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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Hall A, Chatzopoulou M, Frost J. Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements. Bioorg Med Chem 2024; 104:117653. [PMID: 38579492 DOI: 10.1016/j.bmc.2024.117653] [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: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 04/07/2024]
Abstract
Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.
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Affiliation(s)
- Adrian Hall
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK.
| | - Maria Chatzopoulou
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
| | - James Frost
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
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3
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Martino SD, Petri GL, De Rosa M. Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn? J Med Chem 2024; 67:885-921. [PMID: 38179950 DOI: 10.1021/acs.jmedchem.3c01971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.
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Affiliation(s)
- Simona Di Martino
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Giovanna Li Petri
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Maria De Rosa
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
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Kamal S, Shahzad A, Rehman K, Tariq K, Akash MSH, Imran M, Assiri MA. Therapeutic Intervention of Serine Protease Inhibitors against Hepatitis C Virus. Curr Med Chem 2024; 31:2052-2072. [PMID: 37855348 DOI: 10.2174/0109298673234823230921090431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 10/20/2023]
Abstract
Hepatitis C virus (HCV) is a globally prevalent and hazardous disorder that is responsible for inducing several persistent and potentially fatal liver diseases. Current treatment strategies offer limited efficacy, often accompanied by severe and debilitating adverse effects. Consequently, there is an urgent and compelling need to develop novel therapeutic interventions that can provide maximum efficacy in combating HCV while minimizing the burden of adverse effects on patients. One promising target against HCV is the NS3-4A serine protease, a complex composed of two HCV-encoded proteins. This non-covalent heterodimer is crucial in the viral life cycle and has become a primary focus for therapeutic interventions. Although peginterferon, combined with ribavirin, is commonly employed for HCV treatment, its efficacy is hampered by significant adverse effects that can profoundly impact patients' quality of life. In recent years, the development of direct-acting antiviral agents (DAAs) has emerged as a breakthrough in HCV therapy. These agents exhibit remarkable potency against the virus and have demonstrated fewer adverse effects when combined with other DAAs. However, it is important to note that there is a potential for developing resistance to DAAs due to alterations in the amino acid position of the NS3-4A protease. This emphasizes the need for ongoing research to identify strategies that can minimize the emergence of resistance and ensure long-term effectiveness. While the combination of DAAs holds promise for HCV treatment, it is crucial to consider the possibility of drug-drug interactions. These interactions may occur when different DAAs are used concurrently, potentially compromising their therapeutic efficacy. Therefore, carefully evaluating and monitoring potential drug interactions are vital to optimize treatment outcomes. In the pursuit of novel therapeutic interventions for HCV, the field of computational biology and bioinformatics has emerged as a valuable tool. These advanced technologies and methodologies enable the development and design of new drugs and therapeutic agents that exhibit maximum efficacy, reduced risk of resistance, and minimal adverse effects. By leveraging computational approaches, researchers can efficiently screen and optimize potential candidates, accelerating the discovery and development of highly effective treatments for HCV, treatments.
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Affiliation(s)
- Shagufta Kamal
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Asif Shahzad
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, The Women University, Multan, Pakistan
| | - Komal Tariq
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | | | - Muhammad Imran
- Research center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammed Ali Assiri
- Research center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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5
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Ren P, Li S, Wang S, Zhang X, Bai F. Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs. Molecules 2023; 29:225. [PMID: 38202808 PMCID: PMC10780089 DOI: 10.3390/molecules29010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CLpro), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CLpro or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CLpro with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CLpro and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds 1-2, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shiwei Li
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shihang Wang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Xianglei Zhang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Fang Bai
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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6
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Meanwell NA. Applications of Bioisosteres in the Design of Biologically Active Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18087-18122. [PMID: 36961953 DOI: 10.1021/acs.jafc.3c00765] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.
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Affiliation(s)
- Nicholas A Meanwell
- The Baruch S. Blumberg Institute, 3805 Old Easton Rd, Doylestown, Pennsylvania 18902, United States
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Chen Y, Wu Y, Li J, Chen K, Wang W, Ye Z, Feng K, Yang Y, Xu Y, Kang J, Guo X. Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation. Cell Death Discov 2023; 9:244. [PMID: 37452012 PMCID: PMC10349095 DOI: 10.1038/s41420-023-01548-1] [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: 01/27/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023] Open
Abstract
The zinc finger proteins (ZNFs) mediated transcriptional regulation is critical for cell fate transition. However, it is still unclear how the ZNFs realize their specific regulatory roles in the stage-specific determination of cardiomyocyte differentiation. Here, we reported that the zinc fingers and homeoboxes 1 (Zhx1) protein, transiently expressed during the cell fate transition from mesoderm to cardiac progenitors, was indispensable for the proper cardiomyocyte differentiation of mouse and human embryonic stem cells. Moreover, Zhx1 majorly promoted the specification of cardiac progenitors via interacting with hnRNPA1 and co-activated the transcription of a wide range of genes. In-depth mechanistic studies showed that Zhx1 was bound with hnRNPA1 by the amino acid residues (Thr111-His120) of the second Znf domain, thus participating in the formation of cardiac progenitors. Together, our study highlights the unrevealed interaction of Zhx1/hnRNPA1 for activating gene transcription during cardiac progenitor specification and also provides new evidence for the specificity of cell fate determination in cardiomyocyte differentiation.
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Affiliation(s)
- Yang Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Kai Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Wuchan Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zihui Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Ke Feng
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Institute for Advanced Study, Tongji University, Shanghai, 200092, China.
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8
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COVID-19 therapeutics: Clinical application of repurposed drugs and futuristic strategies for target-based drug discovery. Genes Dis 2023; 10:1402-1428. [PMCID: PMC10079314 DOI: 10.1016/j.gendis.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the complicated disease COVID-19. Clinicians are continuously facing huge problems in the treatment of patients, as COVID-19-specific drugs are not available hence the principle of drug repurposing serves as a one-and-only hope. Globally, the repurposing of many drugs is underway; few of them are already approved by the regulatory bodies for their clinical use and most of them are in different phases of clinical trials. Here in this review, our main aim is to discuss in detail the up-to-date information on the target-based pharmacological classification of repurposed drugs, the potential mechanism of actions, and the current clinical trial status of various drugs which are under repurposing since early 2020. At last, we briefly proposed the probable pharmacological and therapeutic drug targets that may be preferred as a futuristic drug discovery approach in the development of effective medicines.
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Broni E, Ashley C, Adams J, Manu H, Aikins E, Okom M, Miller WA, Wilson MD, Kwofie SK. Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors. Int J Mol Sci 2023; 24:ijms24076298. [PMID: 37047270 PMCID: PMC10094735 DOI: 10.3390/ijms24076298] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Joseph Adams
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - Hammond Manu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Ebenezer Aikins
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Mary Okom
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
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10
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Hung CT, Wu BS, Chou CT, Sandford C, Tsai CC. Insight into Stereocontrol in the Asymmetric Intramolecular Allylation with a tert-Butylsulfinamide Nucleophile: Application in the Synthesis of Chiral Isoindoline-1-Carboxylic Acid Esters. J Org Chem 2023; 88:613-625. [PMID: 36548133 DOI: 10.1021/acs.joc.2c02672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The asymmetric induction afforded by a chiral sulfinyl group in a palladium/Brønsted-acid-catalyzed intramolecular allylic amination was investigated. Predictions of the diastereoselectivity for various substrates under assumed total thermodynamic control were obtained from density functional theory (DFT), and the correlation with experimental data demonstrates abrupt changes to kinetic control across the substrate scope. The resulting heterocyclic product was readily converted to valuable isoindoline-1-carboxylic acid esters by a two-step oxidation sequence, providing asymmetric access to a key unnatural α-amino acid scaffold.
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Affiliation(s)
- Chun-Tai Hung
- Department of Chemistry, Tunghai University, Taichung City 40704, Taiwan
| | - Bing-Syuan Wu
- Department of Chemistry, Tunghai University, Taichung City 40704, Taiwan
| | - Chun-Ting Chou
- Department of Chemistry, Tunghai University, Taichung City 40704, Taiwan
| | - Christopher Sandford
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Cheng-Che Tsai
- Department of Chemistry, Tunghai University, Taichung City 40704, Taiwan
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11
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Ren J, Vaid TM, Lee H, Ojeda I, Johnson ME. Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations. J Comput Aided Mol Des 2023; 37:53-65. [PMID: 36427108 PMCID: PMC9839505 DOI: 10.1007/s10822-022-00490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present an investigation of HCV NS3/4A inhibitors based on a sulfonamidobenzamide scaffold. Inhibitor interactions with HCV NS3/4A were explored by molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. All of the inhibitors adopt similar molecular docking poses in the catalytic site of the protease that are stabilized by hydrogen bond interactions with G137 and the catalytic S139, which are known to be important for potency and binding stability. The quantitative assessments of binding free energies from MM/PBSA correlate well with the experimental results, with a high coefficient of determination, R2 of 0.92. Binding free energy decomposition analyses elucidate the different contributions of Q41, F43, H57, R109, K136, G137, S138, S139, A156, M485, and Q526 in binding different inhibitors. The importance of these sidechain contributions was further confirmed by computational alanine scanning mutagenesis. In addition, the sidechains of K136 and S139 show crucial but distinct contributions to inhibitor binding with HCV NS3/4A. The structural basis of the potency has been elucidated, demonstrating the importance of the R155 sidechain conformation. This extensive exploration of binding energies and interactions between these compounds and HCV NS3/4A at the atomic level should benefit future antiviral drug design.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- BeiGene (Beijing) Co., Ltd, No. 30 Science Park Road, Zhong-Guan-Cun Life Sciences Park, Changping District, Beijing, 102206, People's Republic of China
| | - Tasneem M Vaid
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Isabel Ojeda
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
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12
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Suo Y, Xu M, Sun M, Lu W, Wang X, Lu X. Ruthenium-Mediated [2 + 2 + 2] Cyclization: A Route to Forge Indane and Isoindoline Core and Its Application in DNA-Encoded Library Technology. Org Lett 2022; 24:9092-9096. [DOI: 10.1021/acs.orglett.2c03759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Min Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China
| | - Meimei Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
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13
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Masoudi-Sobhanzadeh Y, Esmaeili H, Masoudi-Nejad A. A fuzzy logic-based computational method for the repurposing of drugs against COVID-19. BIOIMPACTS : BI 2022; 12:315-324. [PMID: 35975205 PMCID: PMC9376160 DOI: 10.34172/bi.2021.40] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 03/27/2021] [Accepted: 04/03/2021] [Indexed: 01/09/2023]
Abstract
Introduction: COVID-19 has spread out all around the world and seriously interrupted human activities. Being a newfound disease, not only many aspects of the disease are unknown, but also there is not an effective medication to cure the disease. Besides, designing a drug is a time-consuming process and needs large investment. Hence, drug repurposing techniques, employed to discover the hidden benefits of the existing drugs, maybe a useful option for treating COVID-19. Methods: The present study exploits the drug repositioning concepts and introduces some candidate drugs which may be effective in controlling COVID-19. The suggested method consists of three main steps. First, the required data such as the amino acid sequences of targets and drug-target interactions are extracted from the public databases. Second, the similarity score between the targets (protein/enzymes) and genome of SARS-COV-2 is computed using the proposed fuzzy logic-based method. Since the classical approaches yield outcomes which may not be useful for the real-world applications, the fuzzy technique can address the issue. Third, after ranking targets based on the obtained scores, the usefulness of drugs affecting them is examined for managing COVID-19. Results: The results indicate that antiviral medicines, designed for curing hepatitis C, may also cure COVID-19. According to the findings, ribavirin, simeprevir, danoprevir, and XTL-6865 may be helpful in controlling the disease. Conclusion: It can be concluded that the similarity-based drug repurposing techniques may be the most suitable option for managing emerging diseases such as COVID-19 and can be applied to a wide range of data. Also, fuzzy logic-based scoring methods can produce outcomes which are more consistent with the real-world biological applications than others.
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Affiliation(s)
- Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
,Corresponding authors: Ali Masoudi-Nejad, ; Yosef Masoudi-Sobhanzadeh,
| | - Hosein Esmaeili
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
,Corresponding authors: Ali Masoudi-Nejad, ; Yosef Masoudi-Sobhanzadeh,
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14
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Ullrich S, Sasi VM, Mahawaththa MC, Ekanayake KB, Morewood R, George J, Shuttleworth L, Zhang X, Whitefield C, Otting G, Jackson C, Nitsche C. Challenges of short substrate analogues as SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett 2021; 50:128333. [PMID: 34418570 PMCID: PMC8378659 DOI: 10.1016/j.bmcl.2021.128333] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 12/22/2022]
Abstract
Specific anti-coronaviral drugs complementing available vaccines are urgently needed to fight the COVID-19 pandemic. Given its high conservation across the betacoronavirus genus and dissimilarity to human proteases, the SARS-CoV-2 main protease (Mpro) is an attractive drug target. SARS-CoV-2 Mpro inhibitors have been developed at unprecedented speed, most of them being substrate-derived peptidomimetics with cysteine-modifying warheads. In this study, Mpro has proven resistant towards the identification of high-affinity short substrate-derived peptides and peptidomimetics without warheads. 20 cyclic and linear substrate analogues bearing natural and unnatural residues, which were predicted by computational modelling to bind with high affinity and designed to establish structure-activity relationships, displayed no inhibitory activity at concentrations as high as 100 μM. Only a long linear peptide covering residues P6 to P5' displayed moderate inhibition (Ki = 57 µM). Our detailed findings will inform current and future drug discovery campaigns targeting Mpro.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vishnu M Sasi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Kasuni B Ekanayake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Josemon George
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Laura Shuttleworth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Xiaobai Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Cassidy Whitefield
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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15
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Nageswara Rao D, Zephyr J, Henes M, Chan ET, Matthew AN, Hedger AK, Conway HL, Saeed M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A. Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity against Drug-Resistant Hepatitis C Virus Variants. J Med Chem 2021; 64:11972-11989. [PMID: 34405680 PMCID: PMC9228641 DOI: 10.1021/acs.jmedchem.1c00554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The three pan-genotypic HCV NS3/4A protease inhibitors (PIs) currently in clinical use-grazoprevir, glecaprevir, and voxilaprevir-are quinoxaline-based P2-P4 macrocycles and thus exhibit similar resistance profiles. Using our quinoxaline-based P1-P3 macrocyclic lead compounds as an alternative chemical scaffold, we explored structure-activity relationships (SARs) at the P2 and P4 positions to develop pan-genotypic PIs that avoid drug resistance. A structure-guided strategy was used to design and synthesize two series of compounds with different P2 quinoxalines in combination with diverse P4 groups of varying sizes and shapes, with and without fluorine substitutions. Our SAR data and cocrystal structures revealed the interplay between the P2 and P4 groups, which influenced inhibitor binding and the overall resistance profile. Optimizing inhibitor interactions in the S4 pocket led to PIs with excellent antiviral activity against clinically relevant PI-resistant HCV variants and genotype 3, providing potential pan-genotypic inhibitors with improved resistance profiles.
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Affiliation(s)
- Desaboini Nageswara Rao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Elise T Chan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ashley N Matthew
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Adam K Hedger
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Hasahn L Conway
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts 02118, United States
| | - Alicia Newton
- Monogram Biosciences, South San Francisco, California 94080, United States
| | | | - Wei Huang
- Monogram Biosciences, South San Francisco, California 94080, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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16
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Sharland JC, Wei B, Hardee DJ, Hodges TR, Gong W, Voight EA, Davies HML. Asymmetric synthesis of pharmaceutically relevant 1-aryl-2-heteroaryl- and 1,2-diheteroarylcyclopropane-1-carboxylates. Chem Sci 2021; 12:11181-11190. [PMID: 34522315 PMCID: PMC8386643 DOI: 10.1039/d1sc02474d] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
This study describes general methods for the enantioselective syntheses of pharmaceutically relevant 1-aryl-2-heteroaryl- and 1,2-diheteroarylcyclopropane-1-carboxylates through dirhodium tetracarboxylate-catalysed asymmetric cyclopropanation of vinyl heterocycles with aryl- or heteroaryldiazoacetates. The reactions are highly diastereoselective and high asymmetric induction could be achieved using either (R)-pantolactone as a chiral auxiliary or chiral dirhodium tetracarboxylate catalysts. For meta- or para-substituted aryl- or heteroaryldiazoacetates the optimum catalyst was Rh2(R-p-Ph-TPCP)4. In the case of ortho-substituted aryl- or heteroaryldiazoacetates, the optimum catalyst was Rh2(R-TPPTTL)4. For a highly enantioselective reaction with the ortho-substituted substrates, 2-chloropyridine was required as an additive in the presence of either 4 Å molecular sieves or 1,1,1,3,3,3-hexafluoroisopropanol (HFIP). Under the optimized conditions, the cyclopropanation could be conducted in the presence of a variety of heterocycles, such as pyridines, pyrazines, quinolines, indoles, oxadiazoles, thiophenes and pyrazoles.
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Affiliation(s)
- Jack C Sharland
- Department of Chemistry, Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - Bo Wei
- Department of Chemistry, Emory University 1515 Dickey Drive Atlanta GA 30322 USA
| | - David J Hardee
- Drug Discovery Science and Technology, AbbVie 1 North Waukegan Rd. North Chicago IL 60064 USA
| | - Timothy R Hodges
- Drug Discovery Science and Technology, AbbVie 1 North Waukegan Rd. North Chicago IL 60064 USA
| | - Wei Gong
- Drug Discovery Science and Technology, AbbVie 1 North Waukegan Rd. North Chicago IL 60064 USA
| | - Eric A Voight
- Drug Discovery Science and Technology, AbbVie 1 North Waukegan Rd. North Chicago IL 60064 USA
| | - Huw M L Davies
- Department of Chemistry, Emory University 1515 Dickey Drive Atlanta GA 30322 USA
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17
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Sun MR, Li HL, Ba MY, Cheng W, Zhu HL, Duan YT. Cyclopropyl Scaffold: A Generalist for Marketed Drugs. Mini Rev Med Chem 2021; 21:150-170. [PMID: 32727325 DOI: 10.2174/1389557520666200729161150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/23/2019] [Accepted: 04/26/2020] [Indexed: 11/22/2022]
Abstract
In recent decades, much attention has been given to cyclopropyl scaffolds, which commonly exist in natural products and synthetic organic molecules. Clinical drug molecules with cyclopropyl rings are an area of focus in therapeutic research due to their interesting chemical properties and unique pharmacology activity. These molecular drugs against different targets are applicable in some therapeutic treatment fields including cancer, infection, respiratory disorder, cardiovascular and cerebrovascular diseases, dysphrenia, nervous system disorders, endocrine and metabolic disorders, skin disease, digestive disorders, urogenital diseases, otolaryngological and dental diseases, and eye diseases. This review is a guide for pharmacologists who are in search of valid preclinical/clinical drug compounds where the progress, from 1961 to the present day, of approved marketed drugs containing cyclopropyl scaffold is examined.
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Affiliation(s)
- Mo-Ran Sun
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Hong-Liang Li
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Meng-Yu Ba
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Weyland Cheng
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou University, Zhengzhou 450018, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Yong-Tao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou University, Zhengzhou 450018, China
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18
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Paul SS, Biswas G. Repurposed Antiviral Drugs for the Treatment of COVID-19: Syntheses, Mechanism of Infection and Clinical Trials. Mini Rev Med Chem 2021; 21:1123-1143. [PMID: 33355053 DOI: 10.2174/1389557521666201222145842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/22/2022]
Abstract
COVID-19 is a public health emergency of international concern. Although considerable knowledge has been acquired with time about the viral mechanism of infection and mode of replication, yet no specific drugs or vaccines have been discovered against SARS-CoV-2 to date. There are few small molecule antiviral drugs like Remdesivir and Favipiravir, which have shown promising results in different advanced stages of clinical trials. Chloroquinine, Hydroxychloroquine, and Lopinavir- Ritonavir combination, although initially were hypothesized to be effective against SARSCoV- 2, are now discontinued from the solidarity clinical trials. This review provides a brief description of their chemical syntheses along with their mode of action, and clinical trial results available on Google and in different peer-reviewed journals till 24th October 2020.
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Affiliation(s)
| | - Goutam Biswas
- Department of Chemistry, Cooch Behar Panchanan Barma University, Panchanan Nagar, Cooch Behar 736101, India
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19
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Tarannum H, Chauhan B, Samadder A, Roy H, Nandi S. To Explore the Potential Targets and Current Structure-based Design Strategies Utilizing Co-crystallized Ligand to Combat HCV. Curr Drug Targets 2021; 22:590-604. [PMID: 32720601 DOI: 10.2174/1389450121999200727215020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Hepatitis C Virus (HCV) belongs to the Hepacivirus family. HCV has been designated as a very dreadful virus as it can attack the liver, causing inflammation and even may lead to cancer in chronic conditions. It was estimated that 71 million people around the world have chronic HCV infection. World Health Organization (WHO) reported that about 399000 people died because of chronic cirrhosis and liver cancer globally. In spite of the abundance of availability of drugs for the treatment of HCV, however, the issue of drug resistance surpasses all the possibilities of therapeutic management of HCV. Therefore, to address this issue of 'drug-resistance', various HCV targets were explored to quest the evaluation of the mechanism of the disease progression. METHODS An attempt has been made in the present study to explore the various targets of HCV involved in the mechanism(s) of the disease initiation and progression and to focus on the mode of binding of ligands, which are co-crystallized at the active cavity of different HCV targets. CONCLUSION The present study could predict some crucial features of these ligands, which possibly interacted with various amino acid residues responsible for their biological activity and molecular signaling pathway(s). Such binding mode may be considered as a template for the high throughput screening and designing of active congeneric ligands to combat HCV.
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Affiliation(s)
- Heena Tarannum
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Bhumika Chauhan
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
| | - Asmita Samadder
- Cytogenetics and Molecular Biology Lab., Department of Zoology, University of Kalyani, Kalyani, Nadia, 741235, India
| | - Harekrishna Roy
- Nirmala College of Pharmacy, Mangalagiri, Guntur, Andhra Pradesh, 522503, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research (Affiliated to Uttarakhand Technical University), Kashipur-244713, India
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20
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Dinesh DC, Tamilarasan S, Rajaram K, Bouřa E. Antiviral Drug Targets of Single-Stranded RNA Viruses Causing Chronic Human Diseases. Curr Drug Targets 2021; 21:105-124. [PMID: 31538891 DOI: 10.2174/1389450119666190920153247] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/08/2019] [Accepted: 08/08/2019] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid (RNA) viruses associated with chronic diseases in humans are major threats to public health causing high mortality globally. The high mutation rate of RNA viruses helps them to escape the immune response and also is responsible for the development of drug resistance. Chronic infections caused by human immunodeficiency virus (HIV) and hepatitis viruses (HBV and HCV) lead to acquired immunodeficiency syndrome (AIDS) and hepatocellular carcinoma respectively, which are one of the major causes of human deaths. Effective preventative measures to limit chronic and re-emerging viral infections are absolutely necessary. Each class of antiviral agents targets a specific stage in the viral life cycle and inhibits them from its development and proliferation. Most often, antiviral drugs target a specific viral protein, therefore only a few broad-spectrum drugs are available. This review will be focused on the selected viral target proteins of pathogenic viruses containing single-stranded (ss) RNA genome that causes chronic infections in humans (e.g. HIV, HCV, Flaviviruses). In the recent past, an exponential increase in the number of available three-dimensional protein structures (>150000 in Protein Data Bank), allowed us to better understand the molecular mechanism of action of protein targets and antivirals. Advancements in the in silico approaches paved the way to design and develop several novels, highly specific small-molecule inhibitors targeting the viral proteins.
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Affiliation(s)
| | - Selvaraj Tamilarasan
- Section of Microbial Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Kaushik Rajaram
- Department of Microbiology, Central University of Tamil Nadu, Thiruvarur, India
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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21
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Eng H, Bi YA, West MA, Ryu S, Yamaguchi E, Kosa RE, Tess DA, Griffith DA, Litchfield J, Kalgutkar AS, Varma MVS. Organic Anion-Transporting Polypeptide 1B1/1B3-Mediated Hepatic Uptake Determines the Pharmacokinetics of Large Lipophilic Acids: In Vitro-In Vivo Evaluation in Cynomolgus Monkey. J Pharmacol Exp Ther 2021; 377:169-180. [PMID: 33509903 DOI: 10.1124/jpet.120.000457] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 12/22/2022] Open
Abstract
It is generally presumed that uptake transport mechanisms are of limited significance in hepatic clearance for lipophilic or high passive-permeability drugs. In this study, we evaluated the mechanistic role of the hepato-selective organic anion-transporting polypeptides (OATPs) 1B1/1B3 in the pharmacokinetics of compounds representing large lipophilic acid space. Intravenous pharmacokinetics of 16 compounds with molecular mass ∼400-730 Da, logP ∼3.5-8, and acid pKa <6 were obtained in cynomolgus monkey after dosing without and with a single-dose rifampicin-OATP1B1/1B3 probe inhibitor. Rifampicin (30 mg/kg oral) significantly (P < 0.05) reduced monkey clearance and/or steady-state volume of distribution (VDss) for 15 of 16 acids evaluated. Additionally, clearance of danoprevir was reduced by about 35%, although statistical significance was not reached. A significant linear relationship was noted between the clearance ratio (i.e., ratio of control to treatment groups) and VDss ratio, suggesting hepatic uptake contributes to the systemic clearance and distribution simultaneously. In vitro transport studies using primary monkey and human hepatocytes showed uptake inhibition by rifampicin (100 µM) for compounds with logP ≤6.5 but not for the very lipophilic acids (logP > 6.5), which generally showed high nonspecific binding in hepatocyte incubations. In vitro uptake clearance and fraction transported by OATP1B1/1B3 (ft,OATP1B) were found to be similar in monkey and human hepatocytes. Finally, for compounds with logP ≤6.5, good agreement was noted between in vitro ft,OATP1B and clearance ratio (as well as VDss ratio) in cynomolgus monkey. In conclusion, this study provides mechanistic evidence for the pivotal role of OATP1B-mediated hepatic uptake in the pharmacokinetics across a wide, large lipophilic acid space. SIGNIFICANCE STATEMENT: This study provides mechanistic insight into the pharmacokinetics of a broad range of large lipophilic acids. Organic anion-transporting polypeptides 1B1/1B3-mediated hepatic uptake is of key importance in the pharmacokinetics and drug-drug interactions of almost all drugs and new molecular entities in this space. Diligent in vitro and in vivo transport characterization is needed to avoid the false negatives often noted because of general limitations in the in vitro assays while handling compounds with such physicochemical attributes.
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Affiliation(s)
- Heather Eng
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Yi-An Bi
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Mark A West
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Sangwoo Ryu
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Emi Yamaguchi
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Rachel E Kosa
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - David A Tess
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - David A Griffith
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - John Litchfield
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Amit S Kalgutkar
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
| | - Manthena V S Varma
- ADME Sciences, Medicine Design, Worldwide Research and Development, Pfizer Inc., Groton, Connecticut (H.E., Y.B., M.A.W., S.R., E.Y., R.E.K., M.V.S.V.), and PDM (D.A.T., J.L., A.S.K.) and Medicinal Chemistry, Medicine Design, Worldwide Research and Development (D.A.G.), Pfizer Inc., Cambridge, Massachusetts
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22
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Boonma T, Nutho B, Darai N, Rungrotmongkol T, Nunthaboot N. Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study. J Biomol Struct Dyn 2021; 40:5283-5294. [PMID: 33430709 DOI: 10.1080/07391102.2020.1869587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Hepatitis C virus (HCV) NS3/4A serine protease is a promising drug target for the discovery of anti-HCV drugs. However, its amino acid mutations, particularly A156T, commonly lead to rapid emergence of drug resistance. Paritaprevir and glecaprevir, the newly FDA-approved HCV drugs, exhibit distinct resistance profiles against the A156T mutation of HCV NS3/4A serine protease. To illustrate their different molecular resistance mechanisms, molecular dynamics simulations and binding free energy calculations were carried out on the two compounds complexed with both wild-type (WT) and A156T variants of HCV NS3/4A protease. QM/MM-GBSA-based binding free energy calculations revealed that the binding affinities of paritaprevir and glecaprevir towards A156T NS3/4A were significantly reduced by ∼4 kcal/mol with respect to their WT complexes, which were in line with the experimental resistance folds. Moreover, the relatively weak intermolecular interactions with amino acids such as H57, R155, and T156 of NS3 protein, the steric effect and the destabilized protein binding surface, which is caused by the loss of salt bridge between R123 and D168, are the main contributions for the higher fold-loss in potency of glecaprevir due to A156T mutation. An insight into the difference of molecular mechanism of drug resistance against the A156T substitution among the two classes of serine protease inhibitors could be useful for further optimization of new generation HCV NS3/4A inhibitors with enhanced inhibitory potency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thitiya Boonma
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nitchakan Darai
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand.,Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Nadtanet Nunthaboot
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.,Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
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23
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Xiao L, Wu X, Zhang F, Wang J, Xu X, Li L. Changes of inflammatory cytokines/chemokines during ravidasvir plus ritonavir-boosted danoprevir and ribavirin therapy for patients with genotype 1b hepatitis C infection. J Med Virol 2020; 92:3516-3524. [PMID: 32525562 DOI: 10.1002/jmv.26161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/05/2020] [Accepted: 06/07/2020] [Indexed: 01/02/2023]
Abstract
This study investigated the safety and efficacy of ravidasvir (RDV) plus ritonavir-boosted danoprevir (DNVr) and ribavirin (RBV) regimens for treatment-naïve non-cirrhotic patients with hepatitis C virus (HCV) genotype 1b in mainland China. We also gained insight into HCV-host interactions during anti-HCV treatment. 16 patients with HCV and 10 healthy people enrolled the study. Three of 16 patients received 12-weeks' placebo treatment first and served as the placebo controls. All (n = 16) patients received 12-weeks' RDV plus DNVr and RBV treatment. The adverse effects (AEs), viral loads, alanine transaminase, and aspartate aminotransferase were recorded during study. We also performed multianalyte profiling of 48 cytokines/chemokines in 16 patients with HCV and 10 normal controls. Seventy-five percent patients treated with RDV plus DNVr and RBV experienced AEs. No death, treatment-related serious AEs or AEs leading to discontinuation were reported. The serum HCV-RNA levels remained extremely high in 3 placebo controls after treated with placebo. After RDV plus DNVr and RBV treatment, all patients achieved sustained virologic response (SVR) at posttreatment week 12, but 1 patient experienced viral relapse at SVR 24. The cytokine/chemokine expression pattern was markedly altered in patients with HCV as compared with healthy controls. The interferon-inducible protein-10 (IP-10) decreased after anti-HCV treatment, and dramatically increased in one patient with viral relapse. The regimen of RDV and DNVr plus RBV represents a highly safe and effective treatment option for HCV patients in mainland China. The IP-10 has the potential to be an indicator of innate immune viral recognition.
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Affiliation(s)
- Lanlan Xiao
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoxin Wu
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Fen Zhang
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Wang
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaowei Xu
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- Infections Department, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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24
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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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25
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Kouznetsov VV. COVID-19 treatment: Much research and testing, but far, few magic bullets against SARS-CoV-2 coronavirus. Eur J Med Chem 2020; 203:112647. [PMID: 32693298 PMCID: PMC7362854 DOI: 10.1016/j.ejmech.2020.112647] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/13/2022]
Abstract
The new virus of the of β-Coronaviruses genus, SARS-CoV-2, is the causative agent of coronavirus disease-2019 (COVID-19) and is winning a proverbial chess match against all players simultaneous, including physicians, clinicians, pathologists, doctors, scientists, economists, athletes and politicians. The COVID-19 outbreak has seriously threatened public health, killing the most vulnerable persons and causing general panic. To stop this disease, effective remedies (i.e., drugs, vaccines, personal protection elements, etc.) are urgently required. Unfortunately, no registered specific therapies (including antiviral therapies, immune-modulating agents and vaccines) are currently available to treat coronavirus infections, highlighting an urgent need for therapeutics targeting SARS-CoV-2. In this work, fourteen existing small molecule drugs or/and experimental drugs selected by experts and examined from the point of view of bioavailability via the Lipinski-Veber rules and assessment of their physicochemical descriptors. The aim of this study is to discover selected pattern similarities and peculiar characteristics that could be useful for antiviral drug optimization, drug combination or new antiviral agent design.
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26
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Kouznetsov VV. COVID-19 treatment: Much research and testing, but far, few magic bullets against SARS-CoV-2 coronavirus. Eur J Med Chem 2020. [PMID: 32693298 DOI: 10.1016/j.ejmech.2020.112647.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The new virus of the of β-Coronaviruses genus, SARS-CoV-2, is the causative agent of coronavirus disease-2019 (COVID-19) and is winning a proverbial chess match against all players simultaneous, including physicians, clinicians, pathologists, doctors, scientists, economists, athletes and politicians. The COVID-19 outbreak has seriously threatened public health, killing the most vulnerable persons and causing general panic. To stop this disease, effective remedies (i.e., drugs, vaccines, personal protection elements, etc.) are urgently required. Unfortunately, no registered specific therapies (including antiviral therapies, immune-modulating agents and vaccines) are currently available to treat coronavirus infections, highlighting an urgent need for therapeutics targeting SARS-CoV-2. In this work, fourteen existing small molecule drugs or/and experimental drugs selected by experts and examined from the point of view of bioavailability via the Lipinski-Veber rules and assessment of their physicochemical descriptors. The aim of this study is to discover selected pattern similarities and peculiar characteristics that could be useful for antiviral drug optimization, drug combination or new antiviral agent design.
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Affiliation(s)
- Vladimir V Kouznetsov
- Laboratorio de Química Orgánica y Biomolecular, CMN, Universidad Industrial de Santander, Parque Tecnológico Guatiguará, Piedecuesta, 681011, Colombia.
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27
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Al-Horani RA, Kar S. Potential Anti-SARS-CoV-2 Therapeutics That Target the Post-Entry Stages of the Viral Life Cycle: A Comprehensive Review. Viruses 2020; 12:E1092. [PMID: 32993173 PMCID: PMC7600245 DOI: 10.3390/v12101092] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic continues to challenge health care systems around the world. Scientists and pharmaceutical companies have promptly responded by advancing potential therapeutics into clinical trials at an exponential rate. Initial encouraging results have been realized using remdesivir and dexamethasone. Yet, the research continues so as to identify better clinically relevant therapeutics that act either as prophylactics to prevent the infection or as treatments to limit the severity of COVID-19 and substantially decrease the mortality rate. Previously, we reviewed the potential therapeutics in clinical trials that block the early stage of the viral life cycle. In this review, we summarize potential anti-COVID-19 therapeutics that block/inhibit the post-entry stages of the viral life cycle. The review presents not only the chemical structures and mechanisms of the potential therapeutics under clinical investigation, i.e., listed in clinicaltrials.gov, but it also describes the relevant results of clinical trials. Their anti-inflammatory/immune-modulatory effects are also described. The reviewed therapeutics include small molecules, polypeptides, and monoclonal antibodies. At the molecular level, the therapeutics target viral proteins or processes that facilitate the post-entry stages of the viral infection. Frequent targets are the viral RNA-dependent RNA polymerase (RdRp) and the viral proteases such as papain-like protease (PLpro) and main protease (Mpro). Overall, we aim at presenting up-to-date details of anti-COVID-19 therapeutics so as to catalyze their potential effective use in fighting the pandemic.
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Affiliation(s)
- Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA;
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28
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Zhang W, Lv Y, Yang J, Chen Y, He Y, Huang J. Study Design Characteristics and Pharmacological Mechanisms in International Clinical Trials Registry Platform: Registered Clinical Trials on Antiviral Drugs for COVID-19. Drug Des Devel Ther 2020; 14:3803-3813. [PMID: 32982184 PMCID: PMC7509319 DOI: 10.2147/dddt.s272442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/20/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE This study aimed to evaluate the pharmacological mechanisms of antiviral drugs against the novel coronavirus disease (COVID-19) and the study designs in clinical trials registered with the International Clinical Trials Registry Platform (ICTRP). METHODS Clinical trials involving antiviral drugs for treating COVID-19 were retrieved from the ICTRP database. For each trial, the study design, number of participants, primary endpoints, source register, antiviral mechanism, and results were evaluated. RESULTS On June 10, 2020, 145 eligible clinical trials were retrieved from the ICTRP, of which 99 (68.3%) were randomized trials, 109 (75.2%) were parallel assignment trials, 38 (26.2%) were double or single blinded, 130 (89.7%) involved two groups, and 75 (51.6%) included more than 100 participants; and clinical improvement or recovery and virus-negative conversion were the two most common endpoints, accounting for 40.7% and 18.6%, respectively. The drugs were divided according to the antiviral mechanism into HIV reverse transcriptase inhibitors, RNA-dependent RNA polymerase inhibitors, HIV protease inhibitors (PIs), hepatitis C virus NS3 PIs, and anti-influenza drugs. CONCLUSION The design characteristics of clinical trials of antiviral drugs for treating COVID-19 as well as the mechanism of action and antiviral efficacy of the drugs were evaluated in this study. The results of these trials could constitute a reference for future clinical trials to be executed on COVID-19 treatment and prevention.
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Affiliation(s)
- Weilong Zhang
- Center for Drug Clinical Research, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, People’s Republic of China
| | - Yinghua Lv
- Center for Drug Clinical Research, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, People’s Republic of China
| | - Juan Yang
- Center for Drug Clinical Research, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, People’s Republic of China
| | - Yunhui Chen
- College of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu610075, People’s Republic of China
| | - Yingchun He
- Center for Drug Clinical Research, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, People’s Republic of China
| | - Jihan Huang
- Center for Drug Clinical Research, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai201203, People’s Republic of China
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29
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Sahebnasagh A, Avan R, Saghafi F, Mojtahedzadeh M, Sadremomtaz A, Arasteh O, Tanzifi A, Faramarzi F, Negarandeh R, Safdari M, Khataminia M, Rezai Ghaleno H, Habtemariam S, Khoshi A. Pharmacological treatments of COVID-19. Pharmacol Rep 2020; 72:1446-1478. [PMID: 32816200 PMCID: PMC7439639 DOI: 10.1007/s43440-020-00152-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023]
Abstract
The viral infection due to the new coronavirus or coronavirus disease 2019 (COVID-19), which was reported for the first time in December 2019, was named by the World Health Organization (WHO) as Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV2), because of the very similar genome and also its related symptoms to SARS-CoV1. The ongoing COVID-19 pandemic with significant mortality, morbidity, and socioeconomic impact is considered by the WHO as a global public health emergency. Since there is no specific treatment available for SARS-CoV2 infection, and or COVID-19, several clinical and sub-clinical studies are currently undertaken to find a gold-standard therapeutic regimen with high efficacy and low side effect. Based on the published scientific evidence published to date, we summarized herein the effects of different potential therapies and up-to-date clinical trials. The review is intended to help readers aware of potentially effective COVID-19 treatment and provide useful references for future studies.
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Affiliation(s)
- Adeleh Sahebnasagh
- Clinical Research Center, Department of Internal Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Razieh Avan
- Department of Clinical Pharmacy, Medical Toxicology and Drug Abuse Research Center (MTDRC), Faculty of Pharmacy, Birjand University of Medical Sciences, Birjand, Iran
| | - Fatemeh Saghafi
- Department of Clinical Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mojataba Mojtahedzadeh
- Department of Clinical Pharmacy, Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Afsaneh Sadremomtaz
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD, Groningen, The Netherlands
| | - Omid Arasteh
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Asal Tanzifi
- Sepanta Faragene Azma Research Laboratory. Co. LTD., Gorgan, Iran.,Department of Parasitology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Fatemeh Faramarzi
- Clinical Pharmacy Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Negarandeh
- Student Research Committee, Department of Pharmaceutics, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammadreza Safdari
- Department of Orthopedic Surgery, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Masoud Khataminia
- Student Research Committee, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Rezai Ghaleno
- Department of Surgery, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories and Herbal Analysis Services, University of Greenwich, Central Avenue, Chatham-Maritime, Kent, ME4 4TB, UK
| | - Amirhosein Khoshi
- Department of Clinical Biochemistry, School of Medicine, North Khorasan University of Medical Sciences, Arkan roadway, Bojnurd, Iran.
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30
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Wei B, Hang X, Xie Y, Zhang Y, Wang J, Cao X, Wu JJ, Wang J. Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports. Rev Soc Bras Med Trop 2020; 53:e20200372. [PMID: 32696811 PMCID: PMC7375796 DOI: 10.1590/0037-8682-0372-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/03/2020] [Indexed: 11/22/2022] Open
Abstract
Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a pandemic. We herein report four COVID-19 cases with long-term positive viral ribonucleic acid (RNA) for about 61 days. Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA.
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Affiliation(s)
- Bo Wei
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Xiaofeng Hang
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Ying Xie
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Yuanjing Zhang
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Jianrong Wang
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Xinghao Cao
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
| | - Jinzi J. Wu
- Ascletis Bioscience Co., Ltd., Hangzhou 310051, Zhejiang Province, China
- Ascletis Pharmaceuticals Co., Ltd., Shaoxing 310051, Zhejiang Province, China
| | - Junxue Wang
- Department of infectious diseases, Changzheng Hospital, Naval Medical University, China
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31
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Miao M, Jing X, De Clercq E, Li G. Danoprevir for the Treatment of Hepatitis C Virus Infection: Design, Development, and Place in Therapy. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:2759-2774. [PMID: 32764876 PMCID: PMC7368560 DOI: 10.2147/dddt.s254754] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
On June 8, 2018, an NS3/4A protease inhibitor called danoprevir was approved in China to treat the infections of HCV genotype (GT) 1b – the most common HCV genotype worldwide. Based on phase 2 and 3 clinical trials, the 12-week regimen of ritonavir-boosted danoprevir (danoprevir/r) plus peginterferon alpha-2a and ribavirin offered 97.1% (200/206) of sustained virologic response at post-treatment week 12 (SVR12) in treatment-naïve non-cirrhotic patients infected with HCV genotype 1b. Adverse events such as anemia, fatigue, fever, and headache were associated with the inclusion of peginterferon alpha-2a and ribavirin in the danoprevir-based regimen. Moreover, drug resistance to danoprevir could be traced to amino acid substitutions (Q80K/R, R155K, D168A/E/H/N/T/V) near the drug-binding pocket of HCV NS3 protease. Despite its approval, the clinical use of danoprevir is currently limited to its combination with peginterferon alpha-2a and ribavirin, thereby driving its development towards interferon-free, ribavirin-free regimens with improved tolerability and adherence. In the foreseeable future, pan-genotypic direct-acting antivirals with better clinical efficacy and less adverse events will be available to treat HCV infections worldwide.
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Affiliation(s)
- Miao Miao
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, People's Republic of China
| | - Xixi Jing
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, People's Republic of China
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, People's Republic of China
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32
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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33
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Mei H, Han J, White S, Graham DJ, Izawa K, Sato T, Fustero S, Meanwell NA, Soloshonok VA. Tailor-Made Amino Acids and Fluorinated Motifs as Prominent Traits in Modern Pharmaceuticals. Chemistry 2020; 26:11349-11390. [PMID: 32359086 DOI: 10.1002/chem.202000617] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/23/2020] [Indexed: 12/11/2022]
Abstract
Structural analysis of modern pharmaceutical practices allows for the identification of two rapidly growing trends: the introduction of tailor-made amino acids and the exploitation of fluorinated motifs. Curiously, the former represents one of the most ubiquitous classes of naturally occurring compounds, whereas the latter is the most xenobiotic and comprised virtually entirely of man-made derivatives. Herein, 39 selected compounds, featuring both of these traits in the same molecule, are profiled. The total synthesis, source of the corresponding amino acids and fluorinated residues, and medicinal chemistry aspects and biological properties of the molecules are discussed.
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Affiliation(s)
- Haibo Mei
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Jianlin Han
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, P.R. China
| | - Sarah White
- Oakwood Chemical, Inc., 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Daniel J Graham
- Oakwood Chemical, Inc., 730 Columbia Hwy. N, Estill, SC, 29918, USA
| | - Kunisuke Izawa
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Tatsunori Sato
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Santos Fustero
- Departamento de Química Orgánica, Universidad de Valencia, 46100, Burjassot, Valencia, Spain
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ, 08543-4000, USA
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, Plaza Bizkaia, 48013, Bilbao, Spain
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Tallorin L, Villareal VA, Hsia CY, Rodgers MA, Burri DJ, Pfeil MP, Llopis PM, Lindenbach BD, Yang PL. Hepatitis C virus NS3-4A protease regulates the lipid environment for RNA replication by cleaving host enzyme 24-dehydrocholesterol reductase. J Biol Chem 2020; 295:12426-12436. [PMID: 32641492 PMCID: PMC7458815 DOI: 10.1074/jbc.ra120.013455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Many RNA viruses create specialized membranes for genome replication by manipulating host lipid metabolism and trafficking, but in most cases, we do not know the molecular mechanisms responsible or how specific lipids may impact the associated membrane and viral process. For example, hepatitis C virus (HCV) causes a specific, large-fold increase in the steady-state abundance of intracellular desmosterol, an immediate precursor of cholesterol, resulting in increased fluidity of the membrane where HCV RNA replication occurs. Here, we establish the mechanism responsible for HCV's effect on intracellular desmosterol, whereby the HCV NS3-4A protease controls activity of 24-dehydrocholesterol reductase (DHCR24), the enzyme that catalyzes conversion of desmosterol to cholesterol. Our cumulative evidence for the proposed mechanism includes immunofluorescence microscopy experiments showing co-occurrence of DHCR24 and HCV NS3-4A protease; formation of an additional, faster-migrating DHCR24 species (DHCR24*) in cells harboring a HCV subgenomic replicon RNA or ectopically expressing NS3-4A; and biochemical evidence that NS3-4A cleaves DHCR24 to produce DHCR24* in vitro and in vivo. We further demonstrate that NS3-4A cleaves DHCR24 between residues Cys91 and Thr92 and show that this reduces the intracellular conversion of desmosterol to cholesterol. Together, these studies demonstrate that NS3-4A directly cleaves DHCR24 and that this results in the enrichment of desmosterol in the membranes where NS3-4A and DHCR24 co-occur. Overall, this suggests a model in which HCV directly regulates the lipid environment for RNA replication through direct effects on the host lipid metabolism.
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Affiliation(s)
- Lorillee Tallorin
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Valerie A Villareal
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chih-Yun Hsia
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mary A Rodgers
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Dominique J Burri
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Marc-Philipp Pfeil
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Paula Montero Llopis
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale Medical School, New Haven, Connecticut, USA
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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35
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Tinworth CP, Young RJ. Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data. J Med Chem 2020; 63:10091-10108. [PMID: 32324397 DOI: 10.1021/acs.jmedchem.9b01596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.
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Affiliation(s)
- Christopher P Tinworth
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.,Blue Burgundy Ltd., Bedford, Bedfordshire MK45 2AD, U.K
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36
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Flick AC, Leverett CA, Ding HX, McInturff E, Fink SJ, Helal CJ, DeForest JC, Morse PD, Mahapatra S, O’Donnell CJ. Synthetic Approaches to New Drugs Approved during 2018. J Med Chem 2020; 63:10652-10704. [DOI: 10.1021/acs.jmedchem.0c00345] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Andrew C. Flick
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Carolyn A. Leverett
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hong X. Ding
- Pharmacodia (Beijing) Co., Ltd., Beijing 100085, China
| | - Emma McInturff
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sarah J. Fink
- Takeda Pharmaceutical Company Limited, 125 Binney Street, Cambridge, Massachusetts 02142, United States
| | | | - Jacob C. DeForest
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Peter D. Morse
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Subham Mahapatra
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christopher J. O’Donnell
- Groton Laboratories, Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
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37
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Vafina GF, Khanova MD. Synthesis of Cyclopropylmethyl Esters of Maleopimaric Acid and Diketocage Derivatives of Quinopimaric Acid by a Catalytic Reaction of the Corresponding Allyl Esters with Diazomethane. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020020293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Omar AM, Elfaky MA, Arold ST, Soror SH, Khayat MT, Asfour HZ, Bamane FH, El-Araby ME. 1 H-Imidazole-2,5-Dicarboxamides as NS4A Peptidomimetics: Identification of a New Approach to Inhibit HCV-NS3 Protease. Biomolecules 2020; 10:E479. [PMID: 32245218 PMCID: PMC7175367 DOI: 10.3390/biom10030479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
The nonstructural (NS) protein NS3/4A protease is a critical factor for hepatitis C virus (HCV) maturation that requires activation by NS4A. Synthetic peptide mutants of NS4A were found to inhibit NS3 function. The bridging from peptide inhibitors to heterocyclic peptidomimetics of NS4A has not been considered in the literature and, therefore, we decided to explore this strategy for developing a new class of NS3 inhibitors. In this report, a structure-based design approach was used to convert the bound form of NS4A into 1H-imidazole-2,5-dicarboxamide derivatives as first generation peptidomimetics. This scaffold mimics the buried amino acid sequence Ile-25` to Arg-28` at the core of NS4A21`-33` needed to activate the NS3 protease. Some of the synthesized compounds (Coded MOC) were able to compete with and displace NS4A21`-33` for binding to NS3. For instance, N5-(4-guanidinobutyl)-N2-(n-hexyl)-1H-imidazole-2,5-dicarboxamide (MOC-24) inhibited the binding of NS4A21`-33` with a competition half maximal inhibitory concentration (IC50) of 1.9 ± 0.12 µM in a fluorescence anisotropy assay and stabilized the denaturation of NS3 by increasing the aggregation temperature (40% compared to NS4A21`-33`). MOC-24 also inhibited NS3 protease activity in a fluorometric assay. Molecular dynamics simulations were conducted to rationalize the differences in structure-activity relationship (SAR) between the active MOC-24 and the inactive MOC-26. Our data show that MOC compounds are possibly the first examples of NS4A peptidomimetics that have demonstrated promising activities against NS3 proteins.
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Affiliation(s)
- Abdelsattar M. Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Mahmoud A. Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia;
| | - Stefan T. Arold
- Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia;
| | - Sameh H. Soror
- Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo 11795, Egypt;
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, Cairo 11795, Egypt
| | - Maan T. Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
| | - Hani Z. Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Faida H. Bamane
- Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Moustafa E. El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia; (A.M.O.); (M.T.K.)
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Hu K, Zhu Z, Mathahs MM, Tran H, Bommer J, Testa CA, Schmidt WN. Metalloprotoporphyrin Inhibition of HCV NS3-4A Protease: Structure-Activity Relationships. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:757-771. [PMID: 32158194 PMCID: PMC7048954 DOI: 10.2147/dddt.s201089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022]
Abstract
Background Antiviral actions of tetrapyrroles have been described in a number of systems. Our goal was to evaluate antagonism of the HCV NS3-4A protease by a variety of common porphyrins and characterize structure-activity relationships that may be useful for future drug design of HCV and related Flaviviruses. Methods Using fluorometric assays, common metalloprotoporphyrins (MPP) all inhibited NS3-4A protease with IC50 values in low micromolar ranges [CoPP (1.4 µM) < ZnPP = MnPP = SnPP < CuPP < FePP (6.5 µM) = protoporphyrin]. Results Lineweaver-Burk plots confirmed that MPP: NS3 inhibition was basically competitive. All tested MPPs inhibited HCV genotype 1A, 1B, 2A and 3A recombinant proteases with the same fidelity suggesting wide antagonistic capabilities. However, when the MPPs were tested in cellular incubations with HCV replicons only Zn, Fe and free-base protoporphyrin showed comparable EC50 and IC50 values suggesting that there may be critical differences in MPP uptake and intracellular availability. Meso, deutero, and isohematoporphyrin derivatives, with or without metal substitution, all showed less anti-protease and antiviral activities as compared to protoporphyrins, suggesting that the planar, vinyl side chains are important for protease active site binding. MPPs were also active against three common protease mutants (T54A, A156T, and V36M) with equivalent or better IC50 values as compared to wild type enzyme. Conclusion These findings document the versatility of MPPs as antiviral agents with an expanded sensitivity for HCV genotypes and resistance to some common viral mutations. The results also suggest that further study of MPP structure and function will be useful for the development of new antiviral agents.
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Affiliation(s)
- Katherine Hu
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA 52246, USA.,Department of Internal Medicine of the Roy G. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Zhaowen Zhu
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA 52246, USA.,Department of Internal Medicine of the Roy G. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Meleah M Mathahs
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA 52246, USA.,Department of Internal Medicine of the Roy G. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Huy Tran
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA 52246, USA.,Department of Internal Medicine of the Roy G. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jerry Bommer
- Frontier Scientific, Logan, UT 84321, USA.,Echelon Biosciences Inc, Salt Lake City, UT 84108, USA
| | | | - Warren N Schmidt
- Department of Internal Medicine and Research Service, Veterans Affairs Medical Center, Iowa City, IA 52246, USA.,Department of Internal Medicine of the Roy G. And Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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40
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El-Araby ME, Omar AM, Soror SH, Arold ST, Khayat MT, Asfour HZ, Bamane F, Elfaky MA. Synthetic bulky NS4A peptide variants bind to and inhibit HCV NS3 protease. J Adv Res 2020; 24:251-259. [PMID: 32373358 PMCID: PMC7195562 DOI: 10.1016/j.jare.2020.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/03/2019] [Accepted: 01/02/2020] [Indexed: 01/21/2023] Open
Abstract
NS4A is a non-structural multi-tasking small peptide that is essential for HCV maturation and replication. The central odd-numbered hydrophobic residues of NS4A (Val-23‘ to Leu-31‘)i are essential for activating NS3 upon NS3/4A protease complex formation. This study aims to design new specific allosteric NS3/4A protease inhibitors by mutating Val-23‘, Ile-25‘, and Ile-29‘ into bulkier amino acids. Pep-15, a synthetic peptide, showed higher binding affinity towards HCV-NS3 subtype-4 than native NS4A. The Kd of Pep-15 (80.0 ± 8.0 nM) was twice as high as that of native NS4A (169 ± 37 nM). The mutant Pep-15 inhibited the catalytic activity of HCV-NS3 by forming an inactive complex. Molecular dynamics simulations suggested that a cascade of conformational changes occurred, especially in the catalytic triad arrangements, thereby inactivating NS3. A large shift in the position of Ser-139 was observed, leading to loss of critical hydrogen bonding with His-57. Even though this study is not a classic drug discovery study—nor do we propose Pep-15 as a drug candidate—it serves as a stepping stone towards developing a potent inhibitor of hitherto untargeted HCV subtypes.
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Affiliation(s)
- Moustafa E El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Abdelsattar M Omar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Sameh H Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt.,Center for Scientific Excellence Helwan Structural Biology Research (HSBR), Faculty of Pharmacy, Helwan University, Ain Helwan, P.O. 11795, Cairo, Egypt
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal 23955-6900, Saudi Arabia
| | - Maan T Khayat
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
| | - Hani Z Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Faida Bamane
- Department of Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mahmoud A Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Alsulaymanyah, Jeddah 21589, Saudi Arabia
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41
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Peng C, Atilaw Y, Wang J, Xu Z, Poongavanam V, Shi J, Kihlberg J, Zhu W, Erdélyi M. Conformation of the Macrocyclic Drug Lorlatinib in Polar and Nonpolar Environments: A MD Simulation and NMR Study. ACS OMEGA 2019; 4:22245-22250. [PMID: 31891108 PMCID: PMC6933765 DOI: 10.1021/acsomega.9b03797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 05/02/2023]
Abstract
The replica exchange molecular dynamics (REMD) simulation is demonstrated to readily predict the conformations of the macrocyclic drug lorlatinib, as validated by solution NMR studies. In aqueous solution, lorlatinib adopts a conformer identical to its target bound structure. This conformer is stabilized by an extensive hydrogen bond network to the solvents. In chloroform, lorlatinib populates two conformers with the second one being less polar, which may contribute to lorlatinib's ability to cross cell membranes.
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Affiliation(s)
- Cheng Peng
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yoseph Atilaw
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jinan Wang
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhijian Xu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | | | - Jiye Shi
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jan Kihlberg
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Weiliang Zhu
- Drug
Discovery and Design Center; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy
of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- E-mail: (W.Z.)
| | - Máté Erdélyi
- Department
of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- E-mail: (M.E.)
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42
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Boonma T, Nutho B, Rungrotmongkol T, Nunthaboot N. Understanding of the drug resistance mechanism of hepatitis C virus NS3/4A to paritaprevir due to D168N/Y mutations: A molecular dynamics simulation perspective. Comput Biol Chem 2019; 83:107154. [PMID: 31751885 DOI: 10.1016/j.compbiolchem.2019.107154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/26/2019] [Accepted: 10/21/2019] [Indexed: 02/08/2023]
Abstract
Hepatitis C virus (HCV) NS3/4A protease is an attractive target for the development of antiviral therapy. However, the evolution of antiviral drug resistance is a major problem for treatment of HCV infected patients. Understanding of drug-resistance mechanisms at molecular level is therefore very important for the guidance of further design of antiviral drugs with high efficiency and specificity. Paritaprevir is a potent inhibitor against HCV NS3/4A protease genotype 1a. Unfortunately, this compound is highly susceptible to the substitution at D168 in the protease. In this work, molecular dynamics simulations of paritaprevir complexed with wild-type (WT) and two mutated strains (D168 N and D168Y) were carried out. Due to such mutations, the inhibitor-protein hydrogen bonding between them was weakened and the salt-bridge network among residues R123, R155 and D168 responsible for inhibitor binding was disrupted. Moreover, the per-residue free energy decomposition suggested that the main contributions from key residues such as Q80, V132, K136, G137 and R155 were lost in the D168 N/Y mutations. These lead to a lower binding affinity of paritaprevir for D168 N/Y variants of the HCV NS3/4A protease, consistent with the experimental data. This detailed information could be useful for further design of high potency anti-HCV NS3/4A inhibitors.
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Affiliation(s)
- Thitiya Boonma
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand; Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nadtanet Nunthaboot
- Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand; Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand.
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43
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Meewan I, Zhang X, Roy S, Ballatore C, O’Donoghue AJ, Schooley RT, Abagyan R. Discovery of New Inhibitors of Hepatitis C Virus NS3/4A Protease and Its D168A Mutant. ACS OMEGA 2019; 4:16999-17008. [PMID: 31646247 PMCID: PMC6796237 DOI: 10.1021/acsomega.9b02491] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/02/2019] [Indexed: 06/01/2023]
Abstract
Hepatitis C virus (HCV) is a human pathogen with high morbidity. The HCV NS3/4A protease is essential for viral replication and is one of the top three drug targets. Several drugs targeting the protease have been developed, but drug-resistant mutant strains emerged. Here, we screened a library and synthesized a novel class of small molecules based on a tryptophan derivative scaffold identified as HCV NS3/4A protease inhibitors that are active against both wild type and mutant form of the protease. Only the compounds with predicted binding poses not affected by the most frequent mutations in the active site were selected for experimental validation. The antiviral activities were evaluated by replicon and enzymatic assays. Twenty-two compounds were found to inhibit HCV with EC50 values ranging between 0.64 and 63 μM with compound 22 being the most active. In protease assays, 22 had a comparable inhibition profile for the common mutant HCV GT1b D168A and the wild-type enzyme. However, in the same assay, the potency of the approved drug, simeprevir, decreased 5.7-fold for the mutant enzyme relative to the wild type. The top three inhibitors were also tested against four human serine proteases and were shown to be specific to the viral protease. The fluorescence-based cell viability assay demonstrated a sufficient therapeutic range for the top three candidates.
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Affiliation(s)
- Ittipat Meewan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Xingquan Zhang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Suchismita Roy
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Carlo Ballatore
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Robert T. Schooley
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
| | - Ruben Abagyan
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, Department of Chemistry
and Biochemistry, and School of Medicine, University
of California San Diego, La Jolla, California 92093, United States
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44
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Wei L, Shang J, Ma Y, Xu X, Huang Y, Guan Y, Duan Z, Zhang W, Gao Z, Zhang M, Li J, Jia J, Yang Y, Wen X, Wang M, Jia Z, Ning B, Chen Y, Qi Y, Du J, Jiang J, Tong L, Xie Y, Wu JJ. Efficacy and Safety of 12-week Interferon-based Danoprevir Regimen in Patients with Genotype 1 Chronic Hepatitis C. J Clin Transl Hepatol 2019; 7:221-225. [PMID: 31608213 PMCID: PMC6783684 DOI: 10.14218/jcth.2019.00018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/12/2019] [Accepted: 06/30/2019] [Indexed: 02/05/2023] Open
Abstract
Background and Aims: Genotype (GT) 1 remains the predominant hepatitis c virus (HCV) GT in Chinese patients. Over 80% of those Chinese patients harbor the interferon-sensitive CC allele of IFNL4rs12979860, which is favorable for interferon-based treatment regimens. This phase III clinical trial aimed to evaluate the efficacy and safety of the ritonavir-boosted danoprevir plus pegylated-interferon α-2a and ribavirin regimen for 12 weeks in treatment-naïve mainland Chinese patients infected with HCV GT1 without cirrhosis. Methods: One hundred and forty-one treatment-naïve, non-cirrhotic HCV GT1 Chinese patients (age ≥18 years) were enrolled for this single-arm, multicenter, phase III MANASA study (NCT03020082). Patients received a combination of ritonavir-boosted danoprevir (100 mg/100 mg) twice a day plus subcutaneous injection of weekly pegylated-interferon α-2a (180 μg) and oral ribavirin (1000/1200 mg/day body weight <75/≥75 kg) for 12 weeks. The primary end-point was sustained virologic response rate at 12 weeks after the end of treatment. The secondary end-points were safety outcomes, tolerability, virologic response over time and relapse rate. Results: All enrolled patients were HCV GT1-infected, and most among them (97.9%, 123/141) had the HCV GT1b subtype. Single-nucleotide polymorphism test showed that the majority of patients were of the IFNL4 rs12979860 CC genotype (87.2%, 123/141). Overall, 140 patients completed the 12-week treatment, and 97.1% (136/140) patients achieved sustained virologic response at 12 weeks (per protocol population group, 95% confidence interval: 92.9-99.2%). Only drug-related serious adverse event occurred. Most of the adverse events were grade 1 and grade 2 alanine aminotransferase elevation or liver dysfunction. One patient discontinued treatment because of severe head injury in a car accident. Conclusions: The triple regimen of ritonavir-boosted danoprevir plus pegylated-interferon α-2a and ribavirin produced a sustained virologic response rate of 97.1% after 12 weeks treatment in noncirrhotic HCV GT1-infected Chinese patients, and was safe and well tolerated. Trial Registration Clinical-Trials.gov Identifier: NCT03020082.
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Affiliation(s)
- Lai Wei
- Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, China
- Correspondence to: Lai Wei, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing 100191, China. Tel: +86-1-88326666, Fax: +86-1-68318386, E-mail:
| | - Jia Shang
- People’s Hospital of Henan Province, Henan, China
| | - Yuanji Ma
- West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyuan Xu
- Peking University People’s Hospital, Beijing, China
| | - Yan Huang
- Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yujuan Guan
- Guangzhou Eighth People’s Hospital, Guangzhou, Guangdong, China
| | - Zhongping Duan
- Artificial Liver Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | | | - Zhiliang Gao
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mingxiang Zhang
- The Sixth People’s Hospital of Shenyang, Shenyang, Liaoning, China
| | - Jun Li
- People’s Hospital of Jiangsu Province, Nanjing, Jiangsu, China
| | - Jidong Jia
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yongfeng Yang
- Nanjing Medical University Affiliated Second Hospital, Nanjing, Jiangsu, China
| | | | - Maorong Wang
- Liver Disease Center of PLA, The 81st Hospital of PLA, Nanjing, Jiangsu, China
| | - Zhansheng Jia
- Tangdu Hospital, Air Force Medical University, Xi’an, Shaanxi, China
| | - Bo Ning
- Baoji Central Hospital, Baoji, Shaanxi, China
| | - Yongping Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yue Qi
- The First Hospital Affiliated to Jilin University, Changchun, Jilin, China
| | - Jie Du
- The First Hospital of Changsha, Changsha, Hunan, China
| | - Jianning Jiang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lixin Tong
- The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yao Xie
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jinzi J. Wu
- Ascletis BioScience Co., Ltd., Hangzhou, Zhejiang, China
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Barros RPC, Scotti L, Scotti MT. Exploring Secondary Metabolites Database of Apocynaceae, Menispermaceae, and Annonaceae to Select Potential Anti-HCV Compounds. Curr Top Med Chem 2019; 19:900-913. [PMID: 31074368 DOI: 10.2174/1568026619666190510094228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Hepatitis C is a disease that constitutes a serious global health problem, is often asymptomatic and difficult to diagnose and about 60-80% of infected patients develop chronic diseases over time. As there is no vaccine against hepatitis C virus (HCV), developing new cheap treatments is a big challenge. OBJECTIVE The search for new drugs from natural products has been outstanding in recent years. The aim of this study was to combine structure-based and ligand-based virtual screening (VS) techniques to select potentially active molecules against four HCV target proteins from in-house secondary metabolite dataset (SistematX). MATERIALS AND METHODS From the ChEMBL database, we selected four sets of 1199, 355, 290 and 237chemical structures with inhibitory activity against different targets of HCV to create random forest models with an accuracy value higher than 82% for cross-validation and test sets. Afterward, a ligandbased virtual screen of the entire 1848 secondary metabolites database stored in SistematX was performed. In addition, a structure-based virtual screening was also performed for the same set of secondary metabolites using molecular docking. RESULTS Finally, using consensus analyses approach combining ligand-based and structure-based VS, three alkaloids were selected as potential anti-HCV compounds. CONCLUSION The selected structures are a starting point for further studies in order to develop new anti- HCV compounds based on natural products.
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Affiliation(s)
- Renata P C Barros
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
| | - Marcus T Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa, Brazil
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Taylor JG, Zipfel S, Ramey K, Vivian R, Schrier A, Karki KK, Katana A, Kato D, Kobayashi T, Martinez R, Sangi M, Siegel D, Tran CV, Yang ZY, Zablocki J, Yang CY, Wang Y, Wang K, Chan K, Barauskas O, Cheng G, Jin D, Schultz BE, Appleby T, Villaseñor AG, Link JO. Discovery of the pan-genotypic hepatitis C virus NS3/4A protease inhibitor voxilaprevir (GS-9857): A component of Vosevi ®. Bioorg Med Chem Lett 2019; 29:2428-2436. [PMID: 31133531 DOI: 10.1016/j.bmcl.2019.03.037] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022]
Abstract
Treatment of hepatitis C virus (HCV) infection has been historically challenging due the high viral genetic complexity wherein there are eight distinct genotypes and at least 86 viral subtypes. While HCV NS3/4A protease inhibitors are an established treatment option for genotype 1 infection, limited coverage of genotypes 2 and/or 3 combined with serum alanine transaminase (ALT) elevations for some compounds has limited the broad utility of this therapeutic class. Our discovery efforts were focused on identifying an NS3/4A protease inhibitor with pan-genotypic antiviral activity, improved coverage of resistance associated substitutions, and a decreased risk of hepatotoxicity. Towards this goal, distinct interactions with the conserved catalytic triad of the NS3/4A protease were identified that improved genotype 3 antiviral activity. We further discovered that protein adduct formation strongly correlated with clinical ALT elevation for this therapeutic class. Improving metabolic stability and decreasing protein adduct formation through structural modifications ultimately resulted in voxilaprevir. Voxilaprevir, in combination with sofosbuvir and velpatasvir, has demonstrated pan-genotypic antiviral clinical activity. Furthermore, hepatotoxicity was not observed in Phase 3 clinical trials with voxilaprevir, consistent with our design strategy. Vosevi® (sofosbuvir, velpatasvir, and voxilaprevir) is now an approved pan-genotypic treatment option for the most difficult-to-cure individuals who have previously failed direct acting antiviral therapy.
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Affiliation(s)
- James G Taylor
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States.
| | - Sheila Zipfel
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Kyla Ramey
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Randy Vivian
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Adam Schrier
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Kapil K Karki
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Ashley Katana
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Darryl Kato
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Tetsuya Kobayashi
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Ruben Martinez
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Michael Sangi
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Dustin Siegel
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Chinh V Tran
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Zheng-Yu Yang
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Jeff Zablocki
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Cheng Y Yang
- Drug Metabolism, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Yujin Wang
- Drug Metabolism, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Kelly Wang
- Drug Metabolism, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Katie Chan
- Biology, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Ona Barauskas
- Biology, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Guofeng Cheng
- Biology, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Debi Jin
- Biology, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Brian E Schultz
- Biology, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Todd Appleby
- Structural Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - Armando G Villaseñor
- Structural Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
| | - John O Link
- Medicinal Chemistry, Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, United States
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Cummings MD, Sekharan S. Structure-Based Macrocycle Design in Small-Molecule Drug Discovery and Simple Metrics To Identify Opportunities for Macrocyclization of Small-Molecule Ligands. J Med Chem 2019; 62:6843-6853. [DOI: 10.1021/acs.jmedchem.8b01985] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maxwell D. Cummings
- Janssen Research and Development, LLC, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Sivakumar Sekharan
- Cambridge Crystallographic Data Centre, 252 Nassau Street, Princeton, New Jersey 08542, United States
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Kammarabutr J, Mahalapbutr P, Nutho B, Kungwan N, Rungrotmongkol T. Low susceptibility of asunaprevir towards R155K and D168A point mutations in HCV NS3/4A protease: A molecular dynamics simulation. J Mol Graph Model 2019; 89:122-130. [PMID: 30884449 DOI: 10.1016/j.jmgm.2019.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 01/02/2023]
Abstract
Hepatitis C has become an important health problem that requires expensive treatment and leads to liver tumorigenesis. Hepatitis C virus (HCV), which is the main cause of hepatitis C, has a high mutation rate due to the lack of proofreading activity of the RNA polymerase enzyme. The NS3/4A serine protease is an important target for anti-HCV drug discovery and development because of its crucial role in the cleavage of the polypeptides involved in viral replication. In the present study, all-atom molecular dynamics simulation was performed to elucidate the effect of the single point mutations R155K and D168A in the HCV genotype 1 NS3/4A protease on the structural dynamics, molecular interactions and susceptibility of asunaprevir (ASV), a second-generation NS3/4A protease inhibitor. Principal component analysis indicated that these two mutations converted the direction of motion of residues 123, 155 and 168 in the binding pocket to significantly point outwards from ASV, resulting in a loss of the hydrogen bond network of residues R123···R155···D168. The free energy calculations based on different semiempirical QM/MM-GBSA methods revealed that the binding affinity of ASV with the two mutant forms of the NS3/4A protease was significantly decreased in the order of wild-type < R155K < D168A. This work provided useful structural information regarding the atomistic understanding of acquired drug resistance against ASV caused by the R155K and D168A mutations.
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Affiliation(s)
- Jirayu Kammarabutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Panupong Mahalapbutr
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Bodee Nutho
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Nawee Kungwan
- Department of Chemistry, Faculty of Science, Chiang Mai University, 239 Huay Kaew Road, Muang District, Chiang Mai, 50200, Thailand; Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand; Ph.D. Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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49
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Ji Y, Chen X, Chen H, Zhang X, Fan Z, Xie L, Ma B, Zhu C. Designing of acyl sulphonamide based quinoxalinones as multifunctional aldose reductase inhibitors. Bioorg Med Chem 2019; 27:1658-1669. [PMID: 30858026 DOI: 10.1016/j.bmc.2019.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/06/2019] [Indexed: 02/07/2023]
Abstract
A series of quinoxalinone scaffold-based acyl sulfonamides were designed as aldose reductase inhibitors and evaluated for aldose reductase (ALR2)/aldehyde reductase (ALR1) inhibition and antioxidation. Compounds 9b-g containing styryl side chains at C3-side exhibited good ALR2 inhibitory activity and selectivity. Of them, 9g demonstrated the most potent inhibitory activity with an IC50 value of 0.100 μM, and also exhibited excellent antioxidant activity, even comparable to the typical antioxidant Trolox. Compounds 9 had higher lipid-water partition coefficients relative to the carboxylic acid compounds 8, indicating that they may have better lipophilicity and membrane permeability. Structure-activity relationship (SAR) studies found that acyl trifluoromethanesulfonamide group at N1 and the C3-dihydroxystyryl side chain were the key structure for improving the aldose reductase inhibitory activity and antioxidant activity.
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Affiliation(s)
- Yunpeng Ji
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China
| | - Xin Chen
- ME Genomics Inc., Software Industry Base, Shenzhen 518061, China
| | - Huan Chen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China
| | - Xin Zhang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China
| | - Zhenya Fan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China
| | - Lina Xie
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China
| | - Bing Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China.
| | - Changjin Zhu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5, Zhongguancun South Street, 100081 Beijing, China.
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50
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Ren ZL, He P, Lu WT, Sun M, Ding MW. Synthesis of iminoisoindolinones via a cascade of the three-component Ugi reaction, palladium catalyzed isocyanide insertion, hydroxylation and an unexpected rearrangement reaction. Org Biomol Chem 2019; 16:6322-6331. [PMID: 30131989 DOI: 10.1039/c8ob01728j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A robust ligand-free palladium-catalyzed cascade reaction for the synthesis of diversely substituted iminoisoindolinones has been developed. The cascade reaction involves isocyanide insertion into Ugi-3CR adducts, accompanied by unexpected hydroxylation and rearrangement.
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Affiliation(s)
- Zhi-Lin Ren
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Central China Normal University, Wuhan, 430079, P. R. China.
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