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Tiwari G, Chauhan MS, Sharma D. Estimation of Binding Sites of Efavirenz with 3EO9 Receptor: In Silico Molecular Docking and Molecular Dynamics Studies. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1998148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gargi Tiwari
- Department of Physics, Patna University, Patna, India
| | | | - Dipendra Sharma
- Department of Physics, DDU Gorakhpur University, Gorakhpur, India
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Choi HJ, Wang C, Pan X, Jang J, Cao M, Brazzo JA, Bae Y, Lee K. Emerging machine learning approaches to phenotyping cellular motility and morphodynamics. Phys Biol 2021; 18:10.1088/1478-3975/abffbe. [PMID: 33971636 PMCID: PMC9131244 DOI: 10.1088/1478-3975/abffbe] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/10/2021] [Indexed: 12/22/2022]
Abstract
Cells respond heterogeneously to molecular and environmental perturbations. Phenotypic heterogeneity, wherein multiple phenotypes coexist in the same conditions, presents challenges when interpreting the observed heterogeneity. Advances in live cell microscopy allow researchers to acquire an unprecedented amount of live cell image data at high spatiotemporal resolutions. Phenotyping cellular dynamics, however, is a nontrivial task and requires machine learning (ML) approaches to discern phenotypic heterogeneity from live cell images. In recent years, ML has proven instrumental in biomedical research, allowing scientists to implement sophisticated computation in which computers learn and effectively perform specific analyses with minimal human instruction or intervention. In this review, we discuss how ML has been recently employed in the study of cell motility and morphodynamics to identify phenotypes from computer vision analysis. We focus on new approaches to extract and learn meaningful spatiotemporal features from complex live cell images for cellular and subcellular phenotyping.
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Affiliation(s)
- Hee June Choi
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Chuangqi Wang
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
- Present address. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiang Pan
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Junbong Jang
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Mengzhi Cao
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
| | - Joseph A Brazzo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, United States of America
| | - Yongho Bae
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14203, United States of America
| | - Kwonmoo Lee
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA 01609, United States of America
- Vascular Biology Program and Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
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Nouadi B, Ezaouine A, El Messal M, Blaghen M, Bennis F, Chegdani F. Prediction of Anti-COVID 19 Therapeutic Power of Medicinal Moroccan Plants Using Molecular Docking. Bioinform Biol Insights 2021; 15:11779322211009199. [PMID: 33888980 PMCID: PMC8040561 DOI: 10.1177/11779322211009199] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/21/2021] [Indexed: 01/30/2023] Open
Abstract
The emerging pathogen SARS-CoV2 causing coronavirus disease 2019 (COVID-19) is a global public health challenge. To the present day, COVID-19 had affected more than 40 million people worldwide. The exploration and the development of new bioactive compounds with cost-effective and specific anti-COVID 19 therapeutic power is the prime focus of the current medical research. Thus, the exploitation of the molecular docking technique has become essential in the discovery and development of new drugs, to better understand drug-target interactions in their original environment. This work consists of studying the binding affinity and the type of interactions, through molecular docking, between 54 compounds from Moroccan medicinal plants, dextran sulfate and heparin (compounds not derived from medicinal plants), and 3CLpro-SARS-CoV-2, ACE2, and the post fusion core of 2019-nCoV S2 subunit. The PDB files of the target proteins and prepared herbal compounds (ligands) were subjected for docking to AutoDock Vina using UCSF Chimera, which provides a list of potential complexes based on the criteria of form complementarity of the natural compound with their binding affinities. The results of molecular docking revealed that Taxol, Rutin, Genkwanine, and Luteolin-glucoside have a high affinity with ACE2 and 3CLpro. Therefore, these natural compounds can have 2 effects at once, inhibiting 3CLpro and preventing recognition between the virus and ACE2. These compounds may have a potential therapeutic effect against SARS-CoV2, and therefore natural anti-COVID-19 compounds.
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Affiliation(s)
- Badreddine Nouadi
- Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Abdelkarim Ezaouine
- Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mariame El Messal
- Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Mohamed Blaghen
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences El Jadida, Chouaïb Doukkali University, El Jadida, Morocco
| | - Faiza Bennis
- Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Fatima Chegdani
- Laboratory of Health and Environment, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
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Baig MH, Ahmad K, Rabbani G, Danishuddin M, Choi I. Computer Aided Drug Design and its Application to the Development of Potential Drugs for Neurodegenerative Disorders. Curr Neuropharmacol 2018; 16:740-748. [PMID: 29046156 PMCID: PMC6080097 DOI: 10.2174/1570159x15666171016163510] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/24/2017] [Accepted: 10/10/2017] [Indexed: 12/11/2022] Open
Abstract
Background Neurodegenerative disorders (NDs) are diverse group of disorders characterized by escalating loss of neurons (structural and functional). The development of potential therapeutics for NDs presents an important challenge, as traditional treatments are inefficient and usually are unable to stop or retard the process of neurodegeneration. Computer-Aided Drug Design (CADD) has emerged as an efficient means of developing candidate drugs for the treatment of many disease types. Applications of CADD approach to drug discovery are progressing day by day. The recent tendency in drug design is to rationally design potent therapeutics with multi-targeting effects, higher efficacies, and fewer side effects, especially in terms of toxicity. Methods A wide literature search was performed for writing this review. An updated view on different types of NDs, their effect on human population and a brief introduction to CADD, various approaches involved in this technique, ranging from structural-based to ligand-based drug design has been discussed. The successful application of CADD approaches for the treatment of neurodegenerative disorders is also included in this review. Results In this review, we have briefly described about CADD and its use in the development of the therapeutic drug candidates against NDs. The successful applications, limitations and future prospects of this approach have also been discussed. Conclusion CADD can assist researchers studying interactions between drugs and receptors. We believe this review will be helpful for better understanding of CADD and its applications towards the discovery of new drug candidates against various fatal NDs.
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Affiliation(s)
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Gulam Rabbani
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Mohd Danishuddin
- School of computation and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Korea
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Sun H, Shen Y, Luo G, Cai Y, Xiang Z. An integrated strategy for identifying new targets and inferring the mechanism of action: taking rhein as an example. BMC Bioinformatics 2018; 19:315. [PMID: 30189851 PMCID: PMC6127921 DOI: 10.1186/s12859-018-2346-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/29/2018] [Indexed: 02/19/2023] Open
Abstract
Background Target identification is necessary for the comprehensive inference of the mechanism of action of a compound. The application of computational methods to predict the targets of bioactive compounds saves cost and time in drug research and development. Therefore, we designed an integrated strategy consisting of ligand-protein docking, network analysis, enrichment analysis, and an experimental surface plasmon resonance (SPR) method to identify and validate new targets, and then used enriched pathways to elucidate the underlying pharmacological mechanisms. Here, we used rhein, a compound with various pharmacological activities, as an example to find some of its previously unknown targets and to determine its pharmacological activity. Results A total of nine candidate targets were discovered, including LCK, HSP90AA1, RAB5A, EGFR, CDK2, CDK6, GSK3B, p38, and JNK. LCK was confirmed through SPR experiments, and HSP90AA1, EGFR, CDK6, p38, and JNK were validated through previous reports. Rhein network regulations are complex and interconnected. The therapeutic effect of rhein is the synergistic and comprehensive result of this vast and complex network, and the perturbation of multiple targets gives rhein its various pharmacological activities. Conclusions This study provided a new integrated strategy to identify new targets of bioactive compounds and reveal their molecular mechanisms of action. Electronic supplementary material The online version of this article (10.1186/s12859-018-2346-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Sun
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,Pharmacy Department, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Yiting Shen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Guangwen Luo
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yuepiao Cai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Zheng Xiang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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Doornbos ML, Van der Linden I, Vereyken L, Tresadern G, IJzerman AP, Lavreysen H, Heitman LH. Constitutive activity of the metabotropic glutamate receptor 2 explored with a whole-cell label-free biosensor. Biochem Pharmacol 2018; 152:201-210. [DOI: 10.1016/j.bcp.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/27/2018] [Indexed: 12/14/2022]
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Peng J, Zhao Y, Hong Y, Burkhalter RS, Hogue CL, Tran E, Wei L, Romeo L, Dolley-Sonneville P, Melkoumian Z, Liang X, Fang Y. Chemical Identity and Mechanism of Action and Formation of a Cell Growth Inhibitory Compound from Polycarbonate Flasks. Anal Chem 2018. [DOI: 10.1021/acs.analchem.7b05102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Yaopeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | | | | | | | | | - Lai Wei
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | | | | | | | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
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Hillger JM, Lieuw WL, Heitman LH, IJzerman AP. Label-free technology and patient cells: from early drug development to precision medicine. Drug Discov Today 2017; 22:1808-1815. [PMID: 28778587 DOI: 10.1016/j.drudis.2017.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/10/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
Abstract
Drug development requires physiologically more appropriate model systems and assays to increase understanding of drug action and pathological processes in individual humans. Specifically, patient-derived cells offer great opportunities as representative cellular model systems. Moreover, with novel label-free cellular assays, it is often possible to investigate complex biological processes in their native environment. Combining these two offers distinct opportunities for increasing physiological relevance. Here, we review impedance-based label-free technologies in the context of patient samples, focusing on commonly used cell types, including fibroblasts, blood components, and stem cells. Applications extend as far as tissue-on-a-chip models. Thus, applying label-free technologies to patient samples can produce highly biorelevant data and, with them, unique opportunities for drug development and precision medicine.
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Affiliation(s)
- Julia M Hillger
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Wai-Ling Lieuw
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University, The Netherlands.
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Systems Pharmacology in Small Molecular Drug Discovery. Int J Mol Sci 2016; 17:246. [PMID: 26901192 PMCID: PMC4783977 DOI: 10.3390/ijms17020246] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 12/15/2022] Open
Abstract
Drug discovery is a risky, costly and time-consuming process depending on multidisciplinary methods to create safe and effective medicines. Although considerable progress has been made by high-throughput screening methods in drug design, the cost of developing contemporary approved drugs did not match that in the past decade. The major reason is the late-stage clinical failures in Phases II and III because of the complicated interactions between drug-specific, human body and environmental aspects affecting the safety and efficacy of a drug. There is a growing hope that systems-level consideration may provide a new perspective to overcome such current difficulties of drug discovery and development. The systems pharmacology method emerged as a holistic approach and has attracted more and more attention recently. The applications of systems pharmacology not only provide the pharmacodynamic evaluation and target identification of drug molecules, but also give a systems-level of understanding the interaction mechanism between drugs and complex disease. Therefore, the present review is an attempt to introduce how holistic systems pharmacology that integrated in silico ADME/T (i.e., absorption, distribution, metabolism, excretion and toxicity), target fishing and network pharmacology facilitates the discovery of small molecular drugs at the system level.
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Fang Y. Compound annotation with real time cellular activity profiles to improve drug discovery. Expert Opin Drug Discov 2016; 11:269-80. [PMID: 26787137 DOI: 10.1517/17460441.2016.1143460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In the past decade, a range of innovative strategies have been developed to improve the productivity of pharmaceutical research and development. In particular, compound annotation, combined with informatics, has provided unprecedented opportunities for drug discovery. AREAS COVERED In this review, a literature search from 2000 to 2015 was conducted to provide an overview of the compound annotation approaches currently used in drug discovery. Based on this, a framework related to a compound annotation approach using real-time cellular activity profiles for probe, drug, and biology discovery is proposed. EXPERT OPINION Compound annotation with chemical structure, drug-like properties, bioactivities, genome-wide effects, clinical phenotypes, and textural abstracts has received significant attention in early drug discovery. However, these annotations are mostly associated with endpoint results. Advances in assay techniques have made it possible to obtain real-time cellular activity profiles of drug molecules under different phenotypes, so it is possible to generate compound annotation with real-time cellular activity profiles. Combining compound annotation with informatics, such as similarity analysis, presents a good opportunity to improve the rate of discovery of novel drugs and probes, and enhance our understanding of the underlying biology.
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Affiliation(s)
- Ye Fang
- a Biochemical Technologies, Science and Technology Division , Corning Incorporated , Corning , NY , USA
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Abstract
D-Luciferin (also known as beetle or firefly luciferin) is one of the most widely used bioluminescent reporters for monitoring in vitro or in vivo luciferase activity. The identification of several natural phenols and thieno[3,2-b]thiophene-2-carboxylic acid derivatives as agonists for GPR35, an orphan G protein-coupled receptor, had motivated us to examine the pharmacological activity of D-Luciferin, given that it also contains phenol and carboxylic acid moieties. Here, we describe label-free cell phenotypic assays that ascertain D-Luciferin as a partial agonist for GPR35. The agonistic activity of D-Luciferin at the GPR35 shall evoke careful interpretation of biological data when D-Luciferin or its analogues are used as probes.
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