Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

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Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

10.1101/2021.02.03.429510 ◽

2021 ◽

Author(s):

Abhisek Dwivedy ◽

Richard Mariadasse ◽

Mohammed Ahmad ◽

Sayan Chakraborty ◽

Deepsikha Kar ◽

...

Keyword(s):

Active Site ◽

Drug Target ◽

Kinase Inhibitors ◽

3D Structure ◽

Drug Repurposing ◽

Lead Compounds ◽

Nucleotidyl Transferase ◽

Domain Organisation ◽

First Time

AbstractApart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

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In silico characterization of the NiRAN domain of RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV2

10.31219/osf.io/wd6zu ◽

2020 ◽

Cited By ~ 1

Author(s):

Abhisek Dwivedy ◽

Richard Mariadasse ◽

Mohammed Ahmed ◽

Deepsikha Kar ◽

Jeyaraman Jeyakanthan ◽

...

Keyword(s):

Active Site ◽

In Silico ◽

3D Structure ◽

Drug Repurposing ◽

The Novel ◽

Lead Compounds ◽

Nucleotidyl Transferase ◽

Domain Organisation ◽

Novel Coronavirus ◽

In Silico Characterization

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Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells

Science Signaling ◽

10.1126/scisignal.aat7951 ◽

2018 ◽

Vol 11 (549) ◽

pp. eaat7951 ◽

Cited By ~ 23

Author(s):

Daniel M. Foulkes ◽

Dominic P. Byrne ◽

Wayland Yeung ◽

Safal Shrestha ◽

Fiona P. Bailey ◽

...

Keyword(s):

Cancer Cells ◽

Small Molecule ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Growth Factor Receptor ◽

Drug Repurposing ◽

Protein Kinase Inhibitors ◽

Cellular Mechanisms ◽

Cellular Analysis

A major challenge associated with biochemical and cellular analysis of pseudokinases is a lack of target-validated small-molecule compounds with which to probe function. Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a diverse interactome, including the canonical AKT signaling module. There is substantial evidence that human TRIB2 promotes survival and drug resistance in solid tumors and blood cancers and therefore is of interest as a therapeutic target. The unusual TRIB2 pseudokinase domain contains a unique cysteine-rich C-helix and interacts with a conserved peptide motif in its own carboxyl-terminal tail, which also supports its interaction with E3 ubiquitin ligases. We found that TRIB2 is a target of previously described small-molecule protein kinase inhibitors, which were originally designed to inhibit the canonical kinase domains of epidermal growth factor receptor tyrosine kinase family members. Using a thermal shift assay, we discovered TRIB2-binding compounds within the Published Kinase Inhibitor Set (PKIS) and used a drug repurposing approach to classify compounds that either stabilized or destabilized TRIB2 in vitro. TRIB2 destabilizing agents, including the covalent drug afatinib, led to rapid TRIB2 degradation in human AML cancer cells, eliciting tractable effects on signaling and survival. Our data reveal new drug leads for the development of TRIB2-degrading compounds, which will also be invaluable for unraveling the cellular mechanisms of TRIB2-based signaling. Our study highlights that small molecule–induced protein down-regulation through drug “off-targets” might be relevant for other inhibitors that serendipitously target pseudokinases.

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Imatinib Mesylate Induces BCR-ABL Independent Inhibition of Proteasomal Activity in CML Cells

Blood ◽

10.1182/blood.v112.11.4226.4226 ◽

2008 ◽

Vol 112 (11) ◽

pp. 4226-4226

Author(s):

Stefanie A.E. Held ◽

Peter Brossart

Keyword(s):

Imatinib Mesylate ◽

Cell Lines ◽

Active Site ◽

Antigen Processing ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Multikinase Inhibitor ◽

Proteasomal Activity ◽

Cell Lysates ◽

Hla Class I Molecules

Abstract Imatinib mesylate (IM; Gleevec) is currently used in the treatment of CML and GIST. IM has been described to influence the function and differentiation of antigen presenting cells, to inhibit the effector function of T lymphocytes and to decrease the immunogenicity of CML cells by downregulation of tumor associated antigens. In the present study, we analyzed the possible effects of IM on antigen processing and presentation. To accomplish this we employed active site labelling of proteasomal subunits to measure proteasomal activities in cells treated with IM and other tyrosine kinase inhibitors (TKIs). Proteasomal activity was determined in cell lysates from established CML cell lines and primary cells from CML patients using a biotinylated active site-directed probe, which, covalently binds and labels proteasomal subunits beta-1, beta-2 and beta-5 depending on their activity. In addition, in order to analyze a possible direct effect of IM, isolated 20S and 26S proteasomes were examined. We found that treatment with IM led to a concentration-dependent decrease of proteasomal activity in BCR-ABL positive cells. In line with these results IM reduced the expression of HLA-class I molecules in HLA-A2 transfected K-562 cells. This inhibitory effect was independent of protein expression of proteasome subunits as analyzed by western blotting and it was not due to the induction of apoptosis as only samples with nuclei fragmentation below 40% were utilized. Furthermore, these effects were not inhibited by addition of zVAD, a pan-caspase inhibitor of apoptosis. The inhibition of proteasomal activity was independent of BCR-ABL as analyzed using IM resistant CML cell lines including BA/F-T315I cell line which is transfected with the multiresistent T315I mutation. Application of BCR-ABL specific siRNA to knock down its expression had no significant influence on proteasomal activity. Accordingly, incubation of isolated 20S and 26S proteasomes with IM resulted in a profound inhibition of their activity as determined by reduced proteolytic cleavage of fluorogenic substrates. Interestingly, this inhibition of the proteasomal activity was not IM specific as nilotinib, a TKI with a higher BCR-ABL affinity had similar effects. Furthermore, the multikinase inhibitor sorafenib but not sunitinib reduced the proteasomal activity in cell lysates and isolated proteasomes. Incubation of cells with the mTOR inhibitor rapamycin inhibited the activity of proteasomal subunits while the PI3 kinase inhibitor LY-294002 that acts upstream of rapamycin had no effect. Our results demonstrate that IM and several other TKIs currently applied in the treatment of patients can affect the immunogenicity of malignant cells by a direct inhibition of the proteasomal activity.

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KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery

10.1101/2021.03.28.436965 ◽

2021 ◽

Author(s):

Zhi-Zheng Wang ◽

Xing-Xing Shi ◽

Fan Wang ◽

Ge-Fei Hao ◽

Guang-Fu Yang

Keyword(s):

Drug Targets ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Structural Information ◽

3D Structure ◽

Interaction Space ◽

Design Strategies ◽

Growing Strategy ◽

Fragment Interaction

Protein kinases play a crucial role in many cellular signaling processes, making them one of the most important families of drug targets. But selectivity put a barrier at the design of kinase inhibitors. Fragment-based drug design strategies have been successfully applied to develop novel selective kinase inhibitors. However, the complicate kinase-fragment interaction and fragment-to-lead process pose challenges to fragment-based kinase discovery. Here, we developed a web source KinaFrag to investigate kinase-fragment interaction space and perform fragment-to-lead optimization. KinaFrag contained 31464 fragments from reported kinase inhibitors, which involved 3244 crystal fragment structures and 7783 crystal kinase-fragment complexes. These crystal fragments were classified by their binding cleft and subpockets, and their 3D structure and interactions were displayed in KinaFrag. In addition, the structural information, physicochemical information, similarity information, and substructure relationship information were contained in KinaFrag. Moreover, a computational fragment growing strategy obviously developed by our group was implemented in the KinaFrag. We test this fragment growing strategy using our fragment libraries, and obtained a lead compound of c-Met with ~1000-fold in vitro activity improvement compared with the hit compound. We hope KinaFrag could become a powerful tool for the fragment-based kinase inhibitor design. KinaFrag is freely available at http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/.

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Assembly of VP26 in herpes simplex virus-1 capsid implicated by 3-D structure of recombinant capsid

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100140579 ◽

1995 ◽

Vol 53 ◽

pp. 840-841

Author(s):

Z. Hong Zhou ◽

Jing He ◽

Joanita Jakana ◽

J. D. Tatman ◽

Frazer J. Rixon ◽

...

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

3D Structure ◽

Structure Study ◽

Herpes Simplex Virus 1 ◽

Shell Proteins ◽

Life Threatening ◽

Infected Cells ◽

Simplex Virus ◽

Hsv 1

Herpes simplex virus-1 (HSV-1) is a ubiquitous virus which is implicated in diseases ranging from self-curing cold sores to life-threatening infections. The 2500 Å diameter herpes virion is composed of a glycoprotein spike containing, lipid envelope, enclosing a protein layer (the tegument) in which is embedded the capsid (which contains the dsDNA genome). The B-, and A- and C-capsids, representing different morphogenetic stages in HSV-1 infected cells, are composed of 7, and 5 structural proteins respectively. The three capsid types are organized in similar T=16 icosahedral shells with 12 pentons, 150 hexons, and 320 connecting triplexes. Our previous 3D structure study at 26 Å revealed domain features of all these structural components and suggested probable locations for the outer shell proteins, VP5, VP26, VP19c and VP23. VP5 makes up most of both pentons and hexons. VP26 appeared to bind to the VP5 subunit in hexon but not to that in penton.

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Synthesis of Drugs and Biorelevant N-heterocycles Employing Recent Advances in C-N Bond Formation

Current Organic Chemistry ◽

10.2174/1385272824999200909114144 ◽

2020 ◽

Vol 24 (20) ◽

pp. 2293-2340

Author(s):

Firdoos Ahmad Sofi ◽

Prasad V. Bharatam

Keyword(s):

Kinase Inhibitors ◽

Bond Formation ◽

Comprehensive Review ◽

Biologically Relevant ◽

Lead Compounds ◽

Heterocyclic Molecules ◽

The Past ◽

Anti Cancer ◽

Modern Methods ◽

Bond Formation Reactions

C-N bond formation is a particularly important step in the generation of many biologically relevant heterocyclic molecules. Several methods have been reported for this purpose over the past few decades. Well-known named reactions like Ullmann-Goldberg coupling, Buchwald-Hartwig coupling and Chan-Lam coupling are associated with the C-N bond formation reactions. Several reviews covering this topic have already been published. However, no comprehensive review covering the synthesis of drugs/ lead compounds using the C-N bond formation reactions was reported. In this review, we cover many modern methods of the C-N bond formation reactions, with special emphasis on metal-free and green chemistry methods. We also report specific strategies adopted for the synthesis of drugs, which involve the C-N bond formation reactions. Examples include anti-cancer, antidepressant, anti-inflammatory, anti-atherosclerotic, anti-histaminic, antibiotics, antibacterial, anti-rheumatic, antiepileptic and anti-diabetic agents. Many recently developed lead compounds generated using the C-N bond formation reactions are also covered in this review. Examples include MAP kinase inhibitors, TRKs inhibitors, Polo-like Kinase inhibitors and MPS1 inhibitors.

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Thrombotic microangiopathy in dasatinib-treated patients with chronic myeloid leukemia

Journal of Onco-Nephrology ◽

10.1177/2399369319887979 ◽

2019 ◽

Vol 4 (1-2) ◽

pp. 41-45 ◽

Cited By ~ 1

Author(s):

Takeo Koshida ◽

Sylvia Wu ◽

Hitoshi Suzuki ◽

Rimda Wanchoo ◽

Vanesa Bijol ◽

...

Keyword(s):

Chronic Myeloid Leukemia ◽

Tyrosine Kinase ◽

Tyrosine Kinase Inhibitor ◽

Tyrosine Kinase Inhibitors ◽

Thrombotic Microangiopathy ◽

Myeloid Leukemia ◽

Kinase Inhibitors ◽

Kidney Biopsy ◽

Kinase Inhibitor ◽

Target Effect

Dasatinib is the second-generation tyrosine kinase inhibitor used in the treatment of chronic myeloid leukemia. Proteinuria has been reported with this agent. We describe two kidney biopsy–proven cases of dasatinib-induced thrombotic microangiopathy that responded to stoppage of dasatinib and using an alternate tyrosine kinase inhibitor. Certain specific tyrosine kinase inhibitors lead to endothelial injury and renal-limited thrombotic microangiopathy. Hematologists and nephrologists need to be familiar with this off-target effect of dasatinib.

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Computational evaluation of potent 2-(1H-imidazol-2-yl) pyridine derivatives as potential V600E-BRAF inhibitors

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-020-00111-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Abdullahi Bello Umar ◽

Adamu Uzairu ◽

Gideon Adamu Shallangwa ◽

Sani Uba

Keyword(s):

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Acquired Resistance ◽

Docking Studies ◽

Major Protein ◽

Pharmacological Properties ◽

Braf Inhibitors ◽

Protein Target ◽

Computational Evaluation ◽

Better Than

Abstract Background V600E-BRAF is a major protein target involved in various types of human cancers. However, the acquired resistance of the V600E-BRAF kinase to the vemurafenib and the side effects of other identified drugs initiate the search for efficient inhibitors. In the current paper, virtual docking screening combined with drug likeness and ADMET properties predictions were jointly applied to evaluate potent 2-(1H-imidazol-2-yl) pyridines as V600E-BRAF kinase inhibitors. Results Most of the studied compounds showed better docking scores and favorable interactions with theiV600E-BRAF target. Among the screened compounds, the two most potent (14 and 30) with good rerank scores (−124.079 and − 122.290) emerged as the most effective, and potent V600E-BRAF kinase inhibitors which performed better than vemurafenib (−116.174), an approved V600E-BRAF kinase inhibitor. Thus, the docking studies exhibited that these compounds have shown competing inhibition of V600E-BRAF kinase with vemurafenib at the active site and revealed better pharmacological properties based on Lipinski’s and Veber’s drug-likeness rules for oral bioavailability and ADMET properties. Conclusion The docking result, drug-likeness rules, and ADMET parameters identified compounds (14 and 30) as the best hits against V600E-BRAF kinase with better pharmacological properties. This suggests that these compounds may be developed as potent V600E-BRAF inhibitors.

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Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia

Nature Communications ◽

10.1038/s41467-020-20259-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hu Lei ◽

Han-Zhang Xu ◽

Hui-Zhuang Shan ◽

Meng Liu ◽

Ying Lu ◽

...

Keyword(s):

Tyrosine Kinase ◽

Progenitor Cells ◽

Chronic Myelogenous Leukemia ◽

Drug Targets ◽

Kinase Inhibitors ◽

Kinase Inhibitor ◽

Myelogenous Leukemia ◽

Tki Resistance

AbstractIdentifying novel drug targets to overcome resistance to tyrosine kinase inhibitors (TKIs) and eradicating leukemia stem/progenitor cells are required for the treatment of chronic myelogenous leukemia (CML). Here, we show that ubiquitin-specific peptidase 47 (USP47) is a potential target to overcome TKI resistance. Functional analysis shows that USP47 knockdown represses proliferation of CML cells sensitive or resistant to imatinib in vitro and in vivo. The knockout of Usp47 significantly inhibits BCR-ABL and BCR-ABLT315I-induced CML in mice with the reduction of Lin−Sca1+c-Kit+ CML stem/progenitor cells. Mechanistic studies show that stabilizing Y-box binding protein 1 contributes to USP47-mediated DNA damage repair in CML cells. Inhibiting USP47 by P22077 exerts cytotoxicity to CML cells with or without TKI resistance in vitro and in vivo. Moreover, P22077 eliminates leukemia stem/progenitor cells in CML mice. Together, targeting USP47 is a promising strategy to overcome TKI resistance and eradicate leukemia stem/progenitor cells in CML.

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