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Zhang Q, He Y, Lu YP, Wei QH, Zhang HY, Quan Y. GETdb: A comprehensive database for genetic and evolutionary features of drug targets. Comput Struct Biotechnol J 2024; 23:1429-1438. [PMID: 38616961 PMCID: PMC11015738 DOI: 10.1016/j.csbj.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024] Open
Abstract
The development of an innovative drug is complex and time-consuming, and the drug target identification is one of the critical steps in drug discovery process. Effective and accurate identification of drug targets can accelerate the drug development process. According to previous research, evolutionary and genetic information of genes has been found to facilitate the identification of approved drug targets. In addition, allosteric proteins have great potential as targets due to their structural diversity. However, this information that could facilitate target identification has not been collated in existing drug target databases. Here, we construct a comprehensive drug target database named Genetic and Evolutionary features of drug Targets database (GETdb, http://zhanglab.hzau.edu.cn/GETdb/page/index.jsp). This database not only integrates and standardizes data from dozens of commonly used drug and target databases, but also innovatively includes the genetic and evolutionary information of targets. Moreover, this database features an effective allosteric protein prediction model. GETdb contains approximately 4000 targets and over 29,000 drugs, and is a user-friendly database for searching, browsing and downloading data to facilitate the development of novel targets.
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Affiliation(s)
- Qi Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yang He
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ya-Ping Lu
- Sinopharm Genomics Technology Co., Ltd., Wuhan 430030, PR China
- Sinopharm Medical Laboratory (Wuhan) Co., Ltd., Wuhan 430030, PR China
| | - Qi-Hao Wei
- Sinopharm (Wuhan) Precision Medical Technology Co., Ltd., Wuhan 430030, PR China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China
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2
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Ma B, Shi S, Guo W, Zhang H, Zhao Z, An H. Liensinine, a Novel and Food-Derived Compound, Exerts Potent Antihepatoma Efficacy via Inhibiting the Kv10.1 Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4689-4702. [PMID: 38382537 DOI: 10.1021/acs.jafc.3c06142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Plant metabolites from natural product extracts offer unique advantages against carcinogenesis in the development of drugs. The target-based virtual screening from food-derived compounds represents a promising approach for tumor therapy. In this study, we performed virtual screening to target the presumed inhibitor-binding pocket and identified a highly potent Kv10.1 inhibitor, liensinine (Lien), which can inhibit the channel in a dose-dependent way with an IC50 of 0.24 ± 0.07 μM. Combining molecular dynamics simulations with mutagenesis experiments, our data show that Lien interacts with Kv10.1 by binding with Y539, T543, D551, E553, and H601 in the C-linker domain of Kv10.1. In addition, the interaction of sequence alignment and 3D structural modeling revealed differences between the C-linker domain of the Kv10.1 channel and the Kv11.1 channel. Furthermore, antitumor experiments revealed that Lien suppresses the proliferation and migration of HCC both in vitro and in vivo. In summary, the food-derived compound, Lien, may serve as a lead compound for antihepatoma therapeutic drugs targeting Kv10.1.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Wei Guo
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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3
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Everts M, Drew M. Successfully navigating the valley of death: the importance of accelerators to support academic drug discovery and development. Expert Opin Drug Discov 2024; 19:253-258. [PMID: 37968916 DOI: 10.1080/17460441.2023.2284824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
INTRODUCTION The drug discovery and development 'valley of death' remains a challenge for promising new therapies originating from academic research laboratories. Drug discovery support centers and accelerators have been established to provide monetary and scientific support, but limited available funding along with cultural and expertise gaps remain obstacles for many promising technologies. AREAS COVERED In this meta-opinion article, the authors summarize the literature around obstacles that academic drug discovery projects face, along with potential solutions and best practices. Topics covered include funding challenges, regulatory education, reproducibility, along with cultural and organizational considerations. It describes one accelerator in particular-Critical Path Institute's Translational Therapeutics Accelerator (TRxA)-that aims to overcome several of the mentioned challenges. EXPERT OPINION The 'valley of death' remains a stubborn but not insurmountable part of the academic drug discovery and development landscape. Purposely designed accelerators can help, complementing more traditional intra- and extramural funding support.
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Affiliation(s)
- Maaike Everts
- Translational Therapeutics Accelerator (TRxA), Critical Path Institute, Tucson, AZ, USA
| | - Mark Drew
- Translational Therapeutics Accelerator (TRxA), Critical Path Institute, Tucson, AZ, USA
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Ma B, Shi S, Ren S, Qu C, Zhao Z, An H. Corydaline binds to a druggable pocket of hEAG1 channel and inhibits hepatic carcinoma cell viability. Eur J Pharmacol 2024; 962:176240. [PMID: 38048981 DOI: 10.1016/j.ejphar.2023.176240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
Abstract
Ether-à-go-go (EAG) potassium channels play a crucial role in the regulation of neuronal excitability and cancer progression, rendering them potential drug targets for cancer therapy. However, the scarcity of information regarding the selection sites on hEAG1 has posed a challenge in the discovery of new hEAG1 inhibitors. In this study, we introduced a novel natural product, corydaline, which selectively inhibits the hEAG1 channel without sensitivity to other KCNH channels. The IC50 of corydaline for the hEAG1 channel was 11.3 ± 0.6 μM, whereas the IC50 for hEAG2 and hERG1 were 73.6 ± 9.9 μM and 111.4 ± 8.5 μM, respectively. Molecular dynamics simulations together with site-directed mutagenesis, have unveiled that the site corydaline forms interactions with Lys217, Phe273, Pro276, Trp295 and Arg366, situated within the intracellular transmembrane segments S1-S4 of the voltage-sensor domain, be considered a novel drug pocket for hEAG1. Additionally, the intergaration of sequence alignment and 3D structural modeling revealed differences between the voltage sensor domain of hEAG1 channel and other EAG channels, suggesting the feasibility of a VSD modulation approach that could potentially lead to the selective inhibition of hEAG1 channels. Furthermore, antitumor experiments demonstrated that corydaline can inhibit the proliferation and migration of hepatic carcinoma cells by targeting hEAG1. The identification of this novel druggable pocket offers the possibility for drug screening against diseases linked to abnormal hEAG1 channels.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Shuxi Ren
- School of Sciences, Hebei University of Technology, Tianjin, 300401, China
| | - Chang Qu
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin, 300401, China; Key Laboratory of Molecular Biophysics, Hebei Province, China; Institute of Biophysics, School of Health Sciences and Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
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5
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Ma Z, Augustijn K, De Esch I, Bossink B. Public-private partnerships influencing the initiation and duration of clinical trials for neglected tropical diseases. PLoS Negl Trop Dis 2023; 17:e0011760. [PMID: 37956165 PMCID: PMC10681307 DOI: 10.1371/journal.pntd.0011760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/27/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Public-private partnerships (PPPs) for neglected tropical diseases (NTDs) are often studied as an organizational form that facilitates the management and control of the huge costs of drug research and development. Especially the later stages of drug development, including clinical trials, become very expensive. This present study investigates whether and how the type of PPPs influences the initiation and duration of NTD clinical trials. Using the ClinicalTrials.gov database, a dataset of 1175 NTD clinical studies that started between 2000 and 2021 is analyzed based on affiliation information and project duration. For the NTD clinical trials that resulted from PPPs, the collaborating types were determined and analyzed, including the public sector-, private sector-, governmental sector-, and nongovernmental organization-led collaborations. The determinants for the discontinuation of all stopped clinical trials were categorized into scientific-, funding-, political-, and logistic dimensions. The results reveal that public sector-led PPPs were the most common collaborative types, and logistic and scientific issues were the most frequent determinants of stopped clinical trials. Trial registration: ClinicalTrials.gov.
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Affiliation(s)
- Zhongxuan Ma
- Breakthrough Tech Innovation research group, Amsterdam Institute of Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kevin Augustijn
- Department of Molecular Cell Biology and Immunology, Amsterdam Universitair Medisch Centrum, Amsterdam, The Netherlands
| | - Iwan De Esch
- Division of Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Bart Bossink
- Breakthrough Tech Innovation research group, Amsterdam Institute of Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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6
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Glenn IS, Hall LN, Khalid MM, Ott M, Shoichet BK. Colloidal aggregation confounds cell-based Covid-19 antiviral screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564435. [PMID: 37961552 PMCID: PMC10634915 DOI: 10.1101/2023.10.27.564435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Colloidal aggregation is one of the largest contributors to false-positives in early drug discovery and chemical biology. Much work has focused on its impact on pure-protein screens; here we consider aggregations role in cell-based infectivity assays in Covid-19 drug repurposing. We began by investigating the potential aggregation of 41 drug candidates reported as SARs-CoV-2 entry inhibitors. Of these, 17 formed colloidal-particles by dynamic light scattering and exhibited detergent-dependent enzyme inhibition. To evaluate antiviral efficacy of the drugs in cells we used spike pseudotyped lentivirus and pre-saturation of the colloids with BSA. The antiviral potency of the aggregators was diminished by at least 10-fold and often entirely eliminated in the presence of BSA, suggesting antiviral activity can be attributed to the non-specific nature of the colloids. In confocal microscopy, the aggregates induced fluorescent puncta of labeled spike protein, consistent with sequestration of the protein on the colloidal particles. Addition of either non-ionic detergent or of BSA disrupted these puncta. These observations suggest that colloidal aggregation is common among cell-based anti-viral drug repurposing, and perhaps cell-based assays more broadly, and offers rapid counter-screens to detect and eliminate these artifacts, allowing the community invest resources in compounds with true potential as a Covid-19 therapeutic.
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Affiliation(s)
- Isabella S Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Lauren N Hall
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, CA, USA
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7
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Fashemi BE, van Biljon L, Rodriguez J, Graham O, Mullen M, Khabele D. Ovarian Cancer Patient-Derived Organoid Models for Pre-Clinical Drug Testing. J Vis Exp 2023:10.3791/65068. [PMID: 37782106 PMCID: PMC10881228 DOI: 10.3791/65068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
Ovarian cancer is a fatal gynecologic cancer and the fifth leading cause of cancer death among women in the United States. Developing new drug treatments is crucial to advancing healthcare and improving patient outcomes. Organoids are in-vitro three-dimensional multicellular miniature organs. Patient-derived organoid (PDO) models of ovarian cancer may be optimal for drug screening because they more accurately recapitulate tissues of interest than two-dimensional cell culture models and are inexpensive compared to patient-derived xenografts. In addition, ovarian cancer PDOs mimic the variable tumor microenvironment and genetic background typically observed in ovarian cancer. Here, a method is described that can be used to test conventional and novel drugs on PDOs derived from ovarian cancer tissue and ascites. A luminescence-based adenosine triphosphate (ATP) assay is used to measure viability, growth rate, and drug sensitivity. Drug screens in PDOs can be completed in 7-10 days, depending on the rate of organoid formation and drug treatments.
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Affiliation(s)
| | | | | | | | - Mary Mullen
- Washington University of Medicine in St. Louis
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8
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Muniyandi P, O’Hern C, Popa MA, Aguirre A. Biotechnological advances and applications of human pluripotent stem cell-derived heart models. Front Bioeng Biotechnol 2023; 11:1214431. [PMID: 37560538 PMCID: PMC10407810 DOI: 10.3389/fbioe.2023.1214431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/12/2023] [Indexed: 08/11/2023] Open
Abstract
In recent years, significant biotechnological advancements have been made in engineering human cardiac tissues and organ-like models. This field of research is crucial for both basic and translational research due to cardiovascular disease being the leading cause of death in the developed world. Additionally, drug-associated cardiotoxicity poses a major challenge for drug development in the pharmaceutical and biotechnological industries. Progress in three-dimensional cell culture and microfluidic devices has enabled the generation of human cardiac models that faithfully recapitulate key aspects of human physiology. In this review, we will discuss 3D pluripotent stem cell (PSC)-models of the human heart, such as engineered heart tissues and organoids, and their applications in disease modeling and drug screening.
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Affiliation(s)
- Priyadharshni Muniyandi
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, United States
| | - Colin O’Hern
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, United States
| | - Mirel Adrian Popa
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, United States
- Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Aitor Aguirre
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, United States
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI, United States
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9
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Dera AA, Zaib S, Hussain N, Rana N, Javed H, Khan I. Identification of Potent Inhibitors Targeting EGFR and HER3 for Effective Treatment of Chemoresistance in Non-Small Cell Lung Cancer. Molecules 2023; 28:4850. [PMID: 37375404 DOI: 10.3390/molecules28124850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common form of lung cancer. Despite the existence of various therapeutic options, NSCLC is still a major health concern due to its aggressive nature and high mutation rate. Consequently, HER3 has been selected as a target protein along with EGFR because of its limited tyrosine kinase activity and ability to activate PI3/AKT pathway responsible for therapy failure. We herein used a BioSolveIT suite to identify potent inhibitors of EGFR and HER3. The schematic process involves screening of databases for constructing compound library comprising of 903 synthetic compounds (602 for EGFR and 301 for HER3) followed by pharmacophore modeling. The best docked poses of compounds with the druggable binding site of respective proteins were selected according to pharmacophore designed by SeeSAR version 12.1.0. Subsequently, preclinical analysis was performed via an online server SwissADME and potent inhibitors were selected. Compound 4k and 4m were the most potent inhibitors of EGFR while 7x effectively inhibited the binding site of HER3. The binding energies of 4k, 4m, and 7x were -7.7, -6.3 and -5.7 kcal/mol, respectively. Collectively, 4k, 4m and 7x showed favorable interactions with the most druggable binding sites of their respective proteins. Finally, in silico pre-clinical testing by SwissADME validated the non-toxic nature of compounds 4k, 4m and 7x providing a promising treatment option for chemoresistant NSCLC.
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Affiliation(s)
- Ayed A Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain P.O. Box 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi P.O. Box 144534, United Arab Emirates
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Hira Javed
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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10
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Vázquez J, Ginex T, Herrero A, Morisseau C, Hammock BD, Luque FJ. Screening and Biological Evaluation of Soluble Epoxide Hydrolase Inhibitors: Assessing the Role of Hydrophobicity in the Pharmacophore-Guided Search of Novel Hits. J Chem Inf Model 2023; 63:3209-3225. [PMID: 37141492 PMCID: PMC10207366 DOI: 10.1021/acs.jcim.3c00301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Indexed: 05/06/2023]
Abstract
The human soluble epoxide hydrolase (sEH) is a bifunctional enzyme that modulates the levels of regulatory epoxy lipids. The hydrolase activity is carried out by a catalytic triad located at the center of a wide L-shaped binding site, which contains two hydrophobic subpockets at both sides. On the basis of these structural features, it can be assumed that desolvation is a major factor in determining the maximal achievable affinity that can be attained for this pocket. Accordingly, hydrophobic descriptors may be better suited to the search of novel hits targeting this enzyme. This study examines the suitability of quantum mechanically derived hydrophobic descriptors in the discovery of novel sEH inhibitors. To this end, three-dimensional quantitative structure-activity relationship (3D-QSAR) pharmacophores were generated by combining electrostatic and steric or alternatively hydrophobic and hydrogen-bond parameters in conjunction with a tailored list of 76 known sEH inhibitors. The pharmacophore models were then validated by using two external sets chosen (i) to rank the potency of four distinct series of compounds and (ii) to discriminate actives from decoys, using in both cases datasets taken from the literature. Finally, a prospective study was performed including a virtual screening of two chemical libraries to identify new potential hits, which were subsequently experimentally tested for their inhibitory activity on human, rat, and mouse sEH. The use of hydrophobic-based descriptors led to the identification of six compounds as inhibitors of the human enzyme with IC50 < 20 nM, including two with IC50 values of 0.4 and 0.7 nM. The results support the use of hydrophobic descriptors as a valuable tool in the search of novel scaffolds that encode a proper hydrophilic/hydrophobic distribution complementary to the target's binding site.
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Affiliation(s)
- Javier Vázquez
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia i Ciències de l′Alimentació, Institut de Biomedicina (IBUB), Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
- Pharmacelera,
Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Tiziana Ginex
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia i Ciències de l′Alimentació, Institut de Biomedicina (IBUB), Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
| | - Albert Herrero
- Pharmacelera,
Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Christophe Morisseau
- Department
of Entomology and Nematology, and Comprehensive Cancer Center, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Bruce D. Hammock
- Department
of Entomology and Nematology, and Comprehensive Cancer Center, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - F. Javier Luque
- Departament
de Nutrició, Ciències de l′Alimentació
i Gastronomia, Facultat de Farmàcia i Ciències de l′Alimentació, Institut de Biomecidina (IBUB) and Institut de Química
Teòrica i Computacional (IQTCUB), Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain
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11
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Quan Y, Xiong ZK, Zhang KX, Zhang QY, Zhang W, Zhang HY. Evolution-strengthened knowledge graph enables predicting the targetability and druggability of genes. PNAS NEXUS 2023; 2:pgad147. [PMID: 37188275 PMCID: PMC10178923 DOI: 10.1093/pnasnexus/pgad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Identifying promising targets is a critical step in modern drug discovery, with causative genes of diseases that are an important source of successful targets. Previous studies have found that the pathogeneses of various diseases are closely related to the evolutionary events of organisms. Accordingly, evolutionary knowledge can facilitate the prediction of causative genes and further accelerate target identification. With the development of modern biotechnology, massive biomedical data have been accumulated, and knowledge graphs (KGs) have emerged as a powerful approach for integrating and utilizing vast amounts of data. In this study, we constructed an evolution-strengthened knowledge graph (ESKG) and validated applications of ESKG in the identification of causative genes. More importantly, we developed an ESKG-based machine learning model named GraphEvo, which can effectively predict the targetability and the druggability of genes. We further investigated the explainability of the ESKG in druggability prediction by dissecting the evolutionary hallmarks of successful targets. Our study highlights the importance of evolutionary knowledge in biomedical research and demonstrates the potential power of ESKG in promising target identification. The data set of ESKG and the code of GraphEvo can be downloaded from https://github.com/Zhankun-Xiong/GraphEvo.
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Affiliation(s)
| | | | - Ke-Xin Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, P. R. China
| | - Wen Zhang
- To whom correspondence should be addressed: ;
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12
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Futosi K, Bajza B, Deli D, Erdélyi A, Tusnády S, Mócsai A. Analysis of intracellular tyrosine phosphorylation in circulating neutrophils as a rapid assay for the in vivo effect of oral tyrosine kinase inhibitors. Front Pharmacol 2023; 14:1056154. [PMID: 37089957 PMCID: PMC10117656 DOI: 10.3389/fphar.2023.1056154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023] Open
Abstract
Tyrosine kinases are crucial signaling components of diverse biological processes and are major therapeutic targets in various malignancies and immune-mediated disorders. A critical step of development of novel tyrosine kinase inhibitors is the transition from the confirmation of the in vitro effects of drug candidates to the analysis of their in vivo efficacy. To facilitate this transition, we have developed a rapid in vivo assay for the analysis of the effect of oral tyrosine kinase inhibitors on basal tyrosine phosphorylation of circulating mouse neutrophils. The assay uses a single drop of peripheral blood without sacrificing the mice. Flow cytometry using intracellular staining by fluorescently labeled anti-phosphotyrosine antibodies revealed robust basal tyrosine phosphorylation in resting circulating neutrophils. This signal was abrogated by the use of isotype control antibodies or by pre-saturation of the anti-phosphotyrosine antibodies with soluble phosphotyrosine amino acids or tyrosine-phosphorylated peptides. Basal tyrosine phosphorylation was dramatically reduced in neutrophils of triple knockout mice lacking the Src-family tyrosine kinases Hck, Fgr, and Lyn. Neutrophil tyrosine phosphorylation was also abrogated by oral administration of the Abl/Src-family inhibitor dasatinib, a clinically used anti-leukemic agent. Detailed dose-response and kinetic studies revealed half-maximal reduction of neutrophil tyrosine phosphorylation by 2.9 mg/kg dasatinib, with maximal reduction observed 2 h after inhibitor administration. Taken together, our assay allows highly efficient analysis of the in vivo effect of orally administered tyrosine kinase inhibitors, and may be used as a suitable alternative to other existing approaches.
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Affiliation(s)
- Krisztina Futosi
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
- ELKH-SE Inflammation Physiology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- *Correspondence: Krisztina Futosi,
| | - Boglárka Bajza
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Dorottya Deli
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - András Erdélyi
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Simon Tusnády
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
- ELKH-SE Inflammation Physiology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
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13
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Munir S, Khurshid M, Ahmad M, Ashfaq UA, Zaki MEA. Exploring the Antimicrobial and Pharmacological Potential of NF22 as a Potent Inhibitor of E. coli DNA Gyrase: An In Vitro and In Silico Study. Pharmaceutics 2022; 14:pharmaceutics14122768. [PMID: 36559262 PMCID: PMC9784730 DOI: 10.3390/pharmaceutics14122768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Toward the search for novel antimicrobial agents to control pathogenic E. coli-associated infections, a series of novel norfloxacin derivatives were screened for antimicrobial activities. The norfloxacin derivative, 1-ethyl-6-fluoro-7-(4-(2-(2-(3-hydroxybenzylidene)hydrazinyl)-2-oxoethyl)piperazin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (NF22) demonstrated excellent antibacterial activities against E. coli ATCC 25922 (MIC = 0.0625 μg/mL) and MDR E. coli 1-3 (MIC = 1, 2 and 1 µg/mL). The time-kill kinetic studies have demonstrated that the NF22 was advantageous over norfloxacin and ciprofloxacin in killing the control and MDR E. coli strains. The checkerboard assay showed that NF22 in combination with tetracycline had a synergistic effect against the E. coli strains. The experimental findings are supported by molecular modeling studies on DNA gyrase, explaining the interactions involved for compound NF22, compared to norfloxacin and ciprofloxacin. Further, the compound was also evaluated for various pharmacokinetics (absorption, metabolism, distribution, toxicity and excretion) as well as drug-likeness properties. Our data have highlighted the potential of norfloxacin by restoring its efficacy against E. coli which could lead to the development of new antimicrobial agents.
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Affiliation(s)
- Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
- Correspondence: (U.A.A.); (M.E.A.Z.)
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Correspondence: (U.A.A.); (M.E.A.Z.)
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14
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Lim S, Kim SW, Kim IK, Song BW, Lee S. Organ-on-a-chip: Its use in cardiovascular research. Clin Hemorheol Microcirc 2022; 83:315-339. [DOI: 10.3233/ch-221428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Organ-on-a-chip (OOAC) has attracted great attention during the last decade as a revolutionary alternative to conventional animal models. This cutting-edge technology has also brought constructive changes to the field of cardiovascular research. The cardiovascular system, especially the heart as a well-protected vital organ, is virtually impossible to replicate in vitro with conventional approaches. This made scientists assume that they needed to use animal models for cardiovascular research. However, the frequent failure of animal models to correctly reflect the native cardiovascular system necessitated a search for alternative platforms for preclinical studies. Hence, as a promising alternative to conventional animal models, OOAC technology is being actively developed and tested in a wide range of biomedical fields, including cardiovascular research. Therefore, in this review, the current literature on the use of OOACs for cardiovascular research is presented with a focus on the basis for using OOACs, and what has been specifically achieved by using OOACs is also discussed. By providing an overview of the current status of OOACs in cardiovascular research and its future perspectives, we hope that this review can help to develop better and optimized research strategies for cardiovascular diseases (CVDs) as well as identify novel applications of OOACs in the near future.
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Affiliation(s)
- Soyeon Lim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Republic of Korea
| | - Sang Woo Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Republic of Korea
| | - Il-Kwon Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Republic of Korea
| | - Byeong-Wook Song
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Republic of Korea
| | - Seahyoung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung, Gangwon-do, Republic of Korea
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15
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Li S, Liu Y, Liu M, Wang L, Li X. Comprehensive bioinformatics analysis reveals biomarkers of DNA methylation-related genes in varicose veins. Front Genet 2022; 13:1013803. [PMID: 36506327 PMCID: PMC9732536 DOI: 10.3389/fgene.2022.1013803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
Background: Patients with Varicose veins (VV) show no obvious symptoms in the early stages, and it is a common and frequent clinical condition. DNA methylation plays a key role in VV by regulating gene expression. However, the molecular mechanism underlying methylation regulation in VV remains unclear. Methods: The mRNA and methylation data of VV and normal samples were obtained from the Gene Expression Omnibus (GEO) database. Methylation-Regulated Genes (MRGs) between VV and normal samples were crossed with VV-associated genes (VVGs) obtained by weighted gene co-expression network analysis (WGCNA) to obtain VV-associated MRGs (VV-MRGs). Their ability to predict disease was assessed using receiver operating characteristic (ROC) curves. Biomarkers were then screened using a random forest model (RF), support vector machine model (SVM), and generalized linear model (GLM). Next, gene set enrichment analysis (GSEA) was performed to explore the functions of biomarkers. Furthermore, we also predicted their drug targets, and constructed a competing endogenous RNAs (ceRNA) network and a drug target network. Finally, we verified their mRNA expression using quantitative real-time polymerase chain reaction (qRT-PCR). Results: Total three VV-MRGs, namely Wnt1-inducible signaling pathway protein 2 (WISP2), Cysteine-rich intestinal protein 1 (CRIP1), and Odd-skipped related 1 (OSR1) were identified by VVGs and MRGs overlapping. The area under the curves (AUCs) of the ROC curves for these three VV-MRGs were greater than 0.8. RF was confirmed as the optimal diagnostic model, and WISP2, CRIP1, and OSR1 were regarded as biomarkers. GSEA showed that WISP2, CRIP1, and OSR1 were associated with oxidative phosphorylation, extracellular matrix (ECM), and respiratory system functions. Furthermore, we found that lncRNA MIR17HG can regulate OSR1 by binding to hsa-miR-21-5p and that PAX2 might treat VV by targeting OSR1. Finally, qRT-PCR results showed that the mRNA expression of the three genes was consistent with the results of the datasets. Conclusion: This study identified WISP2, CRIP1, and OSR1 as biomarkers of VV through comprehensive bioinformatics analysis, and preliminary explored the DNA methylation-related molecular mechanism in VV, which might be important for VV diagnosis and exploration of potential molecular mechanisms.
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Affiliation(s)
- Shengyu Li
- Department of Vascular Surgery, Tianjin First Central Hospital, Tianjin, China,*Correspondence: Shengyu Li, ; Xiaofeng Li,
| | - Yuehan Liu
- Department of Functional Examination, Beijing Aerospace General Hospital, Beijing, China
| | - Mingming Liu
- Department of Vascular Surgery, Tianjin First Central Hospital, Tianjin, China
| | - Lizhao Wang
- Department of Vascular Surgery, Tianjin First Central Hospital, Tianjin, China
| | - Xiaofeng Li
- Department of Vascular Surgery, Tianjin First Central Hospital, Tianjin, China,*Correspondence: Shengyu Li, ; Xiaofeng Li,
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16
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Design, Synthesis, Molecular Docking and Antimicrobial Activities of Novel Triazole-ferulic acid ester Hybrid Carbohydrates. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Bakchi B, Krishna AD, Sreecharan E, Ganesh VBJ, Niharika M, Maharshi S, Puttagunta SB, Sigalapalli DK, Bhandare RR, Shaik AB. An overview on applications of SwissADME web tool in the design and development of anticancer, antitubercular and antimicrobial agents: A medicinal chemist's perspective. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Eom S, Kwon T, Lee DY, Park CH, Kim HJ. Copper-Mediated Three-Component Reaction for the Synthesis of N-Acylsulfonamide on DNA. Org Lett 2022; 24:4881-4885. [PMID: 35775977 DOI: 10.1021/acs.orglett.2c01675] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA-encoded library (DEL) technology is a new method for discovering hit compounds for target proteins in the pharmaceutical industry. The N-acylsulfonamide functional group has been reported to exhibit various pharmacological activities, and based on this, the demand for a method that allows its introduction into the DEL platform has increased. In this report, a procedure for synthesizing N-acylsulfonamide functional groups applicable to DEL construction was developed in the presence of a copper reagent and water as a nucleophile from simple alkynes or sulfonyl azides, which are widely commercially available. Furthermore, we prove that a new alternative procedure can be used to construct a DNA-encoded library.
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Affiliation(s)
- Solji Eom
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Taeyeon Kwon
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Da Yeon Lee
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Chi Hoon Park
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
| | - Hyun Jin Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Korea.,Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Korea
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19
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Walter LO, Maioral MF, Silva LO, Speer DB, Campbell SC, Gallimore W, Falkenberg MB, Santos-Silva MC. Involvement of the NF-κB and PI3K/Akt/mTOR pathways in cell death triggered by stypoldione, an o-quinone isolated from the brown algae Stypopodium zonale. ENVIRONMENTAL TOXICOLOGY 2022; 37:1297-1309. [PMID: 35128807 DOI: 10.1002/tox.23484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 01/07/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Multiple myeloma (MM) is a clonal plasma cell malignancy that remains incurable to date. Thus, the aims of this study were to evaluate the involvement of the NF-κB and PI3K/Akt/mTOR pathways in the cytotoxicity of stypoldione, an o-quinone isolated from the brown algae Stypopodium zonale, in MM cells (MM1.S). The cytotoxic effect was evaluated in MM1.S cells and peripheral blood mononuclear cells (PBMCs) by MTT assay. The stypoldione reduced the cell viability of MM1.S cells in a concentration and time-dependent manner (IC50 in MM.1S from 2.55 to 5.38 μM). However, it was also cytotoxic to PBMCs, but at a lower range. Additionally, no significant hemolysis was observed even at concentration up to 10 times the IC50 . Apoptotic cell death was confirmed by cell morphology and Annexin V-FITC assay. Stypoldione induced intrinsic and extrinsic apoptosis by increasing FasR expression and reactive oxygen species (ROS) production, inverting the Bax/Bcl-2 ratio, and inducing ΔΨm loss, which resulted in AIF release and caspase-3 activation. It also increased Ki-67 and survivin expression and inhibited the NF-κB and PI3K/Akt/mTOR pathways. These results suggest that stypoldione is a good candidate for the development of new drugs for MM treatment.
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Affiliation(s)
- Laura O Walter
- Experimental Oncology and Hemopathies Laboratory, Clinical Analysis Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mariana F Maioral
- Experimental Oncology and Hemopathies Laboratory, Clinical Analysis Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Lisandra O Silva
- Experimental Oncology and Hemopathies Laboratory, Clinical Analysis Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Douglas B Speer
- Experimental Oncology and Hemopathies Laboratory, Clinical Analysis Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Sanjay C Campbell
- Department of Chemistry, University of the West Indies, St. Andrew, Jamaica
| | - Winklet Gallimore
- Department of Chemistry, University of the West Indies, St. Andrew, Jamaica
| | - Miriam B Falkenberg
- Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Maria Cláudia Santos-Silva
- Experimental Oncology and Hemopathies Laboratory, Clinical Analysis Department, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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20
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Andersen N, Veuthey T, Blanco MG, Silbestri GF, Rayes D, De Rosa MJ. 1-Mesityl-3-(3-Sulfonatopropyl) Imidazolium Protects Against Oxidative Stress and Delays Proteotoxicity in C. elegans. Front Pharmacol 2022; 13:908696. [PMID: 35685626 PMCID: PMC9171001 DOI: 10.3389/fphar.2022.908696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 11/20/2022] Open
Abstract
Due to the increase in life expectancy worldwide, age-related disorders such as neurodegenerative diseases (NDs) have become more prevalent. Conventional treatments comprise drugs that only attenuate some of the symptoms, but fail to arrest or delay neuronal proteotoxicity that characterizes these diseases. Due to their diverse biological activities, imidazole rings are intensively explored as powerful scaffolds for the development of new bioactive molecules. By using C. elegans, our work aims to explore novel biological roles for these compounds. To this end, we have tested the in vivo anti-proteotoxic effects of imidazolium salts. Since NDs have been largely linked to impaired antioxidant defense mechanisms, we focused on 1-Mesityl-3-(3-sulfonatopropyl) imidazolium (MSI), one of the imidazolium salts that we identified as capable of improving iron-induced oxidative stress resistance in wild-type animals. By combining mutant and gene expression analysis we have determined that this protective effect depends on the activation of the Heat Shock Transcription Factor (HSF-1), whereas it is independent of other canonical cytoprotective molecules such as abnormal Dauer Formation-16 (DAF-16/FOXO) and Skinhead-1 (SKN-1/Nrf2). To delve deeper into the biological roles of MSI, we analyzed the impact of this compound on previously established C. elegans models of protein aggregation. We found that MSI ameliorates β-amyloid-induced paralysis in worms expressing the pathological protein involved in Alzheimer’s Disease. Moreover, this compound also delays age-related locomotion decline in other proteotoxic C. elegans models, suggesting a broad protective effect. Taken together, our results point to MSI as a promising anti-proteotoxic compound and provide proof of concept of the potential of imidazole derivatives in the development of novel therapies to retard age-related proteotoxic diseases.
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Affiliation(s)
- Natalia Andersen
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional Del Sur (UNS), Bahía Blanca, Argentina
| | - Tania Veuthey
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional Del Sur (UNS), Bahía Blanca, Argentina
| | - María Gabriela Blanco
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional Del Sur (UNS), Bahía Blanca, Argentina
| | - Gustavo Fabian Silbestri
- Departamento de Química, INQUISUR, Universidad Nacional Del Sur, UNS-CONICET, Bahía Blanca, Argentina
| | - Diego Rayes
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional Del Sur (UNS), Bahía Blanca, Argentina
- *Correspondence: Diego Rayes, ; María José De Rosa,
| | - María José De Rosa
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB) CCT UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional Del Sur (UNS), Bahía Blanca, Argentina
- *Correspondence: Diego Rayes, ; María José De Rosa,
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21
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Echeverría E, Ripoll S, Fabián L, Shayo C, Monczor F, Fernández NC. Novel inhibitors of phosphorylation independent activity of GRK2 modulate cAMP signaling. Pharmacol Res Perspect 2022; 10:e00913. [PMID: 35184416 PMCID: PMC8858223 DOI: 10.1002/prp2.913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/10/2022] Open
Affiliation(s)
- Emiliana Echeverría
- Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Investigaciones Farmacológicas (ININFA‐UBA‐CONICET) Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
| | - Sonia Ripoll
- Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Investigaciones Farmacológicas (ININFA‐UBA‐CONICET) Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
| | - Lucas Fabián
- Instituto de Química y Metabolismo del Fármaco (IQUIMEFA‐UBA‐CONICET) Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
| | - Carina Shayo
- Laboratorio de Patología y Farmacología Molecular Instituto de Biología y Medicina Experimental (IByME) CONICET Buenos Aires Argentina
| | - Federico Monczor
- Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Investigaciones Farmacológicas (ININFA‐UBA‐CONICET) Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
| | - Natalia C. Fernández
- Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Investigaciones Farmacológicas (ININFA‐UBA‐CONICET) Facultad de Farmacia y Bioquímica Universidad de Buenos Aires Buenos Aires Argentina
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22
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Mermer A, Demirci S, Tatar G. Synthesis of novel pancreatic lipase inhibitors: Biological investigation and in silico studies. J Biomol Struct Dyn 2022; 40:931-940. [PMID: 35068360 DOI: 10.1080/07391102.2021.1950573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The targeted compounds which are Schiff base derivatives were prepared by reaction of 6-(4-phenyl-piperazin-1-yl)pyridine-3-ylamine with 2-hydroxy and 2,6-dichloro benzaldehyde. These compounds were isolated, purified and then spectrally characterized via FT-IR, 1H and 13C NMR, LC MS TOF, and TGA analysis where strong proofs confirmed the formation of the targeted product. The biological activity, which is pancreatic porcine lipase inhibition, of the compounds was investigated and Orlistat was used as standard drug. The compound 3 was found to be as potent as orlistat against PL enzyme with an IC50 value of 0.50 μM. The molecular docking studies were performed for both obtained compounds and orlistat against active side of porcine pancreatic lipase. Also, MM/PBSA binding free energy and molecular dynamics (MD) simulation analyzes were performed for pancreatic porcine lipase with compound 3, which showed potent inhibition according to the results of in vitro studies. Furthermore, The ADME and toxicity analysis of the compounds were examined using web-based online platforms, SwissADME and pkCSM. In the light of biological activity and in silico studies, the compound 3 can be a potential drug candidate with further studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arif Mermer
- Experimental Medicine Research and Application Center, University of Health Sciences Turkey, Uskudar, Istanbul, Turkey
| | - Serpil Demirci
- Department of Medical Services and Techniques, Vocational High School of Health Services, Giresun University, Giresun, Turkey
| | - Gizem Tatar
- Faculty of Medicine, Department of Biostatistics and Medical Informatics, Karadeniz Technical University, Trabzon, Turkey
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23
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Akinpelu OI, Kumalo HM, Mhlongo SI, Mhlongo NN. Identifying the analogues of berberine as promising antitubercular drugs targeting Mtb-FtsZ polymerisation through ligand-based virtual screening and molecular dynamics simulations. J Mol Recognit 2021; 35:e2940. [PMID: 34910337 DOI: 10.1002/jmr.2940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 01/19/2023]
Abstract
Berberine, an active compound in the extract of golden seal (an age-long remedy for many infections) has been confirmed to be responsible for the extract's activity against multi-drug resistant strain of Mycobacterium tuberculosis. There is no available study that shows the exact target of berberine in M tuberculosis, although it is confirmed that berberine inhibits the polymerisation of filamentous temperature-sensitive mutant Z (FtsZ), an important bacteria cytokinesis protein, in Escherichia coli, suggesting that FtsZ could as well be the target of berberine in M tuberculosis. In this study, we carried out ligand-based virtual screening to identify analogues of berberine followed by molecular dynamics (MD) simulations of the complexes of Mtb-FtsZ with berberine (berb1) and the five selected analogues (berb9 [ZINC1709414], berb37 [ZINC238749993], berb38 [ZINC13509022], berb43 [ZINC14765594], and berb48 [ZINC238758595]). Post-MD analyses such as binding free energy, RMSD, RMSF, RoG and hydrogen bond lifetime analysis were used to understand the interactions between these ligands and the receptor. The results suggested that Mtb-FtsZ could likely be the target of berberine in M tuberculosis as it forms a stable complex coupled with a significantly high binding energy. The study also identified other potential inhibitors of MTB-FtsZ polymerisation. Berb38 specifically showed greater interaction with the residues at the binding site of the protein, forming a far more stable complex with the receptor than any of the other compounds under investigation, including berberine itself. ADME properties calculations also predicted all the ligands to be bioactive as orally administered drugs.
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Affiliation(s)
- Olayinka I Akinpelu
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.,School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Sizwe I Mhlongo
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, Medical School, University of KwaZulu-Natal, Durban, South Africa
| | - Ndumiso N Mhlongo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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Human Induced Pluripotent Stem Cell as a Disease Modeling and Drug Development Platform-A Cardiac Perspective. Cells 2021; 10:cells10123483. [PMID: 34943991 PMCID: PMC8699880 DOI: 10.3390/cells10123483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 02/07/2023] Open
Abstract
A comprehensive understanding of the pathophysiology and cellular responses to drugs in human heart disease is limited by species differences between humans and experimental animals. In addition, isolation of human cardiomyocytes (CMs) is complicated because cells obtained by biopsy do not proliferate to provide sufficient numbers of cells for preclinical studies in vitro. Interestingly, the discovery of human-induced pluripotent stem cell (hiPSC) has opened up the possibility of generating and studying heart disease in a culture dish. The combination of reprogramming and genome editing technologies to generate a broad spectrum of human heart diseases in vitro offers a great opportunity to elucidate gene function and mechanisms. However, to exploit the potential applications of hiPSC-derived-CMs for drug testing and studying adult-onset cardiac disease, a full functional characterization of maturation and metabolic traits is required. In this review, we focus on methods to reprogram somatic cells into hiPSC and the solutions for overcome immaturity of the hiPSC-derived-CMs to mimic the structure and physiological properties of the adult human CMs to accurately model disease and test drug safety. Finally, we discuss how to improve the culture, differentiation, and purification of CMs to obtain sufficient numbers of desired types of hiPSC-derived-CMs for disease modeling and drug development platform.
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O'Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK. Colloidal Aggregators in Biochemical SARS-CoV-2 Repurposing Screens. J Med Chem 2021; 64:17530-17539. [PMID: 34812616 DOI: 10.1021/acs.jmedchem.1c01547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To fight COVID-19, much effort has been directed toward in vitro drug repurposing. Here, we investigate the impact of colloidal aggregation, a common screening artifact, in these repurposing campaigns. We tested 56 drugs reported as active in biochemical assays for aggregation by dynamic light scattering and by detergent-based enzyme counter screening; 19 formed colloids at concentrations similar to their literature IC50's, and another 14 were problematic. From a common repurposing library, we further selected another 15 drugs that had physical properties resembling known aggregators, finding that six aggregated at micromolar concentrations. This study suggests not only that many of the drugs repurposed for SARS-CoV-2 in biochemical assays are artifacts but that, more generally, at screening-relevant concentrations, even drugs can act artifactually via colloidal aggregation. Rapid detection of these artifacts will allow the community to focus on those molecules that genuinely have potential for treating COVID-19.
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Affiliation(s)
- Henry R O'Donnell
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94158-2550, United States
| | - Tia A Tummino
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94158-2550, United States.,Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, UCSF, San Francisco, California 94158-2550, United States.,QBI COVID-19 Research Group (QCRG), San Francisco, California 94158-2550, United States
| | - Conner Bardine
- Graduate Program in Chemistry & Chemical Biology, UCSF, San Francisco, California 94158-2550, United States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94158-2550, United States.,QBI COVID-19 Research Group (QCRG), San Francisco, California 94158-2550, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, California 94158-2550, United States.,QBI COVID-19 Research Group (QCRG), San Francisco, California 94158-2550, United States
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26
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Chemical Composition of the Red Sea Green Algae Ulva lactuca: Isolation and In Silico Studies of New Anti-COVID-19 Ceramides. Metabolites 2021; 11:metabo11120816. [PMID: 34940574 PMCID: PMC8707969 DOI: 10.3390/metabo11120816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/27/2021] [Accepted: 11/28/2021] [Indexed: 12/27/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is the disease caused by the virus SARS-CoV-2 responsible for the ongoing pandemic which has claimed the lives of millions of people. This has prompted the scientific research community to act to find treatments against the SARS-CoV-2 virus that include safe antiviral medicinal compounds. The edible green algae U. lactuca. is known to exhibit diverse biological activities such as anti-influenza virus, anti-Japanese encephalitis virus, immunomodulatory, anticoagulant, antioxidant and antibacterial activities. Herein, four new ceramides in addition to two known ones were isolated from Ulva lactuca. The isolated ceramides, including Cer-1, Cer-2, Cer-3, Cer-4, Cer-5 and Cer-6 showed promising antiviral activity against SARS-CoV-2 when investigated using in silico approaches by preventing its attachment to human cells and/or inhibiting its viral replication. Cer-4 and Cer-5 were the most effective in inhibiting the human angiotensin converting enzyme (hACE)-spike protein complex which is essential for the virus to enter the human host. In addition to this, Cer-4 also showed an inhibition of the SARS-CoV-2 protease (Mpro) that is responsible for its viral replication and transcription. In this study, we also used liquid chromatography coupled to electrospray ionization high-resolution mass spectroscopy (LC-ESI-HRMS) to identify several metabolites of U. lactuca, including metabolites such as fatty acids, their glyceride derivatives, terpenoids, sterols and oxysterols from the organic extract. Some of these metabolites also possessed promising antiviral activity, as previously reported.
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Mamidi P, Nayak TK, Kumar A, Kumar S, Chatterjee S, De S, Datey A, Ghosh S, Keshry SS, Singh S, Laha E, Ray A, Chattopadhyay S, Chattopadhyay S. MK2a inhibitor CMPD1 abrogates chikungunya virus infection by modulating actin remodeling pathway. PLoS Pathog 2021; 17:e1009667. [PMID: 34780576 PMCID: PMC8592423 DOI: 10.1371/journal.ppat.1009667] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/15/2021] [Indexed: 02/06/2023] Open
Abstract
Chikungunya virus (CHIKV) epidemics around the world have created public health concern with the unavailability of effective drugs and vaccines. This emphasizes the need for molecular understanding of host-virus interactions for developing effective targeted antivirals. Microarray analysis was carried out using CHIKV strain (Prototype and Indian) infected Vero cells and two host isozymes, MAPK activated protein kinase 2 (MK2) and MAPK activated protein kinase 3 (MK3) were selected for further analysis. The substrate spectrum of both enzymes is indistinguishable and covers proteins involved in cytokines production, endocytosis, reorganization of the cytoskeleton, cell migration, cell cycle control, chromatin remodeling and transcriptional regulation. Gene silencing and drug treatment were performed in vitro and in vivo to unravel the role of MK2/MK3 in CHIKV infection. Gene silencing of MK2 and MK3 abrogated around 58% CHIKV progeny release from the host cell and a MK2 activation inhibitor (CMPD1) treatment demonstrated 68% inhibition of viral infection suggesting a major role of MAPKAPKs during late CHIKV infection in vitro. Further, it was observed that the inhibition in viral infection is primarily due to the abrogation of lamellipodium formation through modulation of factors involved in the actin cytoskeleton remodeling pathway. Moreover, CHIKV-infected C57BL/6 mice demonstrated reduction in the viral copy number, lessened disease score and better survivability after CMPD1 treatment. In addition, reduction in expression of key pro-inflammatory mediators such as CXCL13, RAGE, FGF, MMP9 and increase in HGF (a CHIKV infection recovery marker) was observed indicating the effectiveness of the drug against CHIKV. Taken together it can be proposed that MK2 and MK3 are crucial host factors for CHIKV infection and can be considered as important target for developing effective anti-CHIKV strategies. Chikungunya virus has been a dreaded disease from the first time it occurred in 1952 Tanzania. Since then it has been affecting the different parts of the world at different time periods in large scale. It is typically transmitted to humans by bites of Aedes aegypti and Aedes albopictus mosquitoes. Although, studies have been undertaken to combat its prevalence still there are no effective strategies like vaccines or antivirals against it. Therefore it is essential to understand the virus and host interaction to overcome this hurdle. In this study two host factors MK2 and MK3 have been taken into consideration to see how they affect the multiplication of the virus. The in vitro and in vivo experiments conducted demonstrated that inhibition of MK2 and MK3 not only restricted viral release but also decreased the disease score and allowed better survivability. Therefore, MK2 and MK3 could be considered as the key targets in the anti CHIKV approach.
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Affiliation(s)
| | - Tapas Kumar Nayak
- National Institute of Science Education and Research, Bhubaneswar, India
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Abhishek Kumar
- Institute of Life Sciences, Bhubaneswar, India
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, United States of America
| | - Sameer Kumar
- Institute of Life Sciences, Bhubaneswar, India
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Sanchari Chatterjee
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Saikat De
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ankita Datey
- Institute of Life Sciences, Bhubaneswar, India
- KIIT school of Biotechnology, Bhubaneswar, India
| | - Soumyajit Ghosh
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Supriya Suman Keshry
- Institute of Life Sciences, Bhubaneswar, India
- KIIT school of Biotechnology, Bhubaneswar, India
| | - Sharad Singh
- Institute of Life Sciences, Bhubaneswar, India
- KIIT school of Biotechnology, Bhubaneswar, India
| | - Eshna Laha
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Amrita Ray
- Institute of Life Sciences, Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
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Williams M. Improving Translational Paradigms in Drug Discovery and Development. Curr Protoc 2021; 1:e273. [PMID: 34780124 DOI: 10.1002/cpz1.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Despite improved knowledge regarding disease causality, new drug targets, and enabling technologies, the attrition rate for compounds entering clinical trials has remained consistently high for several decades, with an average 90% failure rate. These failures are manifested in an inability to reproduce efficacy findings from animal models in humans and/or the occurrence of unexpected safety issues, and reflect failures in T1 translation. Similarly, an inability to sequentially demonstrate compound efficacy and safety in Phase IIa, IIb, and III clinical trials represents failures in T2 translation. Accordingly, T1 and T2 translation are colloquially termed 'valleys of death'. Since T2 translation dealt almost exclusively with clinical trials, T3 and T4 translational steps were added, with the former focused on facilitating interactions between laboratory- and population-based research and the latter on 'real world' health outcomes. Factors that potentially lead to T1/T2 compound attrition include: the absence of biomarkers to allow compound effects to be consistently tracked through development; a lack of integration/'de-siloing' of the diverse discipline-based and technical skill sets involved in drug discovery; the industrialization of drug discovery, which via volume-based goals often results in quantity being prioritized over quality; inadequate project governance and strategic oversight; and flawed decision making based on unreliable/irreproducible or incomplete data. A variety of initiatives have addressed this problem, including the NIH National Center for Advancing Translational Sciences (NCATS), which has focused on bringing an unbiased academic perspective to translation, to potentially revitalize the process. This commentary provides an overview of the basic concepts involved in translation, along with suggested changes in the conduct of biomedical research to avoid valleys of death, including the use of Translational Scoring as a tool to avoid translational attrition and the impact of the FDA Accelerated Approval Pathway in lowering the hurdle for drug approval. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Michael Williams
- Department of Biological Chemistry and Pharmacology, College of Medicine, Ohio State University, Columbus, Ohio
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Alkhilaiwi F. Conditionally Reprogrammed Cells and Robotic High-Throughput Screening for Precision Cancer Therapy. Front Oncol 2021; 11:761986. [PMID: 34737964 PMCID: PMC8560709 DOI: 10.3389/fonc.2021.761986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/24/2021] [Indexed: 12/04/2022] Open
Abstract
Cancer is a devastating disease that takes the lives of millions of people globally every year. Precision cancer therapy is based on a patient's tumor histopathology, expression analyses, and/or tumor RNA or DNA analysis. Only 2%-20% of patients with solid tumors benefit from genomics-based precision oncology. Therefore, functional diagnostics and patient-derived cancer models are needed for precision cancer therapy. In this review, we will summarize the potential use of conditional cell reprogramming (CR) and robotic high-throughput screening in precision cancer medicine. Briefly, the CR method includes the co-culturing of irradiated Swiss-3T3-J2 mouse fibroblast cells alongside digested primary non-pathogenic or pathogenic cells with the existence of Rho-associated serine-threonine protein kinase inhibitor called Y-27632, creating an exterior culture environment, allowing the cells to have the ability to gain partial properties of stem cells. On the other hand, quantitative high-throughput screening (qHTS) assays screen thousands of compounds that use cells in a short period of time. The combination of both technologies has the potential to become a driving force for precision cancer therapy.
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Affiliation(s)
- Faris Alkhilaiwi
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
- Regenerative Medicine Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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30
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Puzari U, Fernandes PA, Mukherjee AK. Advances in the Therapeutic Application of Small-Molecule Inhibitors and Repurposed Drugs against Snakebite. J Med Chem 2021; 64:13938-13979. [PMID: 34565143 DOI: 10.1021/acs.jmedchem.1c00266] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The World Health Organization has declared snakebite as a neglected tropical disease. Antivenom administration is the sole therapy against venomous snakebite; however, several limitations of this therapy reinforce the dire need for an alternative and/or additional treatment against envenomation. Inhibitors against snake venoms have been explored from natural resources and are synthesized in the laboratory; however, repurposing of small-molecule therapeutics (SMTs) against the principal toxins of snake venoms to inhibit their lethality and/or obnoxious effect of envenomation has been garnering greater attention owing to their established pharmacokinetic properties, low-risk attributes, cost-effectiveness, ease of administration, and storage stability. Nevertheless, SMTs are yet to be approved and commercialized for snakebite treatment. Therefore, we have systematically reviewed and critically analyzed the scenario of small synthetic inhibitors and repurposed drugs against snake envenomation from 2005 to date and proposed novel approaches and commercialization strategies for the development of efficacious therapies against snake envenomation.
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Affiliation(s)
- Upasana Puzari
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur-784028, Assam, India
| | - Pedro Alexandrino Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua Do Campo Alegre S/N, 4169-007 Porto, Portugal
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, School of Sciences, Tezpur University, Tezpur-784028, Assam, India.,Institute of Advanced Study in Science and Technology, Vigyan Path Garchuk, Paschim Boragaon, Guwahati-781035, Assam, India
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Profiro de Oliveira JH, Arruda IES, Izak Ribeiro de Araújo J, Chaves LL, de La Rocca Soares MF, Soares-Sobrinho JL. Why do few drug delivery systems to combat neglected tropical diseases reach the market? An analysis from the technology's stages. Expert Opin Ther Pat 2021; 32:89-114. [PMID: 34424127 DOI: 10.1080/13543776.2021.1970746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many drugs used to combat schistosomiasis, Chagas disease, and leishmaniasis (SCL) have clinical limitations such as: high toxicity to the liver, kidneys and spleen; reproductive, gastrointestinal, and heart disorders; teratogenicity. In this sense, drug delivery systems (DDSs) have been described in the literature as a viable option for overcoming the limitations of these drugs. An analysis of the level of development (TRL) of patents can help in determine the steps that must be taken for promising technologies to reach the market. AREAS COVERED This study aimed to analyze the stage of development of DDSs for the treatment of SCL described in patents. In addition, we try to understand the main reasons why many DDSs do not reach the market. In this study, we examined DDSs for drugs indicated by WHO and treatment of SCL, by performing a search for patents. EXPERT OPINION In this present work we provide arguments that support the hypothesis that there is a lack of integration between academia and industry to finance and continue research, especially the development of clinical studies. We cite the translational research consortia as the potential alternative for developing DDSs to combat NTDs.
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Affiliation(s)
| | | | | | - Luise Lopes Chaves
- Department of Pharmacy, Federal University of Pernambuco, Recife, Recife-Pernambuco
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Oâ Donnell HR, Tummino TA, Bardine C, Craik CS, Shoichet BK. Colloidal aggregators in biochemical SARS-CoV-2 repurposing screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34494023 DOI: 10.1101/2021.08.31.458413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To fight the SARS-CoV-2 pandemic, much effort has been directed toward drug repurposing, testing investigational and approved drugs against several viral or human proteins in vitro . Here we investigate the impact of colloidal aggregation, a common artifact in early drug discovery, in these repurposing screens. We selected 56 drugs reported to be active in biochemical assays and tested them for aggregation by both dynamic light scattering and by enzyme counter screening with and without detergent; seventeen of these drugs formed colloids at concentrations similar to their literature reported IC 50 s. To investigate the occurrence of colloidal aggregators more generally in repurposing libraries, we further selected 15 drugs that had physical properties resembling known aggregators from a common repurposing library, and found that 6 of these aggregated at micromolar concentrations. An attraction of repurposing is that drugs active on one target are considered de-risked on another. This study suggests not only that many of the drugs repurposed for SARS-CoV-2 in biochemical assays are artifacts, but that, more generally, when screened at relevant concentrations, drugs can act artifactually via colloidal aggregation. Understanding the role of aggregation, and detecting its effects rapidly, will allow the community to focus on those drugs and leads that genuinely have potential for treating COVID-19. Abstract Figure
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Khalid H, Shahid S, Tariq S, Ijaz B, Ashfaq UA, Ahmad M. Discovery of Novel HCV NS5B polymerase inhibitor, 2-(3,4-dimethyl-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-2(4H)-yl)-N-(2-fluorobenzyl)acetamide via molecular docking and experimental approach. Clin Exp Pharmacol Physiol 2021; 48:1653-1661. [PMID: 34386985 DOI: 10.1111/1440-1681.13571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/08/2021] [Indexed: 11/27/2022]
Abstract
Hepatitis C Virus (HCV) is a viral infection posing a severe global threat that left untreated progress to end-stage liver disease, including cirrhosis and Hepatocellular Carcinoma (HCC). Moreover, no prophylactic approach exists so far enabling its prevention. The NS5B polymerase holds special significance as the target of intervention against HCV infection. The current study kindles benzothiazine derivatives against HCV NS5B polymerase through in silico and experimental approaches. Following docking, the compound 2-(3,4-dimethyl-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-2(4H)-yl)-N-(2-fluorobenzyl)acetamide was revealed to form effective binding interaction in the proposed site of HCV NS5B with a score of -10 kcal/mol and subsequently was deciphered through MD simulation study which indicated interaction of residues TYR_382, VAL_381 and HIS_467 through hydrophobic interaction and two residues such as GLU_202 and LYS_209 contributed in the formation of water bridges. The subsequent in silico pharmacological analysis revealed its safe drug profile. The cytotoxicity activity of compound 6c indicated to be non-toxic in HepG2 cells at concentration ranges from 0.001-1.0 µM with > 80% cell viability and diminished expression of the HCV NS5B to 98% at the dose of 1.0 µM and 90 % at 0.5µM. Thus the hit compound 6c might be a potent NS5B polymerase inhibitor required to be validated further through in vivo and preclinical studies.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sana Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Somayya Tariq
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
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Anbazhakan K, Praveena R, Sadasivam K. Theoretical insight on antioxidant potency of kanzakiflavone-2 and its derivatives. Struct Chem 2021. [DOI: 10.1007/s11224-020-01722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ramadan Q, Fardous RS, Hazaymeh R, Alshmmari S, Zourob M. Pharmacokinetics-On-a-Chip: In Vitro Microphysiological Models for Emulating of Drugs ADME. Adv Biol (Weinh) 2021; 5:e2100775. [PMID: 34323392 DOI: 10.1002/adbi.202100775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Despite many ongoing efforts across the full spectrum of pharmaceutical and biotech industries, drug development is still a costly undertaking that involves a high risk of failure during clinical trials. Animal models played vital roles in understanding the mechanism of human diseases. However, the use of these models has been a subject of heated debate, particularly due to ethical matters and the inevitable pathophysiological differences between animals and humans. Current in vitro models lack the sufficient functionality and predictivity of human pharmacokinetics and toxicity, therefore, are not capable to fully replace animal models. The recent development of micro-physiological systems has shown great potential as indispensable tools for recapitulating key physiological parameters of humans and providing in vitro methods for predicting the pharmacokinetics and pharmacodynamics in humans. Integration of Absorption, Distribution, Metabolism, and Excretion (ADME) processes within one close in vitro system is a paramount development that would meet important unmet pharmaceutical industry needs. In this review paper, synthesis of the ADME-centered organ-on-a-chip technology is systemically presented from what is achieved to what needs to be done, emphasizing the requirements of in vitro models that meet industrial needs in terms of the structure and functions.
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Affiliation(s)
- Qasem Ramadan
- Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Roa Saleem Fardous
- Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia.,Strathclyde Institute of Pharmacy and Biomedical Sciences, Strathclyde University, Glasgow, G4 0RE, United Kingdom
| | - Rana Hazaymeh
- Almaarefa University, Riyadh, 13713, Kingdom of Saudi Arabia
| | - Sultan Alshmmari
- Saudi Food and Drug Authority, Riyadh, 13513-7148, Kingdom of Saudi Arabia
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Rathod B, Chak S, Patel S, Shard A. Tumor pyruvate kinase M2 modulators: a comprehensive account of activators and inhibitors as anticancer agents. RSC Med Chem 2021; 12:1121-1141. [PMID: 34355179 PMCID: PMC8292966 DOI: 10.1039/d1md00045d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/25/2021] [Indexed: 12/16/2022] Open
Abstract
Pyruvate kinase M2 (PKM2) catalyzes the conversion of phosphoenolpyruvate (PEP) to pyruvate. It plays a central role in the metabolic reprogramming of cancer cells and is expressed in most human tumors. It is essential in indiscriminate proliferation, survival, and tackling apoptosis in cancer cells. This positions PKM2 as a hot target in cancer therapy. Despite its well-known structure and several reported modulators targeting PKM2 as activators or inhibitors, a comprehensive review focusing on such modulators is lacking. Herein we summarize modulators of PKM2, the assays used to detect their potential, the preferable tense (T) and relaxed (R) states in which the enzyme resides, lacunae in existing modulators, and several strategies that may lead to effective anticancer drug development targeting PKM2.
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Affiliation(s)
- Bhagyashri Rathod
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Shivam Chak
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research Ahmedabad Opposite Air Force Station Gandhinagar Gujarat 382355 India
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De Araújo JS, da Silva PB, Batista MM, Peres RB, Cardoso-Santos C, Kalejaiye TD, Munday JC, De Heuvel E, Sterk GJ, Augustyns K, Salado IG, Matheeussen A, De Esch I, De Koning HP, Leurs R, Maes L, Soeiro MDNC. Evaluation of phthalazinone phosphodiesterase inhibitors with improved activity and selectivity against Trypanosoma cruzi. J Antimicrob Chemother 2021; 75:958-967. [PMID: 31860098 DOI: 10.1093/jac/dkz516] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/15/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi, needs urgent alternative therapeutic options as the treatments currently available display severe limitations, mainly related to efficacy and toxicity. OBJECTIVES As phosphodiesterases (PDEs) have been claimed as novel targets against T. cruzi, our aim was to evaluate the biological aspects of 12 new phthalazinone PDE inhibitors against different T. cruzi strains and parasite forms relevant for human infection. METHODS In vitro trypanocidal activity of the inhibitors was assessed alone and in combination with benznidazole. Their effects on parasite ultrastructural and cAMP levels were determined. PDE mRNA levels from the different T. cruzi forms were measured by quantitative reverse transcription PCR. RESULTS Five TcrPDEs were found to be expressed in all parasite stages. Four compounds displayed strong effects against intracellular amastigotes. Against bloodstream trypomastigotes (BTs), three were at least as potent as benznidazole. In vitro combination therapy with one of the most active inhibitors on both parasite forms (NPD-040) plus benznidazole demonstrated a quite synergistic profile (xΣ FICI = 0.58) against intracellular amastigotes but no interaction (xΣ FICI = 1.27) when BTs were assayed. BTs treated with NPD-040 presented disrupted Golgi apparatus, a swollen flagellar pocket and signs of autophagy. cAMP measurements of untreated parasites showed that amastigotes have higher ability to efflux this second messenger than BTs. NPD-001 and NPD-040 increase the intracellular cAMP content in both BTs and amastigotes, which is also released into the extracellular milieu. CONCLUSIONS The findings demonstrate the potential of PDE inhibitors as anti-T. cruzi drug candidates.
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Affiliation(s)
| | | | - Marcos Meuser Batista
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Raiza Brandão Peres
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Camila Cardoso-Santos
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Titilola D Kalejaiye
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Jane C Munday
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Erik De Heuvel
- Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Geert Jan Sterk
- Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - Irene G Salado
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
| | - An Matheeussen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Iwan De Esch
- Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry P De Koning
- Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Rob Leurs
- Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines & Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
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Human Pluripotent Stem-Cell-Derived Models as a Missing Link in Drug Discovery and Development. Pharmaceuticals (Basel) 2021; 14:ph14060525. [PMID: 34070895 PMCID: PMC8230131 DOI: 10.3390/ph14060525] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human-induced pluripotent stem cells (hiPSCs), have the potential to accelerate the drug discovery and development process. In this review, by analyzing each stage of the drug discovery and development process, we identified the active role of hPSC-derived in vitro models in phenotypic screening, target-based screening, target validation, toxicology evaluation, precision medicine, clinical trial in a dish, and post-clinical studies. Patient-derived or genome-edited PSCs can generate valid in vitro models for dissecting disease mechanisms, discovering novel drug targets, screening drug candidates, and preclinically and post-clinically evaluating drug safety and efficacy. With the advances in modern biotechnologies and developmental biology, hPSC-derived in vitro models will hopefully improve the cost-effectiveness and the success rate of drug discovery and development.
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Rothenaigner I, Hadian K. Brief Guide: Experimental Strategies for High-Quality Hit Selection from Small-Molecule Screening Campaigns. SLAS DISCOVERY 2021; 26:851-854. [PMID: 33882754 PMCID: PMC8293735 DOI: 10.1177/24725552211008862] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Small-molecule screening is a powerful approach to identify modulators of either specific biological targets or cellular pathways with phenotypic endpoints. A myriad of assay technologies are available to assess the activity of enzymes, monitor protein-protein interactions, measure transcription factor activity in reporter assays, or detect cellular features and activities using high-content imaging. A common challenge during small-molecule screening is, however, the presence of hit compounds generating assay interference, thereby producing false-positive hits. Thus, efforts are needed to uncover such interferences to prioritize high-quality hits for further analysis. This process encompasses (1) computational approaches to flag undesirable compounds, and (2) the use of experimental approaches like counter, orthogonal, and cellular fitness screens to identify and eliminate artifacts. In this brief guide, we provide an overview for first-time users, highlighting experimental screening strategies to prioritize high-quality bioactive hits from high-throughput screening/high-content screening (HTS/HCS) campaigns.
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Affiliation(s)
- Ina Rothenaigner
- Helmholtz Zentrum München, Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Neuherberg, Germany
| | - Kamyar Hadian
- Helmholtz Zentrum München, Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Neuherberg, Germany
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40
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Dahlin JL, Auld DS, Rothenaigner I, Haney S, Sexton JZ, Nissink JWM, Walsh J, Lee JA, Strelow JM, Willard FS, Ferrins L, Baell JB, Walters MA, Hua BK, Hadian K, Wagner BK. Nuisance compounds in cellular assays. Cell Chem Biol 2021; 28:356-370. [PMID: 33592188 PMCID: PMC7979533 DOI: 10.1016/j.chembiol.2021.01.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Steve Haney
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park SK10 4TG, UK
| | | | | | | | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02140, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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Wang Y, Yu Z, Yuan H, Chen H, Xie N, Wang Z, Sun Q, Zhang W. Structure-based design of glycyrrhetinic acid derivatives as potent anti-sepsis agents targeting high-mobility group box-1. Bioorg Chem 2020; 106:104461. [PMID: 33223202 DOI: 10.1016/j.bioorg.2020.104461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Novel Glycyrrhetinic Acid (GA) derivatives with fused heterocycles on A ring were structure-based designed and synthesized. Their potential anti-inflammatory effects were investigated by a classical LPS stimulated macrophage model. Surface plasmon resonance (SPR) was used to verify the binding of GA analogues with HMGB1. A preliminary structure-activity relationship was summarized and an analogue GA-60 with ortho-methoxybenzyl pyrozole showed stronger anti-inflammatory effect and higher affinity for HMGB1 with a Kd value of 12.5 μM. In addition, this compound exhibited excellent inhibitory functions on NO (96%), TNF-α (94%), and IL-6 (100%), by interfering with phosphorylation of p38, ERK, JNK MAPKs, as well as that of NF-κB p65 and IKKα/β. Moreover, GA-60 extended the survival of either the classic CLP-induced or LPS-induced sepsis mouse models. Molecular modeling predictions further supported these findings, clearly indicating that inhibiting HMGB1 release, using fused heterocyclic GA derivatives, is a promising strategy for treatment of sepsis.
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Affiliation(s)
- Yuanyuan Wang
- Interdisciplinary Science Research Institute, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zongmin Yu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Department of Medical Service Training Center, No. 965 Hospital, Joint Logistics Support Force of PLA, Jilin 132011, China
| | - Hu Yuan
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi 341000, China
| | - Hao Chen
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China; State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi 341000, China
| | - Ning Xie
- State Key Laboratory of Innovative Natural Medicine and TCM Injections, Jiangxi 341000, China
| | - Zhibin Wang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Qingyan Sun
- Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China.
| | - Weidong Zhang
- Interdisciplinary Science Research Institute, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Shanghai Institute of Pharmaceutical Industry, Shanghai 200040, China; School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
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Veeravarapu H, Tirumalasetty M, Kurati S, Wunnava U, Krishna Kumar Muthyala M. Design, synthesis, antimycobacterial activity and molecular docking studies of novel 3- (N-substituted glycinamido) benzoic acid analogues as anti tubercular agents. Bioorg Med Chem Lett 2020; 30:127603. [PMID: 33039564 DOI: 10.1016/j.bmcl.2020.127603] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/30/2020] [Accepted: 10/03/2020] [Indexed: 01/19/2023]
Abstract
We have recently identified mycolic acid methyl transferase (MmaA1) enzyme inhibitors as potential antitubercular agents using in silico modelling techniques. In continuation of that study, we synthesised a series of novel 3-(N-substituted glycinamido) benzoic acid derivatives with an aim to optimise the lead molecule. The newly synthesised compounds were evaluated for their in vitro antimycobacterial activity against M. tuberculosis H37Rv. Among these, 5 compounds A3, A4, A5, A6 and A10 exhibited most potent activity with an MIC value of 1.6 μg/ml. Further molecular docking studies were carried out to investigate the binding mode of the ligands with MmaA1 protein. The docking studies revealed that the ligands made strong interactions with the catalytic site residues TRP30, TYR 32, GLY 71, TRP 74, GLY 76, ALA 77 and GLU 136 of MmaA1 protein. Druglikeness and leadlikeness properties of the compounds were also studied using computational tools. The results of in silico and in vitro studies indicate that these novel compounds are propitious leads for tuberculosis therapy.
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Affiliation(s)
- Hymavathi Veeravarapu
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - Mohan Tirumalasetty
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - SonyPriya Kurati
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - Umarani Wunnava
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India
| | - Murali Krishna Kumar Muthyala
- Pharmaceutical Chemistry Research Lab, AU College of Pharmaceutical Sciences, Andhra University, Visakhapatnam, India.
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44
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Akinpelu OI, Lawal MM, Kumalo HM, Mhlongo NN. Computational studies of the properties and activities of selected trisubstituted benzimidazoles as potential antitubercular drugs inhibiting MTB-FtsZ polymerization. J Biomol Struct Dyn 2020; 40:1558-1570. [PMID: 33021149 DOI: 10.1080/07391102.2020.1830176] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Trisubstituted benzimidazoles (trisbenz) are significantly active against nonreplicating Mycobacterium tuberculosis (MTB) by inhibiting the polymerization of Filamentous Temperature Sensitive Mutant Z (FtsZ), an essential bacteria cell division protein. In-depth in-silico study of 5 of the most active trisubstituted benzimidazoles; trisbenz 1, 2, 3, 4 and 5, giving insight into their properties, such as stability, bioavailability, interactions with residues at the binding site of MTB-FtsZ and their influence on structural dynamics of the protein have been conducted. This was achieved through the application of in-silico methods including density functional theory (DFT) calculations, ADME properties calculations, molecular docking and molecular dynamics simulations. A DFT approach was applied to predict reactivity properties of potent FtsZ inhibitors, and the results reveal the relative reactivity of these inhibitors as bioactive moieties. The estimated ADME properties predicted all 5 compounds to be bioavailable and suitable for oral administration. Molecular docking, binding free energy, RMSD, RMSF, and hydrogen bond analysis confirmed these 5 compounds as potent MTB-FtsZ inhibitors. Although analyses proved these compounds to be bioactive and potent MTB-FtsZ inhibitors, however, trisbenz 1 appeared to be the most active against this protein while trisbenz 5 was the least active. This study further confirms the experimental study while also giving insight on the compounds mechanism of action and presents their bioavailability properties.
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Affiliation(s)
- Olayinka I Akinpelu
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.,School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Kumalo
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Ndumiso N Mhlongo
- Biomolecular Modelling Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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45
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Paik DT, Chandy M, Wu JC. Patient and Disease-Specific Induced Pluripotent Stem Cells for Discovery of Personalized Cardiovascular Drugs and Therapeutics. Pharmacol Rev 2020; 72:320-342. [PMID: 31871214 PMCID: PMC6934989 DOI: 10.1124/pr.116.013003] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human induced pluripotent stem cells (iPSCs) have emerged as an effective platform for regenerative therapy, disease modeling, and drug discovery. iPSCs allow for the production of limitless supply of patient-specific somatic cells that enable advancement in cardiovascular precision medicine. Over the past decade, researchers have developed protocols to differentiate iPSCs to multiple cardiovascular lineages, as well as to enhance the maturity and functionality of these cells. Despite significant advances, drug therapy and discovery for cardiovascular disease have lagged behind other fields such as oncology. We speculate that this paucity of drug discovery is due to a previous lack of efficient, reproducible, and translational model systems. Notably, existing drug discovery and testing platforms rely on animal studies and clinical trials, but investigations in animal models have inherent limitations due to interspecies differences. Moreover, clinical trials are inherently flawed by assuming that all individuals with a disease will respond identically to a therapy, ignoring the genetic and epigenomic variations that define our individuality. With ever-improving differentiation and phenotyping methods, patient-specific iPSC-derived cardiovascular cells allow unprecedented opportunities to discover new drug targets and screen compounds for cardiovascular disease. Imbued with the genetic information of an individual, iPSCs will vastly improve our ability to test drugs efficiently, as well as tailor and titrate drug therapy for each patient.
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Affiliation(s)
- David T Paik
- Stanford Cardiovascular Institute, Stanford University, Stanford, California
| | - Mark Chandy
- Stanford Cardiovascular Institute, Stanford University, Stanford, California
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, California
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46
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Hinkson IV, Madej B, Stahlberg EA. Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery. Front Pharmacol 2020; 11:770. [PMID: 32694991 PMCID: PMC7339658 DOI: 10.3389/fphar.2020.00770] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/11/2020] [Indexed: 01/08/2023] Open
Abstract
Conventional drug discovery is long and costly, and suffers from high attrition rates, often leaving patients with limited or expensive treatment options. Recognizing the overwhelming need to accelerate this process and increase success, the ATOM consortium was formed by government, industry, and academic partners in October 2017. ATOM applies a team science and open-source approach to foster a paradigm shift in drug discovery. ATOM is developing and validating a precompetitive, preclinical, small molecule drug discovery platform that simultaneously optimizes pharmacokinetics, toxicity, protein-ligand interactions, systems-level models, molecular design, and novel compound generation. To achieve this, the ATOM Modeling Pipeline (AMPL) has been developed to enable advanced and emerging machine learning (ML) approaches to build models from diverse historical drug discovery data. This modular pipeline has been designed to couple with a generative algorithm that optimizes multiple parameters necessary for drug discovery. ATOM's approach is to consider the full pharmacology and therapeutic window of the drug concurrently, through computationally-driven design, thereby reducing the number of molecules that are selected for experimental validation. Here, we discuss the role of collaborative efforts such as consortia and public-private partnerships in accelerating cross disciplinary innovation and the development of open-source tools for drug discovery.
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Affiliation(s)
| | | | - Eric A. Stahlberg
- Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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47
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Prakash P, Vijayasarathi D, Selvam K, Karthi S, Manivasagaperumal R. Pharmacore maping based on docking, ADME/toxicity, virtual screening on 3,5-dimethyl-1,3,4-hexanetriol and dodecanoic acid derivates for anticancer inhibitors. J Biomol Struct Dyn 2020; 39:4490-4500. [DOI: 10.1080/07391102.2020.1778533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Durairaj Vijayasarathi
- Chemical Engineering and Process Development, CSIR- National Chemical Laboratory (NCL), Pune, India
| | | | - Sengodan Karthi
- Sri Paramakalyani Centre for Excellence and Environmental Sciences, Manonmaniam Sundaranar University, Alwarkurichi, India
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48
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Mohan B, Choudhary M, Kumar G, Muhammad S, Das N, Singh K, Al-Sehemi AG, Kumar S. An experimental and computational study of pyrimidine based bis-uracil derivatives as efficient candidates for optical, nonlinear optical, and drug discovery applications. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1771369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bharti Mohan
- Department of Chemistry, National Institute of Technology Patna, Patna, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, India
| | - Gaurav Kumar
- School of Biomedical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
- Department of Clinical Research, School of Biosciences and Biomedical Engineering, Galgotias University, Greater Noida, India
| | - Shabbir Muhammad
- Research Center for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia
| | - Neeladri Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna, India
| | - Khushwant Singh
- Department of Chemistry, Indian Institute of Technology Patna, Patna, India
| | - Abdullah G. Al-Sehemi
- Department of Chemistry, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Santosh Kumar
- Division of Chemical Engineering, Konkuk University, Seoul, South Korea
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49
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Mohan B, Choudhary M, Muhammad S, Das N, Singh K, Jana A, Bharti S, Algarni H, Al-Sehemi AG, Kumar S. Synthesis, characterizations, crystal structures, and theoretical studies of copper(II) and nickel(II) coordination complexes. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1761961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Bharti Mohan
- Department of Chemistry, National Institute of Technology, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology, Patna, Bihar, India
| | - Shabbir Muhammad
- Department of Physics, College of Science, King Khalid University, Abha, Saudi Arabia
- Research Center for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia
| | - Neeladri Das
- Department of Chemistry, Indian Institute of Technology, Patna, Bihar, India
| | - Khushwant Singh
- Department of Chemistry, Indian Institute of Technology, Patna, Bihar, India
| | - Achintya Jana
- Department of Chemistry, Indian Institute of Technology, Patna, Bihar, India
| | - Sulakshna Bharti
- Department of Chemistry, National Institute of Technology, Patna, Bihar, India
| | - H. Algarni
- Department of Physics, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Santosh Kumar
- Division of Chemical Engineering, Konkuk University, Gwangjin-gu, Seoul, South Korea
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Sunyoto T. Partnerships for better neglected disease drug discovery and development: how have we fared? Expert Opin Drug Discov 2020; 15:531-537. [PMID: 32129688 DOI: 10.1080/17460441.2020.1736550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: In the field of neglected disease, mushrooming partnerships have changed the landscape in the last decades. With high diversity in participants, type, scope, and operational models, partnership becomes the ultimate choice for drug discovery and development. This paper aims to reflect on this phenomenon based on experiences and lessons learned, providing insights for the future.Areas covered: Lack of safe and effective drugs for neglected diseases stems from market and public policy failure. Combining resources, skills, and expertise justifies working collaboratively in the R&D quest. The advancement of public-private partnerships (PPP), including product development partnership (PDP) for neglected diseases, is described, herein, including the rationale behind their conception, evolution, expansion, and alternative approaches. The author also discusses the appeals and the pitfalls of partnership in this field.Expert opinion: The progressive partnerships in drug discovery and development for neglected diseases need to be encouraged, especially in alignment with an open science culture. Experiences in partnerships vary with bias for successful ones, rendering more rigorous evaluation and research necessary. Eventually, the focus of improving partnership should not only be on addressing discovery bottlenecks, but also safeguarding access and delivery. Expanding focus to include vaccines and diagnostics is necessary.
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Affiliation(s)
- Temmy Sunyoto
- Public Health Department, Institute of Tropical Medicine, Antwerpen, Belgium
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