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Das A, Sharma HK, Lather V, Pandita D, Agarwal P. Structure-based virtual screening for identification of potential CDC20 inhibitors and their therapeutic evaluation in breast cancer. 3 Biotech 2023; 13:141. [PMID: 37124982 PMCID: PMC10133423 DOI: 10.1007/s13205-023-03554-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Cell division cycle 20 (CDC20), a critical partner of anaphase promoting complex (APC/C), is indispensably required for metaphase-to-anaphase transition. CDC20 overexpression in TNBC breast cancer patients has been found to be correlated with poor prognosis, hence, we aimed to target CDC20 for TNBC therapeutics. In silico molecular docking of large-scale chemical libraries (phytochemicals/synthetic drugs) against CDC20 protein structure identified five synthetic drugs and four phytochemicals as potential hits interacting with CDC20 active site. The molecular selection was done based on docking scores, binding interactions, binding energies and MM/GBSA scores. Further, we analysed ADME profiles for all the hits and identified lidocaine, an aminoamide anaesthetic group of synthetic drug, with high drug-likeness properties. We explored the anti-tumorigenic effects of lidocaine on MDA-MB-231 TNBC breast cancer cells, which resulted in increased growth inhibition in dose-dependent manner. The molecular mechanism behind the cell viability defect mediated by lidocaine was found to be induction of G2/M cell cycle arrest and cellular apoptosis. Notably, lidocaine treatment of TNBC cells also resulted in downregulation of CDC20 gene expression. Thus, this study identifies lidocaine as a potential anti-neoplastic agent for TNBC cells emphasizing CDC20 as a suitable therapeutic target for breast cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03554-7.
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Affiliation(s)
- Amiya Das
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Hitesh Kumar Sharma
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Viney Lather
- Amity Institute of Pharmacy, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Institute of Pharmaceutical Sciences & Research (DIPSAR) Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, Government of NCT of Delhi, New Delhi, 110017 India
- Centre for Advanced Formulation Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, Govt. of NCT of Delhi, New Delhi, 110017 India
| | - Pallavi Agarwal
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida, 201313 India
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Conformational ensemble of the NSP1 CTD in SARS-CoV-2: Perspectives from the free energy landscape. Biophys J 2023:S0006-3495(23)00102-9. [PMID: 36793215 PMCID: PMC9928668 DOI: 10.1016/j.bpj.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/13/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-associated coronavirus 2 plays a crucial role in the translational shutdown and immune evasion inside host cells. Despite its known intrinsic disorder, the C-terminal domain (CTD) of NSP1 has been reported to form a double α-helical structure and block the 40S-ribosomal channel for mRNA translation. Experimental studies indicate that NSP1 CTD functions independently from the globular N-terminal region separated with a long linker domain, underscoring the necessity of exploring the standalone conformational ensemble. In this contribution, we utilize exascale computing resources to yield unbiased molecular dynamics simulation of NSP1 CTD in all-atom resolution starting from multiple initial seed structures. A data-driven approach elicits collective variables (CVs) that are significantly superior to conventional descriptors in capturing the conformational heterogeneity. The free energy landscape as a function of the CV space is estimated using the modified expectation maximized molecular dynamics. Originally developed by us for small peptides, here, we establish the efficacy of expectation maximized molecular dynamics in conjunction with data-driven CV space for a more complex and relevant biomolecular system. The results reveal the existence of two disordered metastable populations in the free energy landscape that are separated from the conformation resembling ribosomal subunit bound state by high kinetic barriers. Chemical shift correlation and secondary structure analysis capture significant differences among key structures of the ensemble. Altogether, these insights can underpin drug development studies and mutational experiments that help induce population shifts to alter translational blocking and understand its molecular basis in further detail.
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Saivish MV, Pacca CC, da Costa VG, de Lima Menezes G, da Silva RA, Nebo L, da Silva GCD, de Aguiar Milhim BHG, da Silva Teixeira I, Henrique T, Mistrão NFB, Hernandes VM, Zini N, de Carvalho AC, Fontoura MA, Rahal P, Sacchetto L, Marques RE, Nogueira ML. Caffeic Acid Has Antiviral Activity against Ilhéus Virus In Vitro. Viruses 2023; 15:494. [PMID: 36851709 PMCID: PMC9961518 DOI: 10.3390/v15020494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Ilhéus virus (ILHV) is a neglected mosquito-borne flavivirus. ILHV infection may lead to Ilhéus fever, an emerging febrile disease like dengue fever with the potential to evolve into a severe neurological disease characterized by meningoencephalitis; no specific treatments are available for this disease. This study assessed the antiviral properties of caffeic acid, an abundant component of plant-based food products that is also compatible with the socioeconomic limitations associated with this neglected infectious disease. The in vitro activity of caffeic acid on ILHV replication was investigated in Vero and A549 cell lines using plaque assays, quantitative RT-PCR, and immunofluorescence assays. We observed that 500 µM caffeic acid was virucidal against ILHV. Molecular docking indicated that caffeic acid might interact with an allosteric binding site on the envelope protein.
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Affiliation(s)
- Marielena Vogel Saivish
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Carolina Colombelli Pacca
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
- Faceres Medical School, São José do Rio Preto 15090-000, SP, Brazil
| | - Vivaldo Gomes da Costa
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
| | - Gabriela de Lima Menezes
- Departamento de Biofísica e Farmacologia, Universidade Federal do Rio Grande do Norte, Natal 59072-970, RN, Brazil
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil
| | | | - Liliane Nebo
- Unidade Especial de Ciências Exatas, Universidade Federal de Jataí, Jataí 75801-615, GO, Brazil
| | - Gislaine Celestino Dutra da Silva
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Bruno Henrique Gonçalves de Aguiar Milhim
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Igor da Silva Teixeira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Tiago Henrique
- Laboratório de Marcadores Moleculares e Bioinformática, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Natalia Franco Bueno Mistrão
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Victor Miranda Hernandes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Nathalia Zini
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Ana Carolina de Carvalho
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Marina Alves Fontoura
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, São José do Rio Preto 15054-000, SP, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA
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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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Mousavi S, Zare S, Mirzaei M, Feizi A. Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Affiliation(s)
- Sarah Mousavi
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Zare
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahmoud Mirzaei
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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6
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Salami Ghaleh S, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Mollapour Sisakht M, Farhadi A, Mousakhan Bakhtiari M, Lee Kuehu D, Deng Y. SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.22.501212. [PMID: 35923310 PMCID: PMC9347281 DOI: 10.1101/2022.07.22.501212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the β-coronavirus . This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus. According to the significant role of non-structural protein 1 (NSP1) in inhibiting host mRNA translation, this study focuses on the link between amino acid sequences of NSP1 and alterations of them spreading around the world. The SARS-CoV-2 NSP1 protein sequences were analyzed and FASTA files were processed by Python language programming libraries. Reference sequences compared with each NSP1 sample to identify every mutation and categorize them were based on continents and frequencies. NSP1 mutations rate divided into continents were different. Based on continental studies, E87D in global vision and also in Europe notably increased. The E87D mutation has significantly risen especially in the last months of the study as the first frequent mutation observed. The remarkable mutations, H110Y and R24C, have the second and third frequencies, respectively. Based on this mutational information, despite NSP1 being a conserved sequence occurrence, these mutations change the rate of flexibility and stability of the NSP1 protein, which can eventually affect inhibiting the host translation. IMPORTANCE In this study, we analyzed 6,510,947 sequences of non-structural protein 1 as a conserved region of SARS-CoV-2. According to the obtained results, 93.4819% of samples had no mutant regions on their amino acid sequences. Heat map data of mutational samples demonstrated high percentages of mutations that occurred in the region of 72 to 126 amino acids indicating a hot spot region of the protein. Increased rates of E87D, H110Y, and R24C mutations in the timeline of our study were reported as significant compared to available mutant samples. Analyzing the details of replacing amino acids in the most frequent E87D mutation reveals the role of this alteration in increasing molecule flexibility and destabilizing the structure of the protein.
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7
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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Synergistic interactions of repurposed drugs that inhibit Nsp1, a major virulence factor for COVID-19. Sci Rep 2022; 12:10174. [PMID: 35715434 PMCID: PMC9204075 DOI: 10.1038/s41598-022-14194-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Nsp1 is one of the first proteins expressed from the SARS-CoV-2 genome and is a major virulence factor for COVID-19. A rapid multiplexed assay for detecting the action of Nsp1 was developed in cultured lung cells. The assay is based on the acute cytopathic effects induced by Nsp1. Virtual screening was used to stratify compounds that interact with two functional Nsp1 sites: the RNA-binding groove and C-terminal helix-loop-helix region. Experimental screening focused on compounds that could be readily repurposed to treat COVID-19. Multiple synergistic combinations of compounds that significantly inhibited Nsp1 action were identified. Among the most promising combinations are Ponatinib, Rilpivirine, and Montelukast, which together, reversed the toxic effects of Nsp1 to the same extent as null mutations in the Nsp1 gene.
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Genomic, proteomic and metabolomic profiling of severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300679 DOI: 10.1016/b978-0-323-91172-6.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) is one of the worst human health problems faced by humanity in recent centuries. An end to this health crisis relies on our ability to monitor viral transmission dynamics to check spread, develop therapeutics and preventatives for treatment of SARS-CoV-2 infection and understand the pathophysiology of the disease for better management of the patients. Omics technologies have played a crucial part in understanding the different aspects of COVID-19 disease. While whole-genome sequencing of SARS-CoV-2 isolates from across the globe has aided in the development of molecular diagnostic assays and informed about the viral evolution, knowledge of structure and function of viral proteome fueled the development of small molecule and biologicals therapeutics as well as vaccines. Concurrently, metabolomic profiling of samples from COVID-19 patients experiencing a varying level of disease severity has provided a snapshot of the pathophysiology of the disease helping device effective treatment regimen. This chapter deals with genomic, proteomic, and metabolomic profiling of SRAS-CoV-2.
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Vasudevan S, Baraniuk JN. Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex. Pathogens 2021; 10:1634. [PMID: 34959589 PMCID: PMC8709492 DOI: 10.3390/pathogens10121634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Non-structural protein 1 (Nsp1) is a virulence factor found in all beta coronaviruses (b-CoVs). Recent studies have shown that Nsp1 of SARS-CoV-2 virus interacts with the nuclear export receptor complex, which includes nuclear RNA export factor 1 (NXF1) and nuclear transport factor 2-like export factor 1 (NXT1). The NXF1-NXT1 complex plays a crucial role in the transport of host messenger RNA (mRNA). Nsp1 interferes with the proper binding of NXF1 to mRNA export adaptors and its docking to the nuclear pore complex. We propose that drugs targeting the binding surface between Nsp1 and NXF1-NXT1 may be a useful strategy to restore host antiviral gene expression. Exploring this strategy forms the main goals of this paper. Crystal structures of Nsp1 and the heterodimer of NXF1-NXT1 have been determined. We modeled the docking of Nsp1 to the NXF1-NXT1 complex, and discovered repurposed drugs that may interfere with this binding. To our knowledge, this is the first attempt at drug-repurposing of this complex. We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1-NXT1 complex. The top hit was ganirelix, with a docking score of -14.49. Ganirelix competitively antagonizes the gonadotropin releasing hormone receptor (GNRHR) on pituitary gonadotrophs, and induces rapid, reversible suppression of gonadotropin secretion. The conformations of Nsp1 and GNRHR make it unlikely that they interact with each other. Additional drug leads were inferred from the structural analysis of this complex, which are discussed in the paper. These drugs offer several options for therapeutically blocking Nsp1 binding to NFX1-NXT1, which may normalize nuclear export in COVID-19 infection.
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Affiliation(s)
- Sona Vasudevan
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20057, USA
| | - James N Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20007, USA
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Abdurrahman L, Fang X, Zhang Y. Molecular Insights of SARS-CoV-2 Infection and Molecular Treatments. Curr Mol Med 2021; 22:621-639. [PMID: 34645374 DOI: 10.2174/1566524021666211013121831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2021] [Accepted: 07/23/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus disease emerged in December 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome-related coronavirus 2 (SARS-CoV-2) and its rapid global spread has brought an international health emergency and urgent responses for seeking efficient prevention and therapeutic treatment. This has led to imperative needs for illustration of the molecular pathogenesis of SARS-CoV-2, identification of molecular targets or receptors, and development of antiviral drugs, antibodies, and vaccines. In this study, we investigated the current research progress in combating SARS-CoV-2 infection. Based on the published research findings, we first elucidated, at the molecular level, SARS-CoV-2 viral structures, potential viral host-cell-invasion and pathogenic mechanisms, main virus-induced immune responses, and emerging SARS-CoV-2 variants. We then focused on the main virus- and host-based potential targets, summarized and categorized effective inhibitory molecules based on drug development strategies for COVID-19, that can guide efforts for the identification of new drugs and treatment for this problematic disease. Current research and development of antibodies and vaccines were also introduced and discussed. We concluded that the main virus entry route- SARS-CoV-2 spike protein interaction with ACE2 receptors has played a key role in guiding the development of therapeutic treatments against COVID-19, four main therapeutic strategies may be considered in developing molecular therapeutics, and drug repurposing is likely to be an easy, fast and low-cost approach in such a short period of time with urgent need of antiviral drugs. Additionally, the quick development of antibody and vaccine candidates has yielded promising results, but the wide-scale deployment of safe and effective COVID-19 vaccines remains paramount in solving the pandemic crisis. As new variants of the virus begun to emerge, the efficacy of these vaccines and treatments must be closely evaluated. Finally, we discussed the possible challenges of developing molecular therapeutics for COVID-19 and suggested some potential future efforts. Despite the limited availability of literatures, our attempt in this work to provide a relatively comprehensive overview of current SARS-CoV-2 studies can be helpful for quickly acquiring the key information of COVID-19 and further promoting this important research to control and diminish the pandemic.
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Affiliation(s)
- Lama Abdurrahman
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Xiaoqian Fang
- Department of Molecular Science, School of Medicine, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
| | - Yonghong Zhang
- Department of Chemistry, The University of Texas Rio Grande Valley, Edinburg, Texas 78539. United States
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12
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Padhi AK, Rath SL, Tripathi T. Accelerating COVID-19 Research Using Molecular Dynamics Simulation. J Phys Chem B 2021; 125:9078-9091. [PMID: 34319118 PMCID: PMC8340580 DOI: 10.1021/acs.jpcb.1c04556] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/12/2021] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has emerged as a global medico-socio-economic disaster. Given the lack of effective therapeutics against SARS-CoV-2, scientists are racing to disseminate suggestions for rapidly deployable therapeutic options, including drug repurposing and repositioning strategies. Molecular dynamics (MD) simulations have provided the opportunity to make rational scientific breakthroughs in a time of crisis. Advancements in these technologies in recent years have become an indispensable tool for scientists studying protein structure, function, dynamics, interactions, and drug discovery. Integrating the structural data obtained from high-resolution methods with MD simulations has helped in comprehending the process of infection and pathogenesis, as well as the SARS-CoV-2 maturation in host cells, in a short duration of time. It has also guided us to identify and prioritize drug targets and new chemical entities, and to repurpose drugs. Here, we discuss how MD simulation has been explored by the scientific community to accelerate and guide translational research on SARS-CoV-2 in the past year. We have also considered future research directions for researchers, where MD simulations can help fill the existing gaps in COVID-19 research.
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Affiliation(s)
- Aditya K. Padhi
- Laboratory for Structural Bioinformatics, Center for
Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi,
Yokohama, Kanagawa 230-0045, Japan
| | - Soumya Lipsa Rath
- Department of Biotechnology, National
Institute of Technology, Warangal, Telangana 506004,
India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory,
Department of Biochemistry, North-Eastern Hill University,
Shillong 793022, India
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13
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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14
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Sundar S, Thangamani L, Piramanayagam S, Rahul CN, Aiswarya N, Sekar K, Natarajan J. Screening of FDA-approved compound library identifies potential small-molecule inhibitors of SARS-CoV-2 non-structural proteins NSP1, NSP4, NSP6 and NSP13: molecular modeling and molecular dynamics studies. ACTA ACUST UNITED AC 2021; 12:161-175. [PMID: 34121824 PMCID: PMC8188161 DOI: 10.1007/s42485-021-00067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/08/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022]
Abstract
COVID-19, the current global pandemic has caused immense damage to human lives and the global economy. It is instigated by the SARS-CoV-2 virus and there is an immediate need for the identification of effective drugs against this deadly virus. SARS-CoV-2 genome codes for four structural proteins, sixteen non-structural proteins (NSPs) and several accessory proteins for its survival inside the host cells. In the present study, through in silico approaches, we aim to identify compounds that are effective against the four NSPs namely, NSP1, NSP4, NSP6 and NSP13 of SARS-CoV-2. The selection criteria of these four NSP proteins are they are least explored and potential targets. First, we have modeled the 3D structures of these proteins using homology modeling methods. Further, through molecular docking studies, we have screened the FDA-approved compounds against these modeled proteins and reported their docking scores. To gain dynamic insights, molecular dynamics studies have also been carried out for the best scored ligand against the NSPs. This study can further pave way for exposing more number of compounds against these proteins and enhance COVID-19 treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00067-w.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - Lokesh Thangamani
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | | | - Natarajan Aiswarya
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka India
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu India
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15
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Singh R, Bhardwaj VK, Das P, Purohit R. A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2. Comput Biol Med 2021; 135:104555. [PMID: 34144270 PMCID: PMC8184359 DOI: 10.1016/j.compbiomed.2021.104555] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
Background Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. Methods Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant (Cedrus deodara) derived α,β,γ-Himachalenes scaffolds. Results The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. Conclusion The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palam-pur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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16
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Hashemi SA, Kyani A, Bathaie SZ. The in silico mechanism of hVKOR interaction with acetaminophen and its metabolite, as well as N-acetyl cysteine: caution on application in COVID-19 patients. J Biomol Struct Dyn 2021; 40:8274-8285. [PMID: 33879035 PMCID: PMC8074654 DOI: 10.1080/07391102.2021.1910570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acetaminophen and N-acetyl cysteine (NAC) are being used as supportive care in patients suffering from coronavirus disease 2019 (COVID-19). The coagulopathy and cerebral hemorrhage have been recently reported in these patients. Prolonged acetaminophen use increases the international normalized ratio (INR) and the risk of bleeding among patients taking anti-coagulants. Inhibition of vitamin K epoxide reductase (VKOR) by acetaminophen and NAC in chronic applications has been reported, however, detailed knowledge of the molecular mechanism and binding sites are not clear. Herein, we built the homology model of human VKOR (hVKOR) using ITASSER server, confirmed, and applied it for docking analysis of its interaction with acetaminophen and its metabolite, N-acetyl-p-benzoquinone imine (NAPQI), and NAC. We also calculated the lipophilicity and predicted the blood-brain-barrier (BBB) permeation of NAPQI by Swiss ADME. Our analysis showed that NAPQI and NAC, but not acetaminophen, bind strongly to the similar sites in hVKOR via both hydrogen and van der Waals bonding; particularly with Cys135. Thus, it interrupted the vitamin K reducing electron transfer pathway. Further, molecular dynamic (MD) simulation study revealed that the interactions of the ligands with hVKOR are stable. In conclusion, our analysis shed a light on the molecular mechanism of acetaminophen-induced coagulopathy previously reported in some clinical cases with chronic acetaminophen use. Furthermore, considering the anti-coagulopathy of NAPQI and NAC but not acetaminophen, the BBB permeation potency of these agents, and the risk of coagulopathy in COVID-19, we suggest a regular prothrombin time (PT) and INR monitoring of these patients taking acetaminophen and/or NAC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ali Hashemi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.,Department of Laboratory Sciences, Chalus Branch, Islamic Azad University, Chalous, Iran
| | - Armita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - S Zahra Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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17
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Vankadari N, Jeyasankar NN, Lopes WJ. Structure of the SARS-CoV-2 Nsp1/5'-Untranslated Region Complex and Implications for Potential Therapeutic Targets, a Vaccine, and Virulence. J Phys Chem Lett 2020; 11:9659-9668. [PMID: 33135884 PMCID: PMC7641045 DOI: 10.1021/acs.jpclett.0c02818] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 is the cause of the ongoing Coronavirus disease 19 (COVID-19) pandemic around the world causing pneumonia and lower respiratory tract infections. In understanding the SARS-CoV-2 pathogenicity and mechanism of action, it is essential to depict the full repertoire of expressed viral proteins. The recent biological studies have highlighted the leader protein Nsp1 of SARS-CoV-2 importance in shutting down the host protein production. Besides, it still enigmatic how Nsp1 regulates for translation. Here we report the novel structure of Nsp1 from SARS-CoV-2 in complex with the SL1 region of 5'UTR of SARS-CoV-2, and its factual interaction is corroborated with enzyme kinetics and experimental binding affinity studies. The studies also address how leader protein Nsp1 of SARS-CoV-2 recognizes its self RNA toward translational regulation by further recruitment of the 40S ribosome. With the aid of molecular dynamics and simulations, we also demonstrated the real-time stability and functional dynamics of the Nsp1/SL1 complex. The studies also report the potential inhibitors and their mode of action to block viral protein/RNA complex formation. This enhance our understanding of the mechanism of the first viral protein Nsp1 synthesized in the human cell to regulate the translation of self and host. Understanding the structure and mechanism of SARS-CoV-2 Nsp1 and its interplay with the viral RNA and ribosome will open the arena for exploring the development of live attenuated vaccines and effective therapeutic targets for this disease.
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Affiliation(s)
- Naveen Vankadari
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
| | - Nandhini Nisha Jeyasankar
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
| | - Wilma Jerom Lopes
- Monash Biomedicine Discovery Institute and
Department of Biochemistry and Molecular Biology and
Faculty of Medicine, Nursing and Health
Science, Monash University, Clayton
Victoria 3800, Australia
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18
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Liu XH, Zhang X, Lu ZH, Zhu YS, Wang T. Potential molecular targets of nonstructural proteins for the development of antiviral drugs against SARS-CoV-2 infection. Biomed Pharmacother 2020; 133:111035. [PMID: 33254013 PMCID: PMC7671653 DOI: 10.1016/j.biopha.2020.111035] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/08/2023] Open
Abstract
The pandemic of SARS-CoV-2 has posed significant threats to public health worldwide. Target-based drug development is a promising approach against SARS-CoV-2 infection. Nonstructural proteins may play critical roles from drug design perspectives. Insights into NSPs of different viruses could streamline novel drug development.
Outbreaks of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2 have produced high pathogenicity and mortality rates in human populations. However, to meet the increasing demand for treatment of these pathogenic coronaviruses, accelerating novel antiviral drug development as much as possible has become a public concern. Target-based drug development may be a promising approach to achieve this goal. In this review, the relevant features of potential molecular targets in human coronaviruses (HCoVs) are highlighted, including the viral protease, RNA-dependent RNA polymerase, and methyltransferases. Additionally, recent advances in the development of antivirals based on these targets are summarized. This review is expected to provide new insights and potential strategies for the development of novel antiviral drugs to treat SARS-CoV-2 infection.
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Affiliation(s)
- Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xiao Zhang
- School of Biological Science, Jining Medical University, Jining, China
| | - Zhen-Hua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - You-Shuang Zhu
- School of Biological Science, Jining Medical University, Jining, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, China.
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19
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SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nat Struct Mol Biol 2020; 27:959-966. [DOI: 10.1038/s41594-020-0511-8] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022]
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20
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da Silva IR, Parise MR, Pereira M, da Silva RA. Prospecting for new catechol- O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson's disease: a study by molecular dynamics and structure-based virtual screening. J Biomol Struct Dyn 2020; 39:5872-5891. [PMID: 32691671 DOI: 10.1080/07391102.2020.1794963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative, chronic, and progressive disease, common in the elderly. The catechol-O-methyltransferase (COMT) is a monomeric enzyme involved in dopamine (DA) degradation, the neurotransmitter in deficit in patients with PD. The reference treatment of PD consists of levodopa (L-dopa) administration, which is the precursor of DA. The inhibition of COMT is an adjuvant treatment in PD since it keeps DA levels constant. The goal of this study was to identify drug candidates capable of inhibiting COMT for the treatment of PD and identify important fragments of these molecules. Initially, we analyzed the flexibility of COMT and defined its main conformations in solution regarding the absence (system I) and presence of the S-adenosyl-L-methionine (SAM) cofactor (system II) through molecular dynamics (MD) simulations. Two regions in these structures were selected for molecular docking, firstly the entire cavity where the cofactor and substrates are bound and secondly the specific biding region of the enzyme substrates. Based on the conformations of the MD, the virtual screening (VS) was performed against FDA Approved and Zinc Natural Products databases aiming at the selection of the best compounds. Subsequently, the absorption, distribution, metabolization, excretion, and toxicity (ADMET) properties, as well as drug-score and drug-likeness indexes of the most promising compounds were analyzed. After a detailed analysis of the compounds selected by structure-based VS, it was possible to highlight the fragments most frequently involved in their stability: 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole, 9H-Benz(c)indole(3,2,1-ij)(1,5)naphthyridin-9-one and (10R,13S)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17dodecahydrocyclopenta[a]phenanthren-3-one. The identification of these potential fragments is essential for the prospection of more specific inhibitors against COMT using the technique of Fragment-based lead discovery (FBLD). Besides, this study allowed us to identify the potential COMT inhibitors through a complete understanding of molecular-level interactions based on the flexibility of this protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Michelle Rocha Parise
- Laboratório de Farmacologia e Fisiologia, Universidade Federal de Jataí, Jataí, Brasil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brasil
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