R S Bhardwaj Free Download

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Original Article

Discovery and in silico evaluation of aminoarylbenzosuberene molecules as novel checkpoint kinase 1 inhibitor determinants

Abstract

Checkpoint kinase 1 (CHK1) is an essential kinase with a critical function in cell cycle arrest. Several potent inhibitors targeting CHK1 have been published, but most of them have failed in clinical trials. Acknowledging the emerging consequence of CHK1 inhibitors in medication of cancer, there is a demand for widening the chemical range of CHK1 inhibitors. In this research, we considered a set of in-house plant based semi-synthetic aminoarylbenzosuberene molecules as potential CHK1 inhibitors. Based on a combined computational research that consolidates molecular docking and binding free energy computations we recognized the crucial determinants for their receptor binding. The drug likeness of these molecules were also scrutinized based on their toxicity and bioavailibilty profile. The computational strategy indicates that the Bch10 could be regarded as a potential CHK1 inhibitor in comparison with top five co-crystallize molecules. Bch10 signifies a promising outlet for the development of potent inhibitors for CHK1.

Introduction

Cancer is one of the world's most fatal diseases recording millions of deaths worldwide every year. A large number of proteins have been proclaimed to be connected in tumor induction and progression [[1], [2], [3], [4], [5]], the most engaging of which are kinases [6]. Tyrosine kinase inhibitors such as the epidermal receptor growth factor (EGFR) are being vended as drugs [7], which has also stirred attention towards serine-threonine kinases due to their significant role in carcinogenesis [8]. These kinases catalyze the serine/threonine residue phosphorylation on the substrate protein. Presently, checkpoint kinase 1 (CHK1) [9], PIM1 [10], MEK1 [11], and Cyclin-dependent kinases [12] have been listed as remarkably engaging targets for the discovery of cancer progression inhibitors.

Every dividing cell in an organism enters a cell division cycle, which is formed of various phases (G1, S, G2, and M) through which a cell proceeds to divide and form daughter cells. The progression of this cycle is halted at some checkpoints, which act as damaged DNA repair checkpoints usually occurring at the phases G1, S, and G2 [13,14]. This is a cellular counter mechanism to various DNA damage (for example, breaks in the continuous chain of DNA, single-base alteration, two base alterations, and cross-linkage) often occurring during the DNA replication process [15]. DNA damage can also occur as a result of exposure to ionizing radiation as well as chemotherapy often subjected to in the case of cancer treatment [15]. This counter-response mechanism is commenced via the serine-threonine protein kinase called the CHK1, which is a lengthy serine-threonine kinase made up of 476 amino acids and activated in case a damage in the DNA chain is detected, thus acting as a global regulator of the mammalian cell cycle. [13]. The activation of CHK1 involves two other upstream kinases, the ataxia telangiectasia Rad3 (ATR) related protein kinase, and the ataxia telangiectasia mutated (ATM) kinase [16,17]. The ATR-CHK1 pathway identifies an array of DNA irregularities, including the damage from virus infection, UV light, inter-strand DNA crosslinking, DNA replication inhibition, and double-strand break end resection [18,19]. These kinases phosphorylate CHK1 at residues S317 and S345 [20]. This phosphorylation activity, in turn, initiates the auto-phosphorylation of residue S296 hence activating the CHK1 [20]. The activated protein further brings about phosphorylation of a diverse array of substrates, one of which is the cell division cycle 25 (CDC25) group of phosphatases. The CDC25 group is accountable for cell cycle progression, where CHK1 mediates the DNA damage checkpoints at the S and G2 phases, and signals the DNA repair protein RAD51 to engage [17,21]. This repairing step is performed before the cell enters mitosis [13]. A successful DNA repair step allows the cell to proceed further into cell division by releasing the checkpoint. Still, if a checkpoint is active for a more extended period, it implies that the damage is severe and ultimately leads to cell death [13,17,22].

This property of CHK1 is exploited by the cancer cells to escape the DNA damaging anticancer therapies by repairing their damaged cancerous DNA, making CHK1 a prominent target for the development of new cancer treatments [17,23,24]. Healthy cells possess multiple checkpoints for DNA repair, where the p53 dependent G1 phase checkpoint is critical. However, most of the cancerous cells lack the G1 phase checkpoint due to mutation and deletion activities which leads to loss of function of the tumor suppressor p53 pathway. These cells solemnly rely on the CHK1 governed S and G2 phase checkpoints for the repair of high levels of damaged DNA strands and its inhibition thereby forms a possible monotherapy for cancerous cells [17,[25], [26], [27], [28], [29], [30], [31]]. The CHK1 is over-expressed in cancerous cells to overcome this replicative stress, thus, increased ATR-CHK1 signaling is observed in these cells [32,33]. It has also been proved experimentally that the intervention of CHK1 via small molecules selectively makes the cancer cells more susceptible to ionizing radiations as well as genotoxic drug molecules [23,32,[34], [35], [36]]. CHK1 inhibition only puts the cancerous cells into replicative stress, whereas the normal cells can surpass this stress due to the presence of an active p53 pathway for DNA repair [25]. The primary role of CHK1 is to regulate the response of the DDR and the cell cycle checkpoint [37,38]. It also governs a plethora of other biological activities, including gene transcription, embryo development, and somatic cell viability. In addition, CHK1 also controls cellular response to infection with the HIV virus, low or high oxygen exposure, stress due to protein misfolding, or heat shock [39,40].

Numerous substances of synthetic and natural roots have been published as inhibitors of the CHK1 in recent years. UCN-01 (7-hydroxystaurosporine) was the first CHK1 inhibitor to enter clinical trials in phase I and II towards a broad variety of tumors.

Many other inhibitors, for instance AZD7762 [41,42], SCH900776 [43,44], and PF-477736 [45] were afterward developed and governed to phase I trial. Unluckily, owing to the low selectivity and the number of side effects of such inhibitors, many of these clinical investigations were discontinued. The objectives of the study were to rank and compare the binding affinity of the in-house semi-synthesized aminoarylbenzosuberene molecules with top co-crystallized inhibitors of CHK1. Secondly, to validate the molecular docking results and in-depth analysis of protein-ligand complexes by performing robust, long-term (250 ns) molecular dynamics simulations. Lastly, identify the most potent inhibitor by calculating the thermodynamic binding free free energy by Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis.

Section snippets

Selection of the target protein and ligand molecules

The crystal structure of the CHK1 was taken from the Protein Data Bank (PDB). The crystal structure (PDB ID: 2YEX) [46] has the best resolution (1.30   Å) and IC₅₀ (0.1 nm) among all 133 crystal structures (Table S1) of CHK1 in the PDB and hence was used in this computational study. The bound YEX and other four molecules (S25, C70, 1AM, and 710) complexed with proteins PDB ID: 3TKI (1.60 Å: 0.05 nm IC₅₀), 3PA3 (1.40 Å: 1 nm IC₅₀), 4HYH (1.70 Å: 1 nm IC₅₀), 2HOG (1.90 Å: 0.3 nm IC₅₀) with best

Protein-ligand interaction analysis

The existing research is a step-by-step perspective to explore novel CHK1 inhibitors. To describe briefly, 17 molecules along with five best resolution and IC₅₀ based standard inhibitors from co-crystallized proteins were anchored into the active site of CHK1 to pointout credible binding poses. The -CDOCKER values were depicted in Table S2. The top ten molecules selected based on -CDOCKER interaction energy as tabulated in Table 1. In the first top-five selected CHK1-Bch complexes, Bch5 formed

Discussions

Molecular docking and MD simulations approaches have rendered perceptions into the ligand-CHK1 receptor interaction manner and in the discovery of potential CHK1 inhibitors. The availability of an inhibitor bound protein structure renders an outstanding opportunity to provide the data linked to their interaction. It will be beneficial to consolidate the derived data in structure-based drug design. Further, it has been noted that ligand-bound protein structures usually show more significant

Conclusions

In this investigation, we adopted an integrated in-silico protocol. It consists of molecular docking, MD simulations, thermodynamic free binding energy estimations, and per residue contribution for achieving profound insight towards the binding mechanism of the selected molecules. The free binding energy elements intimate that electrostatic and van der Waal energies are significant contributors to the binding process. The molecule Bch10 showed higher binding energy with adequate ADMET and

Author contributions

RP conceived of and designed the study. RP, RS, VKB, and JS analyzed and interpreted the data. PD provided chemical molecules for computational studies. RP critically revised it for important intellectual content. All authors gave final approval of the version to be published.

Declaration of Competing Interest

All authors hereby declare that they have no competing interests related to this work.

Acknowledgment

RP gratefully acknowledges the Board of Research in Nuclear Sciences, Department of Atomic Energy, Mumbai, India for financial support vide letter No: 37(1)/14/26/2015/BRNS. VB acknowledges the Department of Science and Technology, New Delhi, India for providing junior research fellowship SERB File No: ECR/2016/000031. We also acknowledge the CSIR-Institute of Himalayan Bioresource Technology, Palampur for providing the facilities to carry out this work. This manuscript represents CSIR-IHBT

References (67)

• et al.

  Structural changes induced by substitution of amino acid 129 in the coat protein of cucumber mosaic virus

  Genomics

  (2020)

• V.K. Bhardwaj et al.

  Structural based study to identify new potential inhibitors for dual specificity tyrosine-phosphorylation- regulated kinase

  Comput. Methods Prog. Biomed.

  (2020)

• M. Shimada et al.

  Chk1 is a histone H3 threonine 11 kinase that regulates DNA damage-induced transcriptional repression

  Cell

  (2008)

• M. Ben-Yehoyada et al.

  Checkpoint signaling from a single DNA interstrand crosslink

  Mol. Cell

  (2009)

• R. Choudhari et al.

  Redundant and nonredundant roles for Cdc42 and Rac1 in lymphomas developed in NPM-ALK transgenic mice

  Blood

  (2016)

• B. Hallberg et al.

  Mechanistic insight into ALK receptor tyrosine kinase in human cancer biology

  Nat. Rev. Cancer

  (2013)

• R. Chiarle et al.

  The anaplastic lymphoma kinase in the pathogenesis of cancer

  Nat. Rev. Cancer

  (2008)

• L. Galluzzi et al.

  Metabolic targets for cancer therapy

  Nat. Rev. Drug Discov.

  (2013)

• T. Bogenrieder et al.

  Axis of evil: molecular mechanisms of cancer metastasis

  Oncogene

  (2003)

• D. Fabbro et al.

  Targeting protein kinases in cancer therapy

  Curr. Opin. Drug Discov. Dev.

  (2002)

J. Hartmann et al.

Tyrosine kinase inhibitors – A review on pharmacology, metabolism and side effects

Curr. Drug Metab.

(2009)

M. Capra et al.

Frequent alterations in the expression of serine/threonine kinases in human cancers

Cancer Res.

(2006)

Z.-F. Tao et al.

Chk1 inhibitors for novel cancer treatment, anticancer

Agents Med. Chem.

(2008)

A.L. Merkel et al.

PIM1 kinase as a target for cancer therapy

Expert Opin. Investig. Drugs

(2012)

C.C.Y. Leow et al.

MEK inhibitors as a chemotherapeutic intervention in multiple myeloma

Blood Cancer J.

(2013)

M. Malumbres et al.

Cell cycle, CDKs and cancer: a changing paradigm

Nat. Rev. Cancer

(2009)

J.D. Osborne et al.

Multiparameter lead optimization to give an oral checkpoint kinase 1 (CHK1) inhibitor clinical candidate: (R)-5-((4-((Morpholin-2-ylmethyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)pyrazine-2-carbonitrile (CCT245737)

J. Med. Chem.

(2016)

Z. Xiao et al.

Chk1 mediates S and G2 arrests through Cdc25A degradation in response to DNA-damaging agents

J. Biol. Chem.

(2003)

Y. Dai et al.

New insights into checkpoint kinase 1 in the DNA damage response signaling network

Clin. Cancer Res.

(2010)

J. Smith et al.

The ATM-Chk2 and ATR-Chk1 pathways in DNA damage signaling and cancer

Adv. Cancer Res.

(2010)

T.P. Matthews et al.

Identification of inhibitors of checkpoint kinase 1 through template screening

J. Med. Chem.

(2009)

M. Cuadrado et al.

ATM regulates ATR chromatin loading in response to DNA double-strand breaks

J. Exp. Med.

(2006)

C.A.L. Clarke et al.

DNA-dependent phosphorylation of Chk1 and Claspin in a human cell-free system

Biochem. J.

(2005)

C.S. Sørensen et al.

The cell-cycle checkpoint kinase Chk1 is required for mammalian homologous recombination repair

Nat. Cell Biol.

(2005)

J. Bartek et al.

Chk1 and Chk2 kinases in checkpoint control and cancer

Cancer Cell

(2003)

T. Chen et al.

Targeting the S and G2 checkpoint to treat cancer

Drug Discov. Today

(2012)

Y. Luo et al.

New opportunities in chemosensitization and radiosensitization: modulating the DNA-damage response

Expert. Rev. Anticancer. Ther.

(2005)

C.X. Ma et al.

Death by releasing the breaks: CHK1 inhibitors as cancer therapeutics

Trends Mol. Med.

(2011)

K.A. Cole et al.

RNAi screen of the protein kinome identifies checkpoint kinase 1 (CHK1) as a therapeutic target in neuroblastoma

Proc. Natl. Acad. Sci. U. S. A.

(2011)

A. Höglund et al.

Therapeutic implications for the induced levels of Chk1 in Myc-expressing cancer cells

Clin. Cancer Res.

(2011)

K. Brooks et al.

A potent Chk1 inhibitor is selectively cytotoxic in melanomas with high levels of replicative stress

Oncogene.

(2013)

L. Albiges et al.

Chk1 as a new therapeutic target in triple-negative breast cancer

Breast

(2014)

P.T. Ferrao et al.

Efficacy of CHK inhibitors as single agents in MYC-driven lymphoma cells

Oncogene

(2012)

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