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Kumari S, Chakraborty S, Ahmad M, Kumar V, Tailor PB, Biswal BK. Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approach. Int J Biol Macromol 2023; 229:515-528. [PMID: 36584781 PMCID: PMC9794403 DOI: 10.1016/j.ijbiomac.2022.12.252] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Given the paucity of antiviral treatments for monkeypox disease, caused by the Monkeypox virus (MPXV), there is a pressing need for the development/identification of new drugs to treat the infection. MPXV possesses a linear dsDNA genome that is replicated by a DNA replication complex of which DNA polymerase (DPol) forms an important component. Owing to the importance of DPol in the viral life cycle, identifying/designing small molecules abolishing its function could yield new antivirals. In this study, we first used the AlphaFold artificial intelligence program to model the 3D structure of the MPXV DPol; like the fold of DPol from other organisms, the MPXV DPol structure has the characteristic exonuclease, thumb, palm, and fingers sub-domains arrangement. Subsequently, we have identified several inhibitors through virtual screening of ZINC and antiviral libraries. Molecules with phenyl scaffold along with alanine-based and tetrazole-based molecules showed the best docking score of -8 to -10 kcal/mol. These molecules bind in the palm and fingers sub-domains interface region, which partially overlaps with the DNA binding path. The delineation of DPol/inhibitor interactions showed that majorly active site residues ASP549, ASP753, TYR550, ASN551, SER552, and ASN665 interact with the inhibitors. These compounds exhibit good Absorption, Distribution, Metabolism and Excretion properties.
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Affiliation(s)
- Swati Kumari
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sayan Chakraborty
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mohammed Ahmad
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Varun Kumar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | - Bichitra K Biswal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Bolz SN, Salentin S, Jennings G, Haupt VJ, Sterneckert J, Schroeder M. Structural binding site comparisons reveal Crizotinib as a novel LRRK2 inhibitor. Comput Struct Biotechnol J 2021; 19:3674-3681. [PMID: 34285770 PMCID: PMC8258795 DOI: 10.1016/j.csbj.2021.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 12/02/2022] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a frequent cause of autosomal dominant Parkinson’s disease (PD) and have been associated with familial and sporadic PD. Reducing the kinase activity of LRRK2 is a promising therapeutic strategy since pathogenic mutations increase the kinase activity. Several small-molecule LRRK2 inhibitors are currently under investigation for the treatment of PD. However, drug discovery and development are always accompanied by high costs and a risk of late failure. The use of already approved drugs for a new indication, which is known as drug repositioning, can reduce the cost and risk. In this study, we applied a structure-based drug repositioning approach to identify new LRRK2 inhibitors that are already approved for a different indication. In a large-scale structure-based screening, we compared the protein–ligand interaction patterns of known LRRK2 inhibitors with protein–ligand complexes in the PDB. The screening yielded 6 drug repositioning candidates. Two of these candidates, Sunitinib and Crizotinib, demonstrated an inhibition potency (IC50) and binding affinity (Kd) in the nanomolar to micromolar range. While Sunitinib has already been known to inhibit LRRK2, Crizotinib is a novel LRRK2 binder. Our results underscore the potential of structure-based methods for drug discovery and development. In light of the recent breakthroughs in cryo-electron microscopy and structure prediction, we believe that structure-based approaches like ours will grow in importance.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, Dresden 01307, Germany
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, Dresden 01307, Germany
| | - Gary Jennings
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, Dresden 01307, Germany
| | - V Joachim Haupt
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, Dresden 01307, Germany
| | - Jared Sterneckert
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstr. 105, Dresden 01307, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, Tatzberg 47/49, Dresden 01307, Germany
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Zhu G, Zhu C, Zhu Y, Sun F. Minireview of progress in the structural study of SARS-CoV-2 proteins. Curr Res Microb Sci 2020; 1:53-61. [PMID: 33236001 PMCID: PMC7323663 DOI: 10.1016/j.crmicr.2020.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/18/2023] Open
Abstract
Major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2. This review summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins. The molecular details of SARS-CoV-2 infection and replication could improve the effective clinical treatment.
A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization, broke out in China and rapidly developed into a global pandemic, with millions of cases and hundreds of thousands of deaths reported globally. The novel coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of COVID-19. On the basis of experience accumulated following previous SARS-CoV and MERS-CoV outbreaks and research, a series of studies have been conducted rapidly, and major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2 in addition its molecular mechanisms of infection and replication. In the present review, we summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins, especially the main protease, RNA-dependent RNA polymerase, spike glycoprotein, and nucleocapsid protein. Results of studies on their associated inhibitors and drugs have also been highlighted.
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Key Words
- 3CLpro, 3C-like protease
- 6-HB, six-helix bundle
- ACE2, angiotensin-converting enzyme 2
- COVID-19
- COVID-19, coronavirus disease 2019
- CatB/L, cysteine proteases-cathepsin B and L
- Drug-screening
- E protein, Envelope protein
- Genome-encoded proteins
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- M protein, Membrane protein
- MERS-CoV, the Middle Eastern respiratory syndrome coronavirus
- Mpro, Main protease
- N protein, Nucleocapsid protein
- NSP, non-structural protein
- ORF, Open reading frame
- PD, peptidase domain
- RBD, receptor-binding domain
- RBM, receptor-binding motif
- RMP, The remdesivir monophosphate
- RdRp, RNA-dependent RNA polymerase
- S protein, Spike glycoprotein
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Structure-based screening
- gRNA, genomic RNA
- sgRNA, subgenomic RNA
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Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Corresponding authors.
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Corresponding authors.
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Patnaik D. Structure-based screening of chemical libraries to identify small molecules that are likely to bind with the SET and RING-associated (SRA) domain of Ubiquitin-like, PHD and Ring Finger-containing 1 (UHRF1). BMC Res Notes 2020; 13:254. [PMID: 32448288 PMCID: PMC7247125 DOI: 10.1186/s13104-020-05103-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/20/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES UHRF1 is a multi-domain protein that recognizes both histone and DNA modification marks on chromatin. UHRF1 is involved in various cellular processes that lead to tumorigenesis and thus attracted considerable attention as a potential anti-cancer drug target. The SRA domain is a unique to the UHRF family. SRA domain recognizes 5-methylcytosine in hemimethylated DNA and necessary for maintenance DNA methylation mediated by DNMT1. Small molecules capable of interacting with the SRA domain may reduce aberrant methylation levels by preventing the interaction of 5-methylcytosine with the SRA domain and thereby blocking substrate access to the catalytic center of DNMT1. The data were collected to identify and predict an initial set of small molecules that are expected to bind to the SRA domain. DATA DESCRIPTION Nearly 2.4 million molecules from various chemical libraries were screened with the SRA domain of UHRF1 using Schrodinger's Small Molecule Drug Discovery Suite. The data is available in the form of a methodology presentation, MS Excel files listing the top hits, and Maestro pose viewer files that provide visualization of how the identified ligands interact with the SRA domain.
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Adasme MF, Parisi D, Sveshnikova A, Schroeder M. Structure-based drug repositioning: Potential and limits. Semin Cancer Biol 2020; 68:192-198. [PMID: 32032699 DOI: 10.1016/j.semcancer.2020.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/08/2020] [Accepted: 01/16/2020] [Indexed: 12/28/2022]
Abstract
Drug repositioning, the assignment of new therapeutic purposes to known drugs, is an established strategy with many repurposed drugs on the market and many more at experimental stage. We review three use cases, a herpes drug with benefits in cancer, a cancer drug with potential in autoimmune disease, and a selective and an unspecific drug binding the same target (GPCR). We explore these use cases from a structural point of view focusing on a deep understanding of the underlying drug-target interactions. We review tools and data needed for such a drug-centric structural repositioning approach. Finally, we show that the availability of data on targets is an important limiting factor to realize the full potential of structural drug-repositioning.
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Affiliation(s)
- Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Daniele Parisi
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany; ESAT-STADIUS, KU Leuven, B-3001 Heverlee, Belgium
| | - Anastasia Sveshnikova
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany.
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Mehta P, Srivastava S, Sharma M, Singh I, Malik R. Identification of chemically diverse GABA A agonists as potential anti-epileptic agents using structure-guided virtual screening, ADMET, quantum mechanics and clinical validation through off-target analysis. Int J Biol Macromol 2018; 119:1113-1128. [PMID: 30098361 DOI: 10.1016/j.ijbiomac.2018.08.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/19/2022]
Abstract
Development of resistance against existing anti-epileptic drugs has alarmed the scientific innovators to find novel potential chemical starting points for the treatment of epilepsy and GABAA inhibition is a promising drug target strategy against epilepsy. The crystal structure of a subtype-selective β3-homopentameric ligand-gated ion channel of GABAA receptor has been used for the first time for screening the Asinex library for discovery of GABAA agonists as potential anti-epileptic agents. Co-crystallized ligand established the involvement of part of the β7-β8 loop (Glu155 and Tyr157) and β9-β10 loop (Phe200 and Tyr205) residues as the crucial amino acids in effective binding, an essential feature, being hydrogen bond or ionic interaction with Glu155 residue. Top ranked hits were further subjected to binding energy estimation, ADMET analysis and ligand efficiency matric calculations as consecutive filters. About 19 compounds qualifying all parameters possessed interaction of one positively charged group with Glu155 with good CNS drug-like properties. Simulation studies were performed on the apo protein, its complex with co-crystallized ligand and the best hit qualifying all screening parameters. The best hit was also analyzed using Quantum mechanical studies, off-target analysis and hit modification. The off-target analysis emphasized that these agents did not have any other predicted side-effects.
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Affiliation(s)
- Pakhuri Mehta
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Shubham Srivastava
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India
| | - Manish Sharma
- School of Pharmacy, Maharishi Markandeshwar University, Sadopur, Ambala, Haryana 134007, India
| | - Inderpal Singh
- Bioinformatics Infrastructure Facility, Department of Biotechnology, Shri Mata Vaishno Devi University (SMVDU), Kakryal, Katra, Jammu & Kashmir 182320, India
| | - Ruchi Malik
- Department of Pharmacy, Central University of Rajasthan, NH-8, Bandar Sindri, Ajmer, Rajasthan 305817, India.
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Chen PC, Masiewicz P, Rybin V, Svergun D, Hennig J. A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions. ACS Comb Sci 2018; 20:197-202. [PMID: 29553252 DOI: 10.1021/acscombsci.8b00007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information on biomolecular interactions independent of prior knowledge, so as to complement affinity-based screening and provide leads for further exploration. This protocol categorizes ligand titrations by computing pairwise agreement between curves, and separately estimates affinities by quantifying complex formation as a departure from the linear sum properties of solution SAXS. The protocol is validated by sparse sequence search around the native poly uridine RNA motifs of the two-RRM domain Sex-lethal protein (Sxl). The screening of 35 RNA motifs between 4 to 10 nucleotides reveals a strong variation of resulting complexes, revealed to be preference-switching between 1:1 and 2:2 binding stoichiometries upon addition of structural modeling. Validation of select sequences in isothermal calorimetry and NMR titration retrieves domain-specific roles and function of a guanine anchor. These findings reinforce the suitability of SAXS as a complement in lead identification.
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Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Vladimir Rybin
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Dmitri Svergun
- EMBL Hamburg, DESY, Building 25A, Notkestraße 85, 22607 Hamburg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
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Abstract
A number of diverse approaches for efficient screening of compound collections in silico are nowadays available, each with their own methodological background, successes and limitations. Implementation of such virtual screening methods has enabled an impressive acceleration in the search toward the most biologically relevant regions of chemical space and has greatly facilitated the discovery of novel biologically active molecules. It is noteworthy that the range of principles on which the available virtual screening methodologies are based is wide enough for several of these methods to be considered as orthogonal to a good extent. We hereby propose a simple and extensible protocol aiming at integrating the diverse information derived by such virtual screening methods in a consensus manner that can achieve an improvement of the hit rate obtained by individual use of those methods. The protocol can be performed in its basic version as described in this work, but it can also be extended manually by integrating a number of different screening tools and their case-specific variations to further increase the performance of virtual screening in prioritizing the most promising compounds for in vitro evaluations.
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Affiliation(s)
- Vassilios Myrianthopoulos
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece.,"Athena" Research and Innovation Center, Athens, Greece
| | - George Lambrinidis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece. .,"Athena" Research and Innovation Center, Athens, Greece.
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Myrianthopoulos V, Cartron PF, Liutkevičiūtė Z, Klimašauskas S, Matulis D, Bronner C, Martinet N, Mikros E. Tandem virtual screening targeting the SRA domain of UHRF1 identifies a novel chemical tool modulating DNA methylation. Eur J Med Chem 2016; 114:390-6. [PMID: 27049577 DOI: 10.1016/j.ejmech.2016.02.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/29/2022]
Abstract
Ubiquitin-like protein UHRF1 that contains PHD and RING finger domain 1 is a key epigenetic protein enabling maintenance of the DNA methylation status through replication. A tandem virtual screening approach was implemented for identifying small molecules able to bind the 5-methylcytosine pocket of UHRF1 and inhibit its functionality. The NCI/DTP small molecules Repository was screened in silico by a combined protocol implementing structure-based and ligand-based methodologies. Consensus ranking was utilized to select a set of 27 top-ranked compounds that were subsequently evaluated experimentally in a stepwise manner for their ability to demethylate DNA in cellulo using PCR-MS and HPLC-MS/MS. The most active molecules were further assessed in a cell-based setting by the Proximity Ligation In Situ Assay and the ApoTome technology. Both evaluations confirmed that the DNMT1/UHRF1 interactions were significantly reduced after 4 h of incubation of U251 glioma cells with the most potent compound NSC232003, showing a 50% interaction inhibition at 15 μM as well as induction of global DNA cytosine demethylation as measured by ELISA. This is the first report of a chemical tool that targets UHRF1 and modulates DNA methylation in a cell context by potentially disrupting DNMT1/UHRF1 interactions. Compound NSC232003, a uracil derivative freely available by the NCI/DTP Repository, provides a versatile lead for developing highly potent and cell-permeable UHRF1 inhibitors that will enable dissection of DNA methylation inheritance.
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