loop (Phe200 and Tyr205) residues as the crucial amino acids in effective binding, an essential feature, being hydrogen bond or ionic interaction with Glu155 residue. Top ranked hits were further subjected to binding energy estimation, ADMET analysis and ligand efficiency matric calculations as consecutive filters. About 19 compounds qualifying all parameters possessed interaction of one positively charged group with Glu155 with good CNS drug-like properties. Simulation studies were performed on the apo protein, its complex with co-crystallized ligand and the best hit qualifying all screening parameters. The best hit was also analyzed using Quantum mechanical studies, off-target analysis and hit modification. The off-target analysis emphasized that these agents did not have any other predicted side-effects.
Collapse
Affiliation(s)
- Pakhuri Mehta
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Shubham Srivastava
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Sadopur, Ambala, Haryana 134007, India
| | - Inderpal Singh
- Bioinformatics Infrastructure Facility, Department of Biotechnology, Shri Mata Vaishno Devi University (SMVDU), Kakryal, Katra, Jammu & Kashmir 182320, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India.
| |
Collapse
|
63
|
Heller AA, Lockwood SY, Janes TM, Spence DM. Technologies for Measuring Pharmacokinetic Profiles. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:79-100. [PMID: 29324183 DOI: 10.1146/annurev-anchem-061417-125611] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The creation of a pharmacokinetic (PK) curve, which follows the plasma concentration of an administered drug as a function of time, is a critical aspect of the drug development process and includes such information as the drug's bioavailability, clearance, and elimination half-life. Prior to a drug of interest gaining clearance for use in human clinical trials, research is performed during the preclinical stages to establish drug safety and dosing metrics from data obtained from the PK studies. Both in vivo animal models and in vitro platforms have limitations in predicting human reaction to a drug due to differences in species and associated simplifications, respectively. As a result, in silico experiments using computer simulation have been implemented to accurately predict PK parameters in human studies. This review assesses these three approaches (in vitro, in vivo, and in silico) when establishing PK parameters and evaluates the potential for in silico studies to be the future gold standard of PK preclinical studies.
Collapse
Affiliation(s)
- A A Heller
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA;
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - S Y Lockwood
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - T M Janes
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA;
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| | - D M Spence
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, USA
| |
Collapse
|
64
|
Kim H, Han H. Computer-Aided Multi-Target Management of Emergent Alzheimer's Disease. Bioinformation 2018; 14:167-180. [PMID: 29983487 PMCID: PMC6016757 DOI: 10.6026/97320630014167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) represents an enormous global health burden in terms of human suffering and economic cost. AD management requires a shift from the prevailing paradigm targeting pathogenesis to design and develop effective drugs with adequate success in clinical trials. Therefore, it is of interest to report a review on amyloid beta (Aβ) effects and other multi-targets including cholinesterase, NFTs, tau protein and TNF associated with brain cell death to be neuro-protective from AD. It should be noted that these molecules have been generated either by target-based or phenotypic methods. Hence, the use of recent advancements in nanomedicine and other natural compounds screening tools as a feasible alternative for circumventing specific liabilities is realized. We review recent developments in the design and identification of neuro-degenerative compounds against AD generated using current advancements in computational multi-target modeling algorithms reflected by theragnosis (combination of diagnostic tests and therapy) concern.
Collapse
Affiliation(s)
- Hyunjo Kim
- Department of Medical Informatics, Ajou Medical University Hospital, Suwon, Kyeounggido province, South Korea
| | - Hyunwook Han
- Department of Informatics, School of Medicine, CHA University, Seongnam, South Korea
- Institute of Basic Medical Sciences, School of Medicine, CHA University, Seongnam, South Korea
| |
Collapse
|
65
|
Matlock M, Dang NL, Swamidass SJ. Learning a Local-Variable Model of Aromatic and Conjugated Systems. ACS CENTRAL SCIENCE 2018; 4:52-62. [PMID: 29392176 PMCID: PMC5785769 DOI: 10.1021/acscentsci.7b00405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 06/01/2023]
Abstract
A collection of new approaches to building and training neural networks, collectively referred to as deep learning, are attracting attention in theoretical chemistry. Several groups aim to replace computationally expensive ab initio quantum mechanics calculations with learned estimators. This raises questions about the representability of complex quantum chemical systems with neural networks. Can local-variable models efficiently approximate nonlocal quantum chemical features? Here, we find that convolutional architectures, those that only aggregate information locally, cannot efficiently represent aromaticity and conjugation in large systems. They cannot represent long-range nonlocality known to be important in quantum chemistry. This study uses aromatic and conjugated systems computed from molecule graphs, though reproducing quantum simulations is the ultimate goal. This task, by definition, is both computable and known to be important to chemistry. The failure of convolutional architectures on this focused task calls into question their use in modeling quantum mechanics. To remedy this heretofore unrecognized deficiency, we introduce a new architecture that propagates information back and forth in waves of nonlinear computation. This architecture is still a local-variable model, and it is both computationally and representationally efficient, processing molecules in sublinear time with far fewer parameters than convolutional networks. Wave-like propagation models aromatic and conjugated systems with high accuracy, and even models the impact of small structural changes on large molecules. This new architecture demonstrates that some nonlocal features of quantum chemistry can be efficiently represented in local variable models.
Collapse
|
66
|
Yamanishi Y. Linear and Kernel Model Construction Methods for Predicting Drug-Target Interactions in a Chemogenomic Framework. Methods Mol Biol 2018; 1825:355-368. [PMID: 30334213 DOI: 10.1007/978-1-4939-8639-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identification of drug-target interactions is a crucial process in drug discovery. In this chapter, we present protocols for recent advancements in machine learning methods for predicting drug-target interactions from heterogeneous biological data in a chemogenomic framework, in which prediction is based on the chemical structure data of drug candidate compounds and translated genomic sequence data of target candidate proteins. Most existing methods are based on either linear modeling or kernel modeling. To illustrate linear modeling, we introduce sparsity-induced binary classifiers and sparse canonical correlation analysis. To illustrate kernel modeling, we introduce pairwise kernel-based support vector machines and kernel-based distance learning. Workflows for using these techniques are presented. We also discuss the characteristics of each method and suggest some directions for future research.
Collapse
Affiliation(s)
- Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| |
Collapse
|
67
|
Abstract
Most drugs produce their phenotypic effects by interacting with target proteins, and understanding the molecular features that underpin drug-target interactions is crucial when designing a novel drug. In this chapter, we introduce the protocols that have driven recent advances in sparse modeling methods for analyzing drug-target interaction networks within a chemogenomic framework. In this approach, the chemical structures of candidate drug compounds are correlated with the genomic sequences of the candidate target proteins. We demonstrate the use of sparse canonical correspondence analysis and sparsity-induced binary classifiers to extract the underlying molecular features that are most strongly involved in drug-target interactions. We focus on drug chemical substructures and protein domains. Workflows for applying these methods are presented, and an application is described in detail. We consider the characteristics of each method and suggest possible directions for future research.
Collapse
|
68
|
Suryanarayanan V, Panwar U, Chandra I, Singh SK. De Novo Design of Ligands Using Computational Methods. Methods Mol Biol 2018; 1762:71-86. [PMID: 29594768 DOI: 10.1007/978-1-4939-7756-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
De novo design technique is complementary to high-throughput virtual screening and is believed to contribute in pharmaceutical development of novel drugs with desired properties at a very low cost and time-efficient manner. In this chapter, we outline the basic de novo design concepts based on computational methods with an example.
Collapse
Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ishwar Chandra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
| |
Collapse
|
69
|
Martínez-Archundia M, Bello M, Correa-Basurto J. Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties. Methods Mol Biol 2018; 1824:403-416. [PMID: 30039421 DOI: 10.1007/978-1-4939-8630-9_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is a synergistic interaction between medicinal chemistry, chemoinformatics, and bioinformatics. The last one includes analyses of sequences as well as structural analysis which employ computational techniques such as docking studies and molecular dynamics (MD) simulations. Over the last years these techniques have allowed the development of new accurate computational tools for drug design. As a result, there have been an increased number of publications where computational methods such as pharmacophore modeling, de novo drug design, evaluation of physicochemical properties, and analysis of ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties have been quite useful for eliminating the compounds with poor physicochemical or toxicological properties. Furthermore, using MD simulations and docking analysis, it is possible to estimate the binding energy of the protein-ligand complexes by using scoring functions, as well as to structurally depict the binding pose of the compounds on proteins, in order to select the best evaluated compounds for subsequent synthetizing and evaluation through biological assays. In this work, we describe some computational tools that have been used for structure-based drug design of new compounds that target histone deacetylases (HDACs), which are known to be potential targets in cancer and parasitic diseases.
Collapse
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P., Ciudad de México, Mexico
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P., Ciudad de México, Mexico.
| | - Jose Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P., Ciudad de México, Mexico.
| |
Collapse
|
70
|
Abstract
Pharmacokinetics is the study of the fate of xenobiotics in a living organism. Physiologically based pharmacokinetic (PBPK) models provide realistic descriptions of xenobiotics' absorption, distribution, metabolism, and excretion processes. They model the body as a set of homogeneous compartments representing organs, and their parameters refer to anatomical, physiological, biochemical, and physicochemical entities. They offer a quantitative mechanistic framework to understand and simulate the time-course of the concentration of a substance in various organs and body fluids. These models are well suited for performing extrapolations inherent to toxicology and pharmacology (e.g., between species or doses) and for integrating data obtained from various sources (e.g., in vitro or in vivo experiments, structure-activity models). In this chapter, we describe the practical development and basic use of a PBPK model from model building to model simulations, through implementation with an easily accessible free software.
Collapse
|
71
|
Mehta P, Srivastava S, Choudhary BS, Sharma M, Malik R. Probing voltage sensing domain of KCNQ2 channel as a potential target to combat epilepsy: a comparative study. J Recept Signal Transduct Res 2017; 37:578-589. [DOI: 10.1080/10799893.2017.1369122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Pakhuri Mehta
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, India
| | - Bhanwar Singh Choudhary
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Ambala, Haryana, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, India
| |
Collapse
|
72
|
Meng FR, You ZH, Chen X, Zhou Y, An JY. Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures. Molecules 2017; 22:molecules22071119. [PMID: 28678206 PMCID: PMC6152073 DOI: 10.3390/molecules22071119] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/27/2017] [Accepted: 07/03/2017] [Indexed: 11/16/2022] Open
Abstract
Knowledge of drug–target interaction (DTI) plays an important role in discovering new drug candidates. Unfortunately, there are unavoidable shortcomings; including the time-consuming and expensive nature of the experimental method to predict DTI. Therefore, it motivates us to develop an effective computational method to predict DTI based on protein sequence. In the paper, we proposed a novel computational approach based on protein sequence, namely PDTPS (Predicting Drug Targets with Protein Sequence) to predict DTI. The PDTPS method combines Bi-gram probabilities (BIGP), Position Specific Scoring Matrix (PSSM), and Principal Component Analysis (PCA) with Relevance Vector Machine (RVM). In order to evaluate the prediction capacity of the PDTPS, the experiment was carried out on enzyme, ion channel, GPCR, and nuclear receptor datasets by using five-fold cross-validation tests. The proposed PDTPS method achieved average accuracy of 97.73%, 93.12%, 86.78%, and 87.78% on enzyme, ion channel, GPCR and nuclear receptor datasets, respectively. The experimental results showed that our method has good prediction performance. Furthermore, in order to further evaluate the prediction performance of the proposed PDTPS method, we compared it with the state-of-the-art support vector machine (SVM) classifier on enzyme and ion channel datasets, and other exiting methods on four datasets. The promising comparison results further demonstrate that the efficiency and robust of the proposed PDTPS method. This makes it a useful tool and suitable for predicting DTI, as well as other bioinformatics tasks.
Collapse
Affiliation(s)
- Fan-Rong Meng
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 21116, China.
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Urumqi 830011, China.
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 21116, China.
| | - Yong Zhou
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 21116, China.
| | - Ji-Yong An
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 21116, China.
| |
Collapse
|
73
|
In Silico Prediction for Intestinal Absorption and Brain Penetration of Chemical Pesticides in Humans. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14070708. [PMID: 28665355 PMCID: PMC5551146 DOI: 10.3390/ijerph14070708] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 01/20/2023]
Abstract
Intestinal absorption and brain permeation constitute key parameters of toxicokinetics for pesticides, conditioning their toxicity, including neurotoxicity. However, they remain poorly characterized in humans. The present study was therefore designed to evaluate human intestine and brain permeation for a large set of pesticides (n = 338) belonging to various chemical classes, using an in silico graphical BOILED-Egg/SwissADME online method based on lipophilicity and polarity that was initially developed for drugs. A high percentage of the pesticides (81.4%) was predicted to exhibit high intestinal absorption, with a high accuracy (96%), whereas a lower, but substantial, percentage (38.5%) displayed brain permeation. Among the pesticide classes, organochlorines (n = 30) constitute the class with the lowest percentage of intestine-permeant members (40%), whereas that of the organophosphorus compounds (n = 99) has the lowest percentage of brain-permeant chemicals (9%). The predictions of the permeations for the pesticides were additionally shown to be significantly associated with various molecular descriptors well-known to discriminate between permeant and non-permeant drugs. Overall, our in silico data suggest that human exposure to pesticides through the oral way is likely to result in an intake of these dietary contaminants for most of them and brain permeation for some of them, thus supporting the idea that they have toxic effects on human health, including neurotoxic effects.
Collapse
|
74
|
Kumar N, Goel N, Chand Yadav T, Pruthi V. Quantum chemical, ADMET and molecular docking studies of ferulic acid amide derivatives with a novel anticancer drug target. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1893-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
75
|
Sindhu T, Srinivasan P. Pharmacophore modeling, comprehensive 3D-QSAR, and binding mode analysis of TGR5 agonists. J Recept Signal Transduct Res 2017; 37:109-123. [DOI: 10.1080/10799893.2016.1189564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Thangaraj Sindhu
- Molecular Biology Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India
| | - Pappu Srinivasan
- Molecular Biology Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamilnadu, India
| |
Collapse
|
76
|
Graepel R, Lamon L, Asturiol D, Berggren E, Joossens E, Paini A, Prieto P, Whelan M, Worth A. The virtual cell based assay: Current status and future perspectives. Toxicol In Vitro 2017; 45:258-267. [PMID: 28108195 PMCID: PMC5742635 DOI: 10.1016/j.tiv.2017.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/15/2016] [Accepted: 01/15/2017] [Indexed: 12/22/2022]
Abstract
In order to replace the use of animals in toxicity testing, there is a need to predict in vivo toxic doses from concentrations that cause toxicological effects in relevant in vitro systems. The Virtual Cell Based Assay (VCBA) estimates time-dependent concentration of a test chemical in the cell and cell culture for a given in vitro system. The concentrations in the different compartments of the cell and test system are derived from ordinary differential equations, physicochemical parameters of the test chemical and properties of the cell line. The VCBA has been developed for a range of cell lines including BALB/c 3T3 cells, HepG2, HepaRG, lung A459 cells, and cardiomyocytes. The model can be used to design and refine in vitro experiments and extrapolate in vitro effective concentrations to in vivo doses that can be applied in risk assessment. In this paper, we first discuss potential applications of the VCBA: i) design of in vitro High Throughput Screening (HTS) experiments; ii) hazard identification (based on acute systemic toxicity); and iii) risk assessment. Further extension of the VCBA is discussed in the second part, exploring potential application to i) manufactured nanomaterials, ii) additional cell lines and endpoints, and considering iii) other opportunities. VCBA as an alternative approach can be applied in the domain of nanotoxicology. VCBA can support better testing strategies in acute toxicity. Refinement of the VCBA taking into account biological oscillators could improve toxicity prediction. Extensions of the VCBA can capture effects related to additional subcellular compartments.
Collapse
Affiliation(s)
- Rabea Graepel
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Lara Lamon
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy.
| | - David Asturiol
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Elisabet Berggren
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Elisabeth Joossens
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Alicia Paini
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Pilar Prieto
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Maurice Whelan
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| | - Andrew Worth
- Chemical Safety and Alternative Methods Unit incorporating EURL ECVAM, Directorate Health, Consumers and Reference Materials, European Commission, Joint Research Centre, Ispra, Italy
| |
Collapse
|
77
|
Synthesis, Molecular Docking Studies, and Antifungal Activity Evaluation of New Benzimidazole-Triazoles as Potential Lanosterol 14α-Demethylase Inhibitors. J CHEM-NY 2017. [DOI: 10.1155/2017/9387102] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Due to anticandidal importance of azole compounds, a new series of benzimidazole-triazole derivatives(5a–5s)were designed and synthesized as ergosterol inhibitors. The chemical structures of the target compounds were characterized by spectroscopic methods. The final compounds were screened for antifungal activity againstCandida glabrata(ATCC 90030),Candida krusei(ATCC 6258),Candida parapsilosis(ATCC 22019), andCandida albicans(ATCC 24433). Compounds5iand5sexhibited significant inhibitory activity againstCandidastrains with MIC50values ranging from 0.78 to 1.56 μg/mL. Cytotoxicity results revealed that IC50values of compounds5iand5sagainst NIH/3T3 are significantly higher than their MIC50values. Effect of the compounds5iand5sagainst ergosterol biosynthesis was determined by LC-MS-MS analysis. Both compounds caused a significant decrease in the ergosterol level. The molecular docking studies were performed to investigate the interaction modes between the compounds and active site of lanosterol 14-α-demethylase (CYP51), which is as a target enzyme for anticandidal azoles. Theoretical ADME predictions were also calculated for final compounds.
Collapse
|
78
|
Malik R, Mehta P, Srivastava S, Choudhary BS, Sharma M. Structure-based screening, ADMET profiling, and molecular dynamic studies on mGlu2 receptor for identification of newer antiepileptic agents. J Biomol Struct Dyn 2016; 35:3433-3448. [DOI: 10.1080/07391102.2016.1257440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Pakhuri Mehta
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Bhanwar Singh Choudhary
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Sadopur, Ambala, Haryana 134007, India
| |
Collapse
|
79
|
Malik R, Choudhary BS, Srivastava S, Mehta P, Sharma M. Identification of novel acetylcholinesterase inhibitors through e-pharmacophore-based virtual screening and molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:3268-3284. [DOI: 10.1080/07391102.2016.1253503] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, Bandarsindri, Ajmer 305817, Rajasthan, India
| | - Bhanwar Singh Choudhary
- Department of Pharmacy, Central University of Rajasthan, Bandarsindri, Ajmer 305817, Rajasthan, India
| | - Shubham Srivastava
- Department of Pharmacy, Central University of Rajasthan, Bandarsindri, Ajmer 305817, Rajasthan, India
| | - Pakhuri Mehta
- Department of Pharmacy, Central University of Rajasthan, Bandarsindri, Ajmer 305817, Rajasthan, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Sadopur, Ambala 134007, Haryana, India
| |
Collapse
|
80
|
Stępnik KE. A concise review of applications of micellar liquid chromatography to study biologically active compounds. Biomed Chromatogr 2016; 31. [DOI: 10.1002/bmc.3741] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Katarzyna E. Stępnik
- Faculty of Chemistry, Chair of Physical Chemistry, Department of Planar Chromatography; Maria Curie-Skłodowska University; M. Curie-Skłodowska Sq. 3 20-031 Lublin Poland
| |
Collapse
|
81
|
Pandey RK, Kumbhar BV, Srivastava S, Malik R, Sundar S, Kunwar A, Prajapati VK. Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:141-158. [DOI: 10.1080/07391102.2015.1135298] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh 305817, Ajmer, Rajasthan, India
| | - Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Shubham Srivastava
- Department of Pharmacy, School of Chemical Sciences, Central University of Rajasthan, Kishangarh 305817, Ajmer, Rajasthan, India
| | - Ruchi Malik
- Department of Pharmacy, School of Chemical Sciences, Central University of Rajasthan, Kishangarh 305817, Ajmer, Rajasthan, India
| | - Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh 305817, Ajmer, Rajasthan, India
| |
Collapse
|
82
|
Nisha J, Ramanathan K, Nawaz Khan F, Dhanasekaran D, Shanthi V. Discovery of a potential lead compound for treating leprosy with dapsone resistance mutation in M. leprae folP1. MOLECULAR BIOSYSTEMS 2016; 12:2178-88. [DOI: 10.1039/c6mb00225k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A potential lead compound to overcome dapsone resistance in M. leprae folP1 was identified by a virtual screening strategy.
Collapse
Affiliation(s)
- J. Nisha
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
| | - K. Ramanathan
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
| | - F. Nawaz Khan
- Department of Chemistry
- School of Advanced Sciences
- VIT University
- Vellore
- India
| | - D. Dhanasekaran
- Department of Microbiology
- Bharathidasan University
- Tiruchirappalli
- India
| | - V. Shanthi
- Department of Biotechnology
- School of BioSciences and Technology
- VIT University
- Vellore
- India
| |
Collapse
|
83
|
Liao Q, Guan N, Wu C, Zhang Q. Predicting Unknown Interactions Between Known Drugs and Targets via Matrix Completion. ADVANCES IN KNOWLEDGE DISCOVERY AND DATA MINING 2016. [DOI: 10.1007/978-3-319-31753-3_47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
84
|
Drug-target interaction prediction from PSSM based evolutionary information. J Pharmacol Toxicol Methods 2015; 78:42-51. [PMID: 26592807 DOI: 10.1016/j.vascn.2015.11.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/01/2015] [Accepted: 11/08/2015] [Indexed: 01/01/2023]
Abstract
The labor-intensive and expensive experimental process of drug-target interaction prediction has motivated many researchers to focus on in silico prediction, which leads to the helpful information in supporting the experimental interaction data. Therefore, they have proposed several computational approaches for discovering new drug-target interactions. Several learning-based methods have been increasingly developed which can be categorized into two main groups: similarity-based and feature-based. In this paper, we firstly use the bi-gram features extracted from the Position Specific Scoring Matrix (PSSM) of proteins in predicting drug-target interactions. Our results demonstrate the high-confidence prediction ability of the Bigram-PSSM model in terms of several performance indicators specifically for enzymes and ion channels. Moreover, we investigate the impact of negative selection strategy on the performance of the prediction, which is not widely taken into account in the other relevant studies. This is important, as the number of non-interacting drug-target pairs are usually extremely large in comparison with the number of interacting ones in existing drug-target interaction data. An interesting observation is that different levels of performance reduction have been attained for four datasets when we change the sampling method from the random sampling to the balanced sampling.
Collapse
|
85
|
Pandey RK, Sharma D, Bhatt TK, Sundar S, Prajapati VK. Developing imidazole analogues as potential inhibitor forLeishmania donovanitrypanothione reductase: virtual screening, molecular docking, dynamics and ADMET approach. J Biomol Struct Dyn 2015; 33:2541-53. [DOI: 10.1080/07391102.2015.1085904] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
86
|
Meng F, Dave V, Chauhan H. Qualitative and quantitative methods to determine miscibility in amorphous drug–polymer systems. Eur J Pharm Sci 2015; 77:106-11. [DOI: 10.1016/j.ejps.2015.05.018] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 11/25/2022]
|
87
|
Clark AM, Dole K, Coulon-Spektor A, McNutt A, Grass G, Freundlich JS, Reynolds RC, Ekins S. Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. J Chem Inf Model 2015; 55:1231-45. [PMID: 25994950 PMCID: PMC4478615 DOI: 10.1021/acs.jcim.5b00143] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
On the order of hundreds of absorption,
distribution, metabolism,
excretion, and toxicity (ADME/Tox) models have been described in the
literature in the past decade which are more often than not inaccessible
to anyone but their authors. Public accessibility is also an issue
with computational models for bioactivity, and the ability to share
such models still remains a major challenge limiting drug discovery.
We describe the creation of a reference implementation of a Bayesian
model-building software module, which we have released as an open
source component that is now included in the Chemistry Development
Kit (CDK) project, as well as implemented in the CDD Vault and
in several mobile apps. We use this implementation to build an array
of Bayesian models for ADME/Tox, in vitro and in vivo bioactivity, and other physicochemical properties.
We show that these models possess cross-validation receiver operator
curve values comparable to those generated previously in prior publications
using alternative tools. We have now described how the implementation
of Bayesian models with FCFP6 descriptors generated in the CDD Vault
enables the rapid production of robust machine learning models from
public data or the user’s own datasets. The current study sets
the stage for generating models in proprietary software (such as CDD)
and exporting these models in a format that could be run in open source
software using CDK components. This work also demonstrates that we
can enable biocomputation across distributed private or public datasets
to enhance drug discovery.
Collapse
Affiliation(s)
- Alex M Clark
- †Molecular Materials Informatics, Inc., 1900 St. Jacques No. 302, Montreal H3J 2S1, Quebec, Canada
| | - Krishna Dole
- ‡Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Anna Coulon-Spektor
- ‡Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - Andrew McNutt
- ‡Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
| | - George Grass
- §G2 Research, Inc., P.O. Box 1242, Tahoe City, California 96145, United States
| | | | - Robert C Reynolds
- #Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, , 1530 Third Avenue South, Birmingham, Alabama 35294-1240, United States
| | - Sean Ekins
- ‡Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States.,∇Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
| |
Collapse
|
88
|
Mousavian Z, Masoudi-Nejad A. Drug-target interaction prediction via chemogenomic space: learning-based methods. Expert Opin Drug Metab Toxicol 2014; 10:1273-87. [PMID: 25112457 DOI: 10.1517/17425255.2014.950222] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Identification of the interaction between drugs and target proteins is a crucial task in genomic drug discovery. The in silico prediction is an appropriate alternative for the laborious and costly experimental process of drug-target interaction prediction. Developing a variety of computational methods opens a new direction in analyzing and detecting new drug-target pairs. AREAS COVERED In this review, we will focus on chemogenomic methods which have established a learning framework for predicting drug-target interactions. Learning-based methods are classified into supervised and semi-supervised, and the supervised learning methods are studied as two separate parts including similarity-based methods and feature-based methods. EXPERT OPINION In spite of many improvements for pharmacology applications by learning-based methods, there are many over simplification settings in construction of predictive models that may lead to over-optimistic results on drug-target interaction prediction.
Collapse
Affiliation(s)
- Zaynab Mousavian
- University of Tehran, Institute of Biochemistry and Biophysics, Laboratory of Systems Biology and Bioinformatics (LBB) , Tehran , Iran +98 21 6695 9256 ; +98 21 6640 4680 ;
| | | |
Collapse
|
89
|
Poongavanam V, Steinmann C, Kongsted J. Inhibitor ranking through QM based chelation calculations for virtual screening of HIV-1 RNase H inhibition. PLoS One 2014; 9:e98659. [PMID: 24897431 PMCID: PMC4045755 DOI: 10.1371/journal.pone.0098659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
Quantum mechanical (QM) calculations have been used to predict the binding affinity of a set of ligands towards HIV-1 RT associated RNase H (RNH). The QM based chelation calculations show improved binding affinity prediction for the inhibitors compared to using an empirical scoring function. Furthermore, full protein fragment molecular orbital (FMO) calculations were conducted and subsequently analysed for individual residue stabilization/destabilization energy contributions to the overall binding affinity in order to better understand the true and false predictions. After a successful assessment of the methods based on the use of a training set of molecules, QM based chelation calculations were used as filter in virtual screening of compounds in the ZINC database. By this, we find, compared to regular docking, QM based chelation calculations to significantly reduce the large number of false positives. Thus, the computational models tested in this study could be useful as high throughput filters for searching HIV-1 RNase H active-site molecules in the virtual screening process.
Collapse
Affiliation(s)
- Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- * E-mail:
| | - Casper Steinmann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| |
Collapse
|
90
|
Fotaki N. Pros and cons of methods used for the prediction of oral drug absorption. Expert Rev Clin Pharmacol 2014; 2:195-208. [DOI: 10.1586/17512433.2.2.195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
91
|
Drug-target and disease networks: polypharmacology in the post-genomic era. In Silico Pharmacol 2013; 1:17. [PMID: 25505661 PMCID: PMC4230718 DOI: 10.1186/2193-9616-1-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/17/2022] Open
Abstract
With the growing understanding of complex diseases, the focus of drug discovery has shifted away from the well-accepted “one target, one drug” model, to a new “multi-target, multi-drug” model, aimed at systemically modulating multiple targets. Identification of the interaction between drugs and target proteins plays an important role in genomic drug discovery, in order to discover new drugs or novel targets for existing drugs. Due to the laborious and costly experimental process of drug-target interaction prediction, in silico prediction could be an efficient way of providing useful information in supporting experimental interaction data. An important notion that has emerged in post-genomic drug discovery is that the large-scale integration of genomic, proteomic, signaling and metabolomic data can allow us to construct complex networks of the cell that would provide us with a new framework for understanding the molecular basis of physiological or pathophysiological states. An emerging paradigm of polypharmacology in the post-genomic era is that drug, target and disease spaces can be correlated to study the effect of drugs on different spaces and their interrelationships can be exploited for designing drugs or cocktails which can effectively target one or more disease states. The future goal, therefore, is to create a computational platform that integrates genome-scale metabolic pathway, protein–protein interaction networks, gene transcriptional analysis in order to build a comprehensive network for multi-target multi-drug discovery.
Collapse
|
92
|
Zheng M, Liu X, Xu Y, Li H, Luo C, Jiang H. Computational methods for drug design and discovery: focus on China. Trends Pharmacol Sci 2013; 34:549-59. [PMID: 24035675 PMCID: PMC7126378 DOI: 10.1016/j.tips.2013.08.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/07/2013] [Accepted: 08/13/2013] [Indexed: 01/09/2023]
Abstract
In the past decades, China's computational drug design and discovery research has experienced fast development through various novel methodologies. Application of these methods spans a wide range, from drug target identification to hit discovery and lead optimization. In this review, we firstly provide an overview of China's status in this field and briefly analyze the possible reasons for this rapid advancement. The methodology development is then outlined. For each selected method, a short background precedes an assessment of the method with respect to the needs of drug discovery, and, in particular, work from China is highlighted. Furthermore, several successful applications of these methods are illustrated. Finally, we conclude with a discussion of current major challenges and future directions of the field.
Collapse
Affiliation(s)
- Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | | | | | | | | | | |
Collapse
|
93
|
Zhivkova Z, Doytchinova I. Quantitative Structure – Clearance Relationships of Acidic Drugs. Mol Pharm 2013; 10:3758-68. [DOI: 10.1021/mp400251k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zvetanka Zhivkova
- Faculty of Pharmacy, Medical University of Sofia, Sofia 1000, Bulgaria
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, Sofia 1000, Bulgaria
| |
Collapse
|
94
|
Alhalaweh A, Alzghoul A, Kaialy W. Data mining of solubility parameters for computational prediction of drug–excipient miscibility. Drug Dev Ind Pharm 2013; 40:904-9. [DOI: 10.3109/03639045.2013.789906] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
95
|
Cami A, Manzi S, Arnold A, Reis BY. Pharmacointeraction network models predict unknown drug-drug interactions. PLoS One 2013; 8:e61468. [PMID: 23620757 PMCID: PMC3631217 DOI: 10.1371/journal.pone.0061468] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/11/2013] [Indexed: 12/20/2022] Open
Abstract
Drug-drug interactions (DDIs) can lead to serious and potentially lethal adverse events. In recent years, several drugs have been withdrawn from the market due to interaction-related adverse events (AEs). Current methods for detecting DDIs rely on the accumulation of sufficient clinical evidence in the post-market stage – a lengthy process that often takes years, during which time numerous patients may suffer from the adverse effects of the DDI. Detection methods are further hindered by the extremely large combinatoric space of possible drug-drug-AE combinations. There is therefore a practical need for predictive tools that can identify potential DDIs years in advance, enabling drug safety professionals to better prioritize their limited investigative resources and take appropriate regulatory action. To meet this need, we describe Predictive Pharmacointeraction Networks (PPINs) – a novel approach that predicts unknown DDIs by exploiting the network structure of all known DDIs, together with other intrinsic and taxonomic properties of drugs and AEs. We constructed an 856-drug DDI network from a 2009 snapshot of a widely-used drug safety database, and used it to develop PPIN models for predicting future DDIs. We compared the DDIs predicted based solely on these 2009 data, with newly reported DDIs that appeared in a 2012 snapshot of the same database. Using a standard multivariate approach to combine predictors, the PPIN model achieved an AUROC (area under the receiver operating characteristic curve) of 0.81 with a sensitivity of 48% given a specificity of 90%. An analysis of DDIs by severity level revealed that the model was most effective for predicting “contraindicated” DDIs (AUROC = 0.92) and less effective for “minor” DDIs (AUROC = 0.63). These results indicate that network based methods can be useful for predicting unknown drug-drug interactions.
Collapse
Affiliation(s)
- Aurel Cami
- Division of Emergency Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.
| | | | | | | |
Collapse
|
96
|
Zhou W, Huang C, Li Y, Duan J, Wang Y, Yang L. A systematic identification of multiple toxin–target interactions based on chemical, genomic and toxicological data. Toxicology 2013; 304:173-84. [DOI: 10.1016/j.tox.2012.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 11/26/2022]
|
97
|
Telpoukhovskaia MA, Patrick BO, Rodríguez-Rodríguez C, Orvig C. Exploring the multifunctionality of thioflavin- and deferiprone-based molecules as acetylcholinesterase inhibitors for potential application in Alzheimer's disease. MOLECULAR BIOSYSTEMS 2013; 9:792-805. [DOI: 10.1039/c3mb25600f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
98
|
Abstract
The identification of drug-target interactions from heterogeneous biological data is critical in the drug development. In this chapter, we review recently developed in silico chemogenomic approaches to infer unknown drug-target interactions from chemical information of drugs and genomic information of target proteins. We review several kernel-based statistical methods from two different viewpoints: binary classification and dimension reduction. In the results, we demonstrate the usefulness of the methods on the prediction of drug-target interactions from chemical structure data and genomic sequence data. We also discuss the characteristics of each method, and show some perspectives toward future research direction.
Collapse
|
99
|
Xu X, Yang W, Li Y, Wang Y. Discovery of estrogen receptor modulators: a review of virtual screening and SAR efforts. Expert Opin Drug Discov 2012; 5:21-31. [PMID: 22823969 DOI: 10.1517/17460440903490395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
IMPORTANCE OF THE FIELD Virtual screening (VS) coupled with structural biology is a significantly important approach to increase the number and enhance the success of projects in lead identification stage of drug discovery process. Recent advances and future directions in estrogen therapy have resulted in great demand for identifying the potential estrogen receptor (ER) modulators with more activity and selectivity. AREAS COVERED IN THIS REVIEW This review presents the current state of the art in VS and structure-activity relationship of ER modulators in recent discovery, and discusses the strengths and weaknesses of the technology. WHAT THE READER WILL GAIN Readers will gain an overview of the current platforms of in silico screening for discovery of ER modulators; they will learn which structural information is significantly correlated with the bioactivity of ER modulators and what novel strategies should be considered for the creation of more effective chemical structures. TAKE HOME MESSAGE With the goal of reducing toxicity and/or improving efficacy, challenges to the successful modeling of endocrine agents are proposed, providing new paradigms for the design of ER inhibitors.
Collapse
Affiliation(s)
- Xue Xu
- Northwest A&F University, Center of Bioinformatics, Yangling, Shaanxi, 712100, China
| | | | | | | |
Collapse
|
100
|
Gönen M. Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization. Bioinformatics 2012; 28:2304-10. [PMID: 22730431 DOI: 10.1093/bioinformatics/bts360] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION Identifying interactions between drug compounds and target proteins has a great practical importance in the drug discovery process for known diseases. Existing databases contain very few experimentally validated drug-target interactions and formulating successful computational methods for predicting interactions remains challenging. RESULTS In this study, we consider four different drug-target interaction networks from humans involving enzymes, ion channels, G-protein-coupled receptors and nuclear receptors. We then propose a novel Bayesian formulation that combines dimensionality reduction, matrix factorization and binary classification for predicting drug-target interaction networks using only chemical similarity between drug compounds and genomic similarity between target proteins. The novelty of our approach comes from the joint Bayesian formulation of projecting drug compounds and target proteins into a unified subspace using the similarities and estimating the interaction network in that subspace. We propose using a variational approximation in order to obtain an efficient inference scheme and give its detailed derivations. Finally, we demonstrate the performance of our proposed method in three different scenarios: (i) exploratory data analysis using low-dimensional projections, (ii) predicting interactions for the out-of-sample drug compounds and (iii) predicting unknown interactions of the given network. AVAILABILITY Software and Supplementary Material are available at http://users.ics.aalto.fi/gonen/kbmf2k. CONTACT mehmet.gonen@aalto.fi SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mehmet Gönen
- Helsinki Institute for Information Technology HIIT, Department of Information and Computer Science, Aalto University School of Science, FI-00076 Aalto, Espoo, Finland.
| |
Collapse
|