1
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Singh S, Ahmad F, Aruri H, Das S, Parajuli P, Gavande NS, Singh PK, Kumar A. Novel quinoline substituted autophagy inhibitors attenuate Zika virus replication in ocular cells. Virus Res 2024; 347:199419. [PMID: 38880335 PMCID: PMC11239713 DOI: 10.1016/j.virusres.2024.199419] [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: 04/24/2024] [Revised: 05/26/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Zika virus (ZIKV) is a re-emerging RNA virus that is known to cause ocular and neurological abnormalities in infants. ZIKV exploits autophagic processes in infected cells to enhance its replication and spread. Thus, autophagy inhibitors have emerged as a potent therapeutic target to combat RNA viruses, with Hydroxychloroquine (HCQ) being one of the most promising candidates. In this study, we synthesized several novel small-molecule quinoline derivatives, assessed their antiviral activity, and determined the underlying molecular mechanisms. Among the nine synthesized analogs, two lead candidates, labeled GL-287 and GL-382, significantly attenuated ZIKV replication in human ocular cells, primarily by inhibiting autophagy. These two compounds surpassed the antiviral efficacy of HCQ and other existing autophagy inhibitors, such as ROC-325, DC661, and GNS561. Moreover, unlike HCQ, these novel analogs did not exhibit cytotoxicity in the ocular cells. Treatment with compounds GL-287 and GL-382 in ZIKV-infected cells increased the abundance of LC3 puncta, indicating the disruption of the autophagic process. Furthermore, compounds GL-287 and GL-382 effectively inhibited the ZIKV-induced innate inflammatory response in ocular cells. Collectively, our study demonstrates the safe and potent antiviral activity of novel autophagy inhibitors against ZIKV.
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Affiliation(s)
- Sneha Singh
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Faraz Ahmad
- Department of Ophthalmology, Mason Eye Institute, University of Missouri School of Medicine, Columbia, MO, USA
| | - Hariprasad Aruri
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Susmita Das
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Prahlad Parajuli
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48201, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201, USA.
| | - Pawan Kumar Singh
- Department of Ophthalmology, Mason Eye Institute, University of Missouri School of Medicine, Columbia, MO, USA.
| | - Ashok Kumar
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA; Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.
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2
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Sanches IH, Braga RC, Alves VM, Andrade CH. Enhancing hERG Risk Assessment with Interpretable Classificatory and Regression Models. Chem Res Toxicol 2024; 37:910-922. [PMID: 38781421 PMCID: PMC11187631 DOI: 10.1021/acs.chemrestox.3c00400] [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: 12/15/2023] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
The human Ether-à-go-go-Related Gene (hERG) is a transmembrane protein that regulates cardiac action potential, and its inhibition can induce a potentially deadly cardiac syndrome. In vitro tests help identify hERG blockers at early stages; however, the high cost motivates searching for alternative, cost-effective methods. The primary goal of this study was to enhance the Pred-hERG tool for predicting hERG blockage. To achieve this, we developed new QSAR models that incorporated additional data, updated existing classificatory and multiclassificatory models, and introduced new regression models. Notably, we integrated SHAP (SHapley Additive exPlanations) values to offer a visual interpretation of these models. Utilizing the latest data from ChEMBL v30, encompassing over 14,364 compounds with hERG data, our binary and multiclassification models outperformed both the previous iteration of Pred-hERG and all publicly available models. Notably, the new version of our tool introduces a regression model for predicting hERG activity (pIC50). The optimal model demonstrated an R2 of 0.61 and an RMSE of 0.48, surpassing the only available regression model in the literature. Pred-hERG 5.0 now offers users a swift, reliable, and user-friendly platform for the early assessment of chemically induced cardiotoxicity through hERG blockage. The tool provides versatile outcomes, including (i) classificatory predictions of hERG blockage with prediction reliability, (ii) multiclassificatory predictions of hERG blockage with reliability, (iii) regression predictions with estimated pIC50 values, and (iv) probability maps illustrating the contribution of chemical fragments for each prediction. Furthermore, we implemented explainable AI analysis (XAI) to visualize SHAP values, providing insights into the contribution of each feature to binary classification predictions. A consensus prediction calculated based on the predictions of the three developed models is also present to assist the user's decision-making process. Pred-hERG 5.0 has been designed to be user-friendly, making it accessible to users without computational or programming expertise. The tool is freely available at http://predherg.labmol.com.br.
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Affiliation(s)
- Igor H. Sanches
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for the Research and Advancement in Fragments and Molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP 05508-220, Brazil
| | | | - Vinicius M. Alves
- University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Carolina Horta Andrade
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculty of Pharmacy, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for Excellence in Artificial Intelligence (CEIA), Institute of Informatics, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
- Center
for the Research and Advancement in Fragments and Molecular Targets
(CRAFT), School of Pharmaceutical Sciences at Ribeirao Preto, University of São Paulo, Ribeirão Preto, SP 05508-220, Brazil
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3
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Brown AP, Friedrichs GS, Tang HM, Traebert M, Weber V, Yao N, Yan GX. Electrophysiological Changes in the Rabbit Ventricular Wedge and Human-Induced Pluripotent Stem-Cell Derived (IPSC) Cardiomyocytes Translate to Severe Arrhythmia Observed in a Canine Toxicology Study, Not Predicted by Standard In Vitro Ion Channel Assays. Int J Toxicol 2024; 43:231-242. [PMID: 38327194 DOI: 10.1177/10915818241230900] [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: 02/09/2024]
Abstract
During drug discovery, small molecules are typically assayed in vitro for secondary pharmacology effects, which include ion channels relevant to cardiac electrophysiology. Compound A was an irreversible inhibitor of myeloperoxidase investigated for the treatment of peripheral artery disease. Oral doses in dogs at ≥5 mg/kg resulted in cardiac arrhythmias in a dose-dependent manner (at Cmax, free ≥1.53 μM) that progressed in severity with time. Nevertheless, a panel of 13 different cardiac ion channel (K, Na, and Ca) assays, including hERG, failed to identify pharmacologic risks of the molecule. Compound A and a related Compound B were evaluated for electrophysiological effects in the isolated rabbit ventricular wedge assay. Compounds A and B prolonged QT and Tp-e intervals at ≥1 and ≥.3 μM, respectively, and both prolonged QRS at ≥5 μM. Compound A produced early after depolarizations and premature ventricular complexes at ≥5 μM. These data indicate both compounds may be modulating hERG (Ikr) and Nav1.5 ion channels. In human IPSC cardiomyocytes, Compounds A and B prolonged field potential duration at ≥3 μM and induced cellular dysrhythmia at ≥10 and ≥3 μM, respectively. In a rat toxicology study, heart tissue: plasma concentration ratios for Compound A were ≥19X at 24 hours post-dose, indicating significant tissue distribution. In conclusion, in vitro ion channel assays may not always identify cardiovascular electrophysiological risks observed in vivo, which can be affected by tissue drug distribution. Risk for arrhythmia may increase with a "trappable" ion channel inhibitor, particularly if cardiac tissue drug levels achieve a critical threshold for pharmacologic effects.
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Affiliation(s)
- Alan P Brown
- Novartis Biomedical Research, Cambridge, MA, USA
| | | | | | | | | | - Nancy Yao
- Novartis Biomedical Research, East Hanover, NJ, USA
| | - Gan-Xin Yan
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
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4
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Rohatgi A, Gupta P. Benzoic acid derivatives as potent antibiofilm agents against Klebsiella pneumoniae biofilm. J Biosci Bioeng 2023; 136:190-197. [PMID: 37479559 DOI: 10.1016/j.jbiosc.2023.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Klebsiella pneumoniae is responsible for a significant proportion of human urinary tract infections, and its biofilm is a major virulence. One potential approach to controlling biofilm-associated infections is targeting the adhesin MrkD1P to disrupt biofilm formation. We employed Schrodinger's Maestro tool with the OPLS 2005 force field to dock compounds with the target protein. Two benzoic acid derivatives, 3-hydroxy benzoic acid and 2,5-dihydroxybenzoic acid, had strong binding free energies (-55.57 and -18.68 kcal/mol) and were the most potent compounds. The in-vitro experiments were conducted to validate the in-silico results. The results showed that both compounds effectively inhibited biofilm formation at low concentrations (4 and 8 mg/mL, respectively) and had antibiofilm activity, restricting cell attachment. Both compounds demonstrated a strong biofilm inhibitory effect, with 97% and 89% reduction in biofilm by 3-hydroxy benzoic acid and 2,5-dihydroxybenzoic acid, respectively. These findings suggest that natural compounds can be a potential source of new drugs to combat biofilm-associated infections. The study highlights the potential of targeting adhesin MrkD1P as an effective approach to controlling biofilm-associated infections caused by K. pneumoniae. The results may have implications for the development of new therapies for biofilm-associated infections and pave the way for future research in this area.
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Affiliation(s)
- Anuj Rohatgi
- Department of Biotechnology, National Institute of Technology, Raipur 492010, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology, Raipur 492010, India.
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5
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Goel H, Yu W, MacKerell AD. hERG Blockade Prediction by Combining Site Identification by Ligand Competitive Saturation and Physicochemical Properties. CHEMISTRY (BASEL, SWITZERLAND) 2022; 4:630-646. [PMID: 36712295 PMCID: PMC9881610 DOI: 10.3390/chemistry4030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ether-a-go-go-related gene (hERG) potassium channel is well-known contributor to drug-induced cardiotoxicity and therefore an extremely important target when performing safety assessments of drug candidates. Ligand-based approaches in connection with quantitative structure active relationships (QSAR) analyses have been developed to predict hERG toxicity. Availability of the recent published cryogenic electron microscopy (cryo-EM) structure for the hERG channel opened the prospect for using structure-based simulation and docking approaches for hERG drug liability predictions. In recent time, the idea of combining structure- and ligand-based approaches for modeling hERG drug liability has gained momentum offering improvements in predictability when compared to ligand-based QSAR practices alone. The present article demonstrates uniting the structure-based SILCS (site-identification by ligand competitive saturation) approach in conjunction with physicochemical properties to develop predictive models for hERG blockade. This combination leads to improved model predictability based on Pearson's R and percent correct (represents rank-ordering of ligands) metric for different validation sets of hERG blockers involving diverse chemical scaffold and wide range of pIC50 values. The inclusion of the SILCS structure-based approach allows determination of the hERG region to which compounds bind and the contribution of different chemical moieties in the compounds to blockade, thereby facilitating the rational ligand design to minimize hERG liability.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
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6
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Creanza TM, Delre P, Ancona N, Lentini G, Saviano M, Mangiatordi GF. Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study. J Chem Inf Model 2021; 61:4758-4770. [PMID: 34506150 PMCID: PMC9282647 DOI: 10.1021/acs.jcim.1c00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Drug-induced blockade of the human
ether-à-go-go-related
gene (hERG) channel is today considered the main
cause of cardiotoxicity in postmarketing surveillance. Hence, several
ligand-based approaches were developed in the last years and are currently
employed in the early stages of a drug discovery process for in silico cardiac safety assessment of drug candidates.
Herein, we present the first structure-based classifiers able to discern hERG binders from nonbinders. LASSO regularized support
vector machines were applied to integrate docking scores and protein–ligand
interaction fingerprints. A total of 396 models were trained and validated
based on: (i) high-quality experimental bioactivity information returned
by 8337 curated compounds extracted from ChEMBL (version 25) and (ii)
structural predictor data. Molecular docking simulations were performed
using GLIDE and GOLD software programs and four different hERG structural models, namely, the recently published structures
obtained by cryoelectron microscopy (PDB codes: 5VA1 and 7CN1) and
two published homology models selected for comparison. Interestingly,
some classifiers return performances comparable to ligand-based models
in terms of area under the ROC curve (AUCMAX = 0.86 ±
0.01) and negative predictive values (NPVMAX = 0.81 ±
0.01), thus putting forward the herein proposed computational workflow
as a valuable tool for predicting hERG-related cardiotoxicity
without the limitations of ligand-based models, typically affected
by low interpretability and a limited applicability domain. From a
methodological point of view, our study represents the first example
of a successful integration of docking scores and protein–ligand
interaction fingerprints (IFs) through a support vector machine (SVM)
LASSO regularized strategy. Finally, the study highlights the importance
of using hERG structural models accounting for ligand-induced
fit effects and allowed us to select the best-performing protein conformation
(made available in the Supporting Information, SI) to be employed
for a reliable structure-based prediction of hERG-related cardiotoxicity.
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Affiliation(s)
- Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Pietro Delre
- Chemistry Department, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.,CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy
| | - Michele Saviano
- CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
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7
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Thomas L, Birangal SR, Ray R, Sekhar Miraj S, Munisamy M, Varma M, S V CS, Banerjee M, Shenoy GG, Rao M. Prediction of potential drug interactions between repurposed COVID-19 and antitubercular drugs: an integrational approach of drug information software and computational techniques data. Ther Adv Drug Saf 2021; 12:20420986211041277. [PMID: 34471515 PMCID: PMC8404633 DOI: 10.1177/20420986211041277] [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: 12/03/2020] [Accepted: 07/24/2021] [Indexed: 01/02/2023] Open
Abstract
Introduction: Tuberculosis is a major respiratory disease globally with a higher prevalence in Asian and African countries than rest of the world. With a larger population of tuberculosis patients anticipated to be co-infected with COVID-19 infection, an ongoing pandemic, identifying, preventing and managing drug–drug interactions is inevitable for maximizing patient benefits for the current repurposed COVID-19 and antitubercular drugs. Methods: We assessed the potential drug–drug interactions between repurposed COVID-19 drugs and antitubercular drugs using the drug interaction checker of IBM Micromedex®. Extensive computational studies were performed at a molecular level to validate and understand the drug–drug interactions found from the Micromedex drug interaction checker database at a molecular level. The integrated knowledge derived from Micromedex and computational data was collated and curated for predicting potential drug–drug interactions between repurposed COVID-19 and antitubercular drugs. Results: A total of 91 potential drug–drug interactions along with their severity and level of documentation were identified from Micromedex between repurposed COVID-19 drugs and antitubercular drugs. We identified 47 pharmacodynamic, 42 pharmacokinetic and 2 unknown DDIs. The majority of our molecular modelling results were in line with drug–drug interaction data obtained from the drug information software. QT prolongation was identified as the most common type of pharmacodynamic drug–drug interaction, whereas drug–drug interactions associated with cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (P-gp) inhibition and induction were identified as the frequent pharmacokinetic drug–drug interactions. The results suggest antitubercular drugs, particularly rifampin and second-line agents, warrant high alert and monitoring while prescribing with the repurposed COVID-19 drugs. Conclusion: Predicting these potential drug–drug interactions, particularly related to CYP3A4, P-gp and the human Ether-à-go-go-Related Gene proteins, could be used in clinical settings for screening and management of drug–drug interactions for delivering safer chemotherapeutic tuberculosis and COVID-19 care. The current study provides an initial propulsion for further well-designed pharmacokinetic-pharmacodynamic-based drug–drug interaction studies. Plain Language Summary
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Affiliation(s)
- Levin Thomas
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sumit Raosaheb Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Rajdeep Ray
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sonal Sekhar Miraj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Murali Munisamy
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Muralidhar Varma
- Department of Infectious Diseases, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | | | - Mithu Banerjee
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | - Gautham G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Mahadev Rao
- Professor and Head, Department of Pharmacy Practice, Coordinator, Centre for Translational Research, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
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8
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Hamilton MM, Mseeh F, McAfoos TJ, Leonard PG, Reyna NJ, Harris AL, Xu A, Han M, Soth MJ, Czako B, Theroff JP, Mandal PK, Burke JP, Virgin-Downey B, Petrocchi A, Pfaffinger D, Rogers NE, Parker CA, Yu SS, Jiang Y, Krapp S, Lammens A, Trevitt G, Tremblay MR, Mikule K, Wilcoxen K, Cross JB, Jones P, Marszalek JR, Lewis RT. Discovery of IACS-9779 and IACS-70465 as Potent Inhibitors Targeting Indoleamine 2,3-Dioxygenase 1 (IDO1) Apoenzyme. J Med Chem 2021; 64:11302-11329. [PMID: 34292726 DOI: 10.1021/acs.jmedchem.1c00679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme that mediates the rate-limiting step in the metabolism of l-tryptophan to kynurenine, has been widely explored as a potential immunotherapeutic target in oncology. We developed a class of inhibitors with a conformationally constrained bicyclo[3.1.0]hexane core. These potently inhibited IDO1 in a cellular context by binding to the apoenzyme, as elucidated by biochemical characterization and X-ray crystallography. A SKOV3 tumor model was instrumental in differentiating compounds, leading to the identification of IACS-9779 (62) and IACS-70465 (71). IACS-70465 has excellent cellular potency, a robust pharmacodynamic response, and in a human whole blood assay was more potent than linrodostat (BMS-986205). IACS-9779 with a predicted human efficacious once daily dose below 1 mg/kg to sustain >90% inhibition of IDO1 displayed an acceptable safety margin in rodent toxicology and dog cardiovascular studies to support advancement into preclinical safety evaluation for human development.
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Affiliation(s)
- Matthew M Hamilton
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Faika Mseeh
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Timothy J McAfoos
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Paul G Leonard
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Naphtali J Reyna
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Angela L Harris
- TRACTION (Translational Research to Advance Therapeutics and Innovation in Oncology), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Alan Xu
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Michelle Han
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Michael J Soth
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Barbara Czako
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jay P Theroff
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Pijus K Mandal
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason P Burke
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Brett Virgin-Downey
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Alessia Petrocchi
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Dana Pfaffinger
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Norma E Rogers
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Connor A Parker
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Simon S Yu
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yongying Jiang
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Stephan Krapp
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
| | - Alfred Lammens
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
| | - Graham Trevitt
- XenoGesis Ltd, BioCity Nottingham, Pennyfoot Street, Nottingham, Nottinghamshire NG1 1GF, U.K
| | - Martin R Tremblay
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Keith Mikule
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Keith Wilcoxen
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Jason B Cross
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Philip Jones
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Joseph R Marszalek
- TRACTION (Translational Research to Advance Therapeutics and Innovation in Oncology), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Richard T Lewis
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
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9
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Wan H, Aravamuthan V, Pearlstein RA. Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory. ACS Pharmacol Transl Sci 2020; 3:1111-1143. [PMID: 33330838 PMCID: PMC7671103 DOI: 10.1021/acsptsci.0c00089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/01/2023]
Abstract
![]()
The
SARS-CoV-2 main protease (Mpro) is of major interest
as an antiviral drug target. Structure-based virtual screening efforts,
fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2
Mpro crystal structures, are underway in many laboratories.
However, little is known about the dynamic enzyme mechanism, which
is needed to inform both assay development and structure-based inhibitor
design. Here, we apply biodynamics theory to characterize the structural
dynamics of substrate-induced Mpro activation under nonequilibrium conditions. The catalytic cycle
is governed by concerted dynamic structural
rearrangements of domain 3 and the m-shaped loop (residues 132–147)
on which Cys145 (comprising the thiolate nucleophile and half of the
oxyanion hole) and Gly143 (comprising the second half of the oxyanion
hole) reside. In particular, we observed the following: (1) Domain
3 undergoes dynamic rigid-body rotation about the domain 2–3
linker, alternately visiting two primary conformational states (denoted
as M1pro ↔
M2pro); (2)
The Gly143-containing crest of the m-shaped loop undergoes up and
down translations caused by conformational changes within the rising
stem of the loop (Lys137–Asn142) in response to domain 3 rotation
and dimerization (denoted as M1/downpro ↔ 2·M2/uppro) (noting that the Cys145-containing
crest is fixed in the up position). We propose that substrates associate
to the M1/downpro state, which promotes the M2/downpro state, dimerization (denoted as 2·M2/uppro–substrate),
and catalysis. Here, we explore the state transitions of Mpro under nonequilibrium conditions, the mechanisms by which they are
powered, and the implications thereof for efficacious inhibition under in vivo conditions.
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Affiliation(s)
- Hongbin Wan
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vibhas Aravamuthan
- Vibhas Aravamuthan - NIBR Informatics, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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Pearlstein RA, Wan H, Aravamuthan V. Toward in vivo relevant drug design. Drug Discov Today 2020; 26:637-650. [PMID: 33132106 DOI: 10.1016/j.drudis.2020.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 11/28/2022]
Abstract
Current early and preclinical drug discovery are rooted in decades-old empirical principles describing structure-free energy and structure-function relationships under equilibrium conditions that frequently break down under in vivo conditions. Improved prediction of efficacy and toxicity depends on a paradigm shift to in vivo-relevant principles describing the true nonequilibrium/nonlinear dynamic (NLD) nature of cellular systems. Here, we outline a holistic, in vivo-relevant first principles theory ('Biodynamics'), in which cellular function/dysfunction, and pharmaco-/toxicodynamic effects are considered as emergent behaviors of multimolecular systems powered by covalent and noncovalent free energy sources. The reduction to practice of Biodynamics theory consists of in silico simulations performed at the atomistic and molecular systems levels, versus empirical models fit to in vitro data under the classical paradigm.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Hongbin Wan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vibhas Aravamuthan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
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