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      Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs

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      Author(s): ∗ ,
      Publication date (Electronic):
      Journal: Bioorganic & Medicinal Chemistry
      Publisher: Elsevier Ltd.
      Keywords: SARS-CoV, Drugs, Binding, Proteinase

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          Abstract

          The binding analysis of SARS-CoV main proteinase with HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine) suggests that these existing drugs can be used as starting points for designing SARS-CoV proteinase inhibitors.

          Abstract

          The SARS-associated coronavirus (SARS-CoV) main proteinase is a key enzyme in viral polyprotein processing. To allow structure-based design of drugs directed at SARS-CoV main proteinase, we predicted its binding pockets and affinities with existing HIV, psychotic and parasite drugs (lopinavir, ritonavir, niclosamide and promazine), which show signs of inhibiting the replication of SARS-CoV. Our results suggest that these drugs and another two HIV inhibitors (PNU and UC2) could be used as templates for designing SARS-CoV proteinase inhibitors.

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          Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs.

          Kanchan Anand, John Ziebuhr, Parvesh Wadhwani … (2003)
          A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.
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            Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS ☆

            Kuo-Chen Chou, Dong-Qing Wei, Wei-Zhu Zhong (2003)
            In order to stimulate the development of drugs against severe acute respiratory syndrome (SARS), based on the atomic coordinates of the SARS coronavirus main proteinase determined recently [Science 13 (May) (2003) (online)], studies of docking KZ7088 (a derivative of AG7088) and the AVLQSGFR octapeptide to the enzyme were conducted. It has been observed that both the above compounds interact with the active site of the SARS enzyme through six hydrogen bonds. Also, a clear definition of the binding pocket for KZ7088 has been presented. These findings may provide a solid basis for subsite analysis and mutagenesis relative to rational design of highly selective inhibitors for therapeutic application. Meanwhile, the idea of how to develop inhibitors of the SARS enzyme based on the knowledge of its own peptide substrates (the so-called “distorted key” approach) was also briefly elucidated.
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              Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.

              Craig W Ritchie (2003)
              This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e.g., Lactobacillus HPr kinase, hemagglutinin, bovine rotavirus VP6). Here we describe several enhancements to our original spherical polar Fourier docking correlation algorithm. For example, a novel surface sphere smothering algorithm is introduced to generate multiple local coordinate systems around the surface of a large receptor molecule, which may be used to define a small number of initial ligand-docking orientations distributed over the receptor surface. High-resolution spherical polar docking correlations are performed over the resulting receptor surface patches, and candidate docking solutions are refined by using a novel soft molecular mechanics energy minimization procedure. Overall, this approach identified two good solutions at rank 5 or less for two of the seven CAPRI complexes. Subsequent analysis of our results shows that Hex 3.1 is able to place good solutions within a list of
              Article 0 comments Cited 41 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Xue Wu Zhang
                Journal
                Journal ID (nlm-ta): Bioorg Med Chem
                Journal ID (iso-abbrev): Bioorg. Med. Chem
                Title: Bioorganic & Medicinal Chemistry
                Publisher: Elsevier Ltd.
                ISSN (Print): 0968-0896
                ISSN (Electronic): 1464-3391
                Publication date PMC-release: 10 April 2004
                Publication date (Print): 15 May 2004
                Publication date (Electronic): 10 April 2004
                Volume: 12
                Issue: 10
                Pages: 2517-2521
                Affiliations
                HKU-Pasteur Research Center, 8 Sassoon Road, Pokfulam, Hong Kong
                Author notes
                [∗ ]Corresponding author. Tel.: +852-2816-8407; fax: +852-2872-5782 xwzhang@ 123456hkucc.hku.hk
                Article
                Publisher ID: S0968-0896(04)00221-4
                DOI: 10.1016/j.bmc.2004.03.035
                PMC ID: 7126105
                PubMed ID: 15110833
                SO-VID: fe15153d-b95c-4271-9ca5-25324ae875aa
                Copyright statement: Copyright © 2004 Elsevier Ltd. All rights reserved.
                License:

                Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

                History
                Date received : 20 February 2004
                Date revision received : 16 March 2004
                Date accepted : 16 March 2004
                Categories
                Subject: Article

                ScienceOpen disciplines: Pharmaceutical chemistry
                Keywords: sars-cov,drugs,binding,proteinase
                Data availability:
                ScienceOpen disciplines: Pharmaceutical chemistry
                Keywords: sars-cov, drugs, binding, proteinase

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