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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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Perrier A, Eluard M, Petitjean M, Vanet A. In Silico Design of New Inhibitors Against Hemagglutinin of Influenza. J Phys Chem B 2018; 123:582-592. [DOI: 10.1021/acs.jpcb.8b10767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Aurélie Perrier
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas Mann, F-75205 Paris Cedex 13, France
- Epôle de Génoinformatique, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
| | - Matthias Eluard
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France
- Epôle de Génoinformatique, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
- Pathologies de la replication de l’ADN, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
| | - Michel Petitjean
- Epôle de Génoinformatique, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
- MTi, UMR-S 973, INSERM, University Denis Diderot, Paris 7, F-75013 Paris, France
| | - Anne Vanet
- Epôle de Génoinformatique, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
- Pathologies de la replication de l’ADN, Institut Jacques Monod, UMR7592, CNRS, F-75013 Paris, France
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A New Strategy to Reduce Influenza Escape: Detecting Therapeutic Targets Constituted of Invariance Groups. Viruses 2017; 9:v9030038. [PMID: 28257108 PMCID: PMC5371793 DOI: 10.3390/v9030038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/03/2017] [Accepted: 02/23/2017] [Indexed: 12/26/2022] Open
Abstract
The pathogenicity of the different flu species is a real public health problem worldwide. To combat this scourge, we established a method to detect drug targets, reducing the possibility of escape. Besides being able to attach a drug candidate, these targets should have the main characteristic of being part of an essential viral function. The invariance groups that are sets of residues bearing an essential function can be detected genetically. They consist of invariant and synthetic lethal residues (interdependent residues not varying or slightly varying when together). We analyzed an alignment of more than 10,000 hemagglutinin sequences of influenza to detect six invariance groups, close in space, and on the protein surface. In parallel we identified five potential pockets on the surface of hemagglutinin. By combining these results, three potential binding sites were determined that are composed of invariance groups located respectively in the vestigial esterase domain, in the bottom of the stem and in the fusion area. The latter target is constituted of residues involved in the spring-loaded mechanism, an essential step in the fusion process. We propose a model describing how this potential target could block the reorganization of the hemagglutinin HA2 secondary structure and prevent viral entry into the host cell.
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Petitjean M, Badel A, Veitia RA, Vanet A. Synthetic lethals in HIV: ways to avoid drug resistance : Running title: Preventing HIV resistance. Biol Direct 2015; 10:17. [PMID: 25888435 PMCID: PMC4399722 DOI: 10.1186/s13062-015-0044-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background RNA viruses rapidly accumulate genetic variation, which can give rise to synthetic lethal (SL) and deleterious (SD) mutations. Synthetic lethal mutations (non-lethal when alone but lethal when combined in one genome) have been studied to develop cancer therapies. This principle can also be used against fast-evolving RNA-viruses. Indeed, targeting protein sites involved in SD + SL interactions with a drug would render any mutation of such sites, lethal. Results Here, we set up a strategy to detect intragenic pairs of SL and SD at the surface of the protein to predict less escapable drug target sites. For this, we detected SD + SL, studying HIV protease (PR) and reverse transcriptase (RT) sequence alignments from two groups of VIH+ individuals: treated with drugs (T) or not (NT). Using a series of statistical approaches, we were able to propose bona fide SD + SL couples. When focusing on spatially close co-variant SD + SL couples at the surface of the protein, we found 5 SD + SL groups (2 in the protease and 3 in the reverse transcriptase), which could be good candidates to form pockets to accommodate potential drugs. Conclusions Thus, designing drugs targeting these specific SD + SL groups would not allow the virus to mutate any residue involved in such groups without losing an essential function. Moreover, we also show that the selection pressure induced by the treatment leads to the appearance of new mutations, which change the mutational landscape of the protein. This drives the existence of differential SD + SL couples between the drug-treated and non-treated groups. Thus, new anti-viral drugs should be designed differently to target such groups. Reviewers This article was reviewed by Neil Greenspan Csaba Pal and István Simon. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0044-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michel Petitjean
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France. .,MTI, INSERM UMR-S 973, F-75013, Paris, France.
| | - Anne Badel
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France. .,MTI, INSERM UMR-S 973, F-75013, Paris, France.
| | - Reiner A Veitia
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France. .,CNRS, UMR7592, Institut Jacques Monod, F-75013, Paris, France.
| | - Anne Vanet
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013, Paris, France. .,CNRS, UMR7592, Institut Jacques Monod, F-75013, Paris, France. .,Atelier de Bio Informatique, F-75005, Paris, France.
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Petitjean M, Vanet A. VIRAPOPS2 supports the influenza virus reassortments. SOURCE CODE FOR BIOLOGY AND MEDICINE 2014; 9:18. [PMID: 25183993 PMCID: PMC4144320 DOI: 10.1186/1751-0473-9-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 08/07/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND For over 400 years, due to the reassortment of their segmented genomes, influenza viruses evolve extremely quickly and cause devastating epidemics. This reassortment arises because two flu viruses can infect the same cell and therefore the new virions' genomes will be composed of segment reassortments of the two parental strains. A treatment developed against parents could then be ineffective if the virions' genomes are different enough from their parent's genomes. It is therefore essential to simulate such reassortment phenomena to assess the risk of apparition of new flu strain. FINDINGS So we decided to upgrade the forward simulator VIRAPOPS, containing already the necessary options to handle non-segmented viral populations. This new version can mimic single or successive reassortments, in birds, humans and/or swines. Other options such as the ability to treat populations of positive or negative sense viral RNAs, were also added. Finally, we propose output options giving statistics of the results. CONCLUSION In this paper we present a new version of VIRAPOPS which now manages the viral segment reassortments and the negative sense single strain RNA viruses, these two issues being the cause of serious public health problems.
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Affiliation(s)
- Michel Petitjean
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013 Paris, France ; MTI, INSERM UMR-S 973, F-75013 Paris, France
| | - Anne Vanet
- Univ Paris Diderot, Sorbonne Paris Cité, F-75013 Paris, France ; CNRS, UMR7592, Institut Jacques Monod, F-75013 Paris, France ; Atelier de Bio Informatique, F-75005 Paris, France
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Petitjean M, Vanet A. VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. Bioinformatics 2013; 30:578-80. [PMID: 24336644 DOI: 10.1093/bioinformatics/btt724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists. AVAILABILITY AND IMPLEMENTATION Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
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Affiliation(s)
- Michel Petitjean
- Department of Biology, Univ Paris Diderot, Sorbonne Paris Cité, MTI, INSERM UMR-S 973, CNRS, UMR7592, Institut Jacques Monod, F-75013 Paris and Atelier de Bio Informatique, F-75005 Paris, France
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Kranthi T, Rao SB, Manimaran P. Identification of synthetic lethal pairs in biological systems through network information centrality. MOLECULAR BIOSYSTEMS 2013; 9:2163-7. [PMID: 23728082 DOI: 10.1039/c3mb25589a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The immense availability of protein interaction data, provided with an abstract network approach is valuable for the improved interpretation of biological processes and protein functions globally. The connectivity of a protein and its structure are related to its functional properties. Highly connected proteins are often functionally cardinal and the knockout of such proteins leads to lethality. In this paper, we propose a new approach based on graph information centrality measures to identify the synthetic lethal pairs in biological systems. To illustrate the efficacy of our approach, we have applied it to a human cancer protein interaction network. It is found that the lethal pairs obtained were analogous to the experimental and computational inferences, implying that our approach can serve as a surrogate for predicting the synthetic lethality.
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Affiliation(s)
- T Kranthi
- C R Rao Advanced Institute of Mathematics, Statistics and Computer Science, University of Hyderabad Campus, GachiBowli, Hyderabad - 500046, India.
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Braz ASK, Tufanetto P, Perahia D, Scott LPB. Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors. Proteins 2012; 80:2680-91. [DOI: 10.1002/prot.24151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/31/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
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