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Han D, Zhao F, Chen Y, Xue Y, Bao K, Chang Y, Lu J, Wang M, Liu T, Gao Q, Cui W, Xu Y. Distinct Characteristic Binding Modes of Benzofuran Core Inhibitors to Diverse Genotypes of Hepatitis C Virus NS5B Polymerase: A Molecular Simulation Study. Int J Mol Sci 2024; 25:8028. [PMID: 39125602 PMCID: PMC11311972 DOI: 10.3390/ijms25158028] [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: 06/21/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The benzofuran core inhibitors HCV-796, BMS-929075, MK-8876, compound 2, and compound 9B exhibit good pan-genotypic activity against various genotypes of NS5B polymerase. To elucidate their mechanism of action, multiple molecular simulation methods were used to investigate the complex systems of these inhibitors binding to GT1a, 1b, 2a, and 2b NS5B polymerases. The calculation results indicated that these five inhibitors can not only interact with the residues in the palm II subdomain of NS5B polymerase, but also with the residues in the palm I subdomain or the palm I/III overlap region. Interestingly, the binding of inhibitors with longer substituents at the C5 position (BMS-929075, MK-8876, compound 2, and compound 9B) to the GT1a and 2b NS5B polymerases exhibits different binding patterns compared to the binding to the GT1b and 2a NS5B polymerases. The interactions between the para-fluorophenyl groups at the C2 positions of the inhibitors and the residues at the binding pockets, together with the interactions between the substituents at the C5 positions and the residues at the reverse β-fold (residues 441-456), play a key role in recognition and the induction of the binding. The relevant studies could provide valuable information for further research and development of novel anti-HCV benzofuran core pan-genotypic inhibitors.
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Affiliation(s)
- Di Han
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Fang Zhao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yifan Chen
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yiwei Xue
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Ke Bao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yuxiao Chang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Meiting Wang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China;
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China;
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
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Koh WLC, Poh SE, Lee CK, Chan THM, Yan G, Kong KW, Lau L, Lee WYT, Cheng C, Hoon S, Seow Y. Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms. Bioengineering (Basel) 2023; 10:bioengineering10050520. [PMID: 37237590 DOI: 10.3390/bioengineering10050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder widespread deployment. Separate preparations of DNA and RNA also increases costs. In this study, we developed a rapid unbiased metagenomics next-generation sequencing (mNGS) workflow with a human background depletion method (HostEL) and a combined DNA/RNA library preparation kit (AmpRE) to address this issue. We enriched and detected bacterial and fungal standards spiked in plasma at physiological levels with low-depth sequencing (<1 million reads) for analytical validation. Clinical validation also showed 93% of plasma samples agreed with the clinical diagnostic test results when the diagnostic qPCR had a Ct < 33. The effect of different sequencing times was evaluated with the 19 h iSeq 100 paired end run, a more clinically palatable simulated iSeq 100 truncated run and the rapid 7 h MiniSeq platform. Our results demonstrate the ability to detect both DNA and RNA pathogens with low-depth sequencing and that iSeq 100 and MiniSeq platforms are compatible with unbiased low-depth metagenomics identification with the HostEL and AmpRE workflow.
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Affiliation(s)
- Winston Lian Chye Koh
- Bioinformatic Institute, A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore
| | - Si En Poh
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Tim Hon Man Chan
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Gabriel Yan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Division of Microbiology, Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Kiat Whye Kong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Lalita Lau
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | | | - Clark Cheng
- Paths Diagnostics Pte Limited, Singapore 349317, Singapore
| | - Shawn Hoon
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Yiqi Seow
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
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Fluorescence-based simultaneous dual oligo sensing of HCV genotypes 1 and 3 using magnetite nanoparticles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112463. [PMID: 35567883 DOI: 10.1016/j.jphotobiol.2022.112463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid tests (NATs) have gained an important position in biosensing in the context of the increasing need to meet the stringent requirements for accurate diagnosis of infectious diseases with high sensitivity and selectivity. Recently, the development of new strategies towards multiplex detection of analytes in a single assay is gaining impetus since such an approach would lead to high throughput analysis, leading to substantial benefits in terms of time, infrastructure, labor, and cost. In this work, we demonstrate a facile fluorescence-based simultaneous dual oligo sensing of genotypes 1 and 3 by employing two target sequences (36-mers each) derived from the NS4B and NS5A regions of HCV genome, respectively. A set of 18-mer amine-tagged probes and another set of 18-mer fluorescently-labeled probes that were complementary to each half of the 36-mer target sequences were designed. The amine-tagged probes were immobilized over aldehyde-derivatized magnetite nanoparticles (NPs) via imine bond formation, which was characterized using X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS) mapping techniques. The successful hybridization between the two probes with their target followed by magnetic removal of the NPs from the solution enabled quantitative analysis of the target by measuring the fluorescence intensity of the residual concentration of the fluorescently-tagged probe. In this manner, the targets corresponding to genotypes 1 and 3 were simultaneously detected with the detection limit in the range of 10-15 nM. The current strategy can potentially be amalgamated with existing nanotechnology-based techniques towards multiplex oligo sensing of several pathogens.
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Mohammed AS, Balapure A, Khan AA, Khaja MN, Ganesan R, Dutta JR. Genotyping simplified: rationally designed antisense oligonucleotide-mediated PCR amplification-free colorimetric sensing of viral RNA in HCV genotypes 1 and 3. Analyst 2021; 146:4767-4774. [PMID: 34231566 DOI: 10.1039/d1an00590a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular diagnosis of viral genotyping devoid of polymerase chain reaction (PCR) amplification in clinical cohorts has hitherto been challenging. Here we present a simplified molecular diagnostic strategy for direct genotyping of hepatitis C virus (HCV) 1 and 3 (prevalent worldwide) using a combination of rationally designed genotype-specific antisense oligonucleotides (ASOs) and plasmonic gold nanoparticles. The ASOs specific to genotypes 1 and 3 have been designed from the nonstructural region 5A (NS5A) of the viral genome using the ClustalW multiple sequence alignment tool. A total of 79 clinical samples including 18 HCV genotype 1, 18 HCV genotype 3, one HIV positive, one HBV positive, and 41 healthy controls have been tested against both the designed ASOs. The study reveals 100% specificity and sensitivity with the employed samples and thereby opens up new avenues for PCR-free direct genotyping of other viruses as well, through the rational design of ASOs.
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Affiliation(s)
- Almas Shamaila Mohammed
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
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Shahid I, Alzahrani AR, Al-Ghamdi SS, Alanazi IM, Rehman S, Hassan S. Hepatitis C Diagnosis: Simplified Solutions, Predictive Barriers, and Future Promises. Diagnostics (Basel) 2021; 11:1253. [PMID: 34359335 PMCID: PMC8305142 DOI: 10.3390/diagnostics11071253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
The simplification of current hepatitis C diagnostic algorithms and the emergence of digital diagnostic devices will be very crucial to achieving the WHO's set goals of hepatitis C diagnosis (i.e., 90%) by 2030. From the last decade, hepatitis C diagnosis has been revolutionized by the advent and approval of state-of-the-art HCV diagnostic platforms which have been efficiently implemented in high-risk HCV populations in developed nations as well as in some low-to-middle income countries (LMICs) to identify millions of undiagnosed hepatitis C-infected individuals. Point-of-care (POC) rapid diagnostic tests (RDTs; POC-RDTs), RNA reflex testing, hepatitis C self-test assays, and dried blood spot (DBS) sample analysis have been proven their diagnostic worth in real-world clinical experiences both at centralized and decentralized diagnostic settings, in mass hepatitis C screening campaigns, and hard-to-reach aboriginal hepatitis C populations in remote areas. The present review article overviews the significance of current and emerging hepatitis C diagnostic packages to subvert the public health care burden of this 'silent epidemic' worldwide. We also highlight the challenges that remain to be met about the affordability, accessibility, and health system-related barriers to overcome while modulating the hepatitis C care cascade to adopt a 'test and treat' strategy for every hepatitis C-affected individual. We also elaborate some key measures and strategies in terms of policy and progress to be part of hepatitis C care plans to effectively link diagnosis to care cascade for rapid treatment uptake and, consequently, hepatitis C cure.
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Affiliation(s)
- Imran Shahid
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia; (A.R.A.); (S.S.A.-G.); (I.M.A.)
| | - Abdullah R. Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia; (A.R.A.); (S.S.A.-G.); (I.M.A.)
| | - Saeed S. Al-Ghamdi
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia; (A.R.A.); (S.S.A.-G.); (I.M.A.)
| | - Ibrahim M. Alanazi
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia; (A.R.A.); (S.S.A.-G.); (I.M.A.)
| | - Sidra Rehman
- Functional Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 45550, Pakistan;
| | - Sajida Hassan
- Viral Hepatitis Program, Laboratory of Medicine, University of Washington, Seattle, WA 98195, USA;
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Yu S, Nimse SB, Kim J, Song KS, Kim T. Development of a Lateral Flow Strip Membrane Assay for Rapid and Sensitive Detection of the SARS-CoV-2. Anal Chem 2020; 92:14139-14144. [PMID: 32967427 PMCID: PMC7539551 DOI: 10.1021/acs.analchem.0c03202] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/23/2020] [Indexed: 01/12/2023]
Abstract
The infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has threatened public health worldwide. The easy human-to-human transmission of this virus has rapidly evolved into a global pandemic. Therefore, to control the community spread of the virus, it is crucial to identify the infected individuals, including asymptomatic people. Hence, a specific and rapid assay is crucial for the early diagnosis and active monitoring of individuals potentially exposed to SARS-CoV-2 for controlling the COVID-19 outbreak. In this study, we have developed the novel lateral flow strip membrane (LFSM) assay that allows the simultaneous detection of RdRp, ORF3a, and N genes using the PCR product obtained by using the single-tube reverse transcription polymerase chain reaction (RT-PCR). The LFSM assay allows detection of SARS-CoV-2 in 30 min at 25 °C after the RT-PCR with the detection limit of 10 copies/test for each gene. The clinical performance of the LFSM assay for the detection of SARS-Cov-2 was evaluated using 162 clinical samples previously detected by using the commercial assay. The percent positive agreement, percent negative agreement, and overall percent agreement of the LFSM assay with the commercial assay were 100% (94.2-100%), 99.0% (94.6-100%), and 99.4% (96.6-100%), respectively. Therefore, the results of the LFSM assay showed significantly high concordance with the commercial assay for the detection of SARS-CoV-2 in clinical specimens. Therefore, we conclude that the developed LFSM assay can be used alone or complementary to the RT-PCR or other methods for the diagnosis and monitoring of the patients to curb community transmission and the pandemic.
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Affiliation(s)
- Sangheon Yu
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Satish Balasaheb Nimse
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Junghoon Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
| | - Keum-Soo Song
- Biometrix Technology, Inc.,
2-2 Bio Venture Plaza 56, Chuncheon 24232, Korea
| | - Taisun Kim
- Institute of Applied Chemistry and Department of
Chemistry, Hallym University, Chuncheon 24252,
Korea
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