1
|
Khidre RE, Salem MA, Ameen TA, Abdelgawad AAM. Triazoloquinolines II: Synthesis, Reactions, and Pharmacological Properties of [1,2,4]Triazoloquinoline and 1,2,4-Triazoloisoquinoline Derivatives. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2008457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Rizk E. Khidre
- Chemistry Department, Faculty of Science, Jazan University, Jazan, Saudi Arabia
- Chemical Industries Division, National Research Centre, Giza, Egypt
| | - Mounir A. Salem
- Chemistry Department, Synthetic Heterocycles Laboratory, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Tahah A. Ameen
- Chemistry Department, Faculty of Science, Jazan University, Jazan, Saudi Arabia
- Chemistry Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ahmed A. M. Abdelgawad
- Chemistry Department, Faculty of Science, Jazan University, Jazan, Saudi Arabia
- Medicinal and Aromatic Plants Department, Desert Research Center, Cairo, Egypt
| |
Collapse
|
2
|
Singh R, Bhardwaj VK, Sharma J, Das P, Purohit R. Discovery and in silico evaluation of aminoarylbenzosuberene molecules as novel checkpoint kinase 1 inhibitor determinants. Genomics 2020; 113:707-715. [PMID: 33065246 DOI: 10.1016/j.ygeno.2020.10.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 10/01/2020] [Indexed: 01/12/2023]
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.
Collapse
Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP 176061, India; Biotechnology division, CSIR-IHBT, Palampur, HP 176061, India; Academy of Scientific & Innovative Research (AcSIR), CSIR-IHBT Campus, Palampur, HP 176061, India.
| |
Collapse
|
3
|
Prediction of Toxoplasma gondii virulence factor ROP18 competitive inhibitors by virtual screening. Parasit Vectors 2019; 12:98. [PMID: 30867024 PMCID: PMC6416898 DOI: 10.1186/s13071-019-3341-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 02/26/2019] [Indexed: 02/06/2023] Open
Abstract
Background Rhoptry protein 18 (ROP18) is a key virulence factor of Toxoplasma gondii. The host’s immune responses mediated by immune-related GTPases (IRGs) could be blocked by ROP18’s kinase activity. ROP18 also interacts with various substrates, such as activating transcription factor 6 beta (ATF6β) and affects multiple physiological functions within host cells, thereby inducing intense virulence. In this study, competitive inhibitors targeted to ROP18 were subjected to virtual screening based on the principle of structure-based drug design (SBDD). Methods The preparation of the ROP18 structure was conducted using the “Structure Prepare” function of Molecular Operating Environment (MOE) software. The ATP-binding pocket was selected as the starting point for virtual screening. Construction of the pharmacophore model used Extended Hückel Theory (EHT) half-quantitative measurement and construction, as well as the characteristics of Type I kinase inhibitors. The pharmacophore model of ROP18 was imported into the Specs database for small molecule similarity screening using EHT pharmacophore measurement. Hit compounds were selected using the functions of London dG and generalized-born volume integral/weighted surface area (GBVI/WSA) scoring. The top 100 hits were analyzed by molecular docking and structure activity relationships (SAR) analysis. Results The final pharmacophore comprised three typical characteristics: three hydrogen bond acceptors/donors, two ring aromatic features occupying the hydrophobic core, and one cation group feature targeted to the terminus of ATP. A total of 1314 hit compounds analogous to ROP18 pharmacophore were passed through the Specs. After two rounds of docking, 25 out of 100 hits were identified as belonging to two main scaffold types: phthalimide ring structure, thiazole ring and styrene structure. Additionally, the screen also identified 13 inhibitors with distinct scaffold types. The docking models and SAR analysis demonstrated that these hits could engage in multiple hydrogen bonds, salt bridges halogen bonds, and hydrophobic interactions with ROP18, and para-position halo substituents on the benzene ring may enhance their affinity scoring. Conclusions A pharmacophore against the ROP18 ATP-binding pocket was successfully constructed, and 25 representative inhibitors from 15 scaffold clusters were screened using the Specs database. Our results provide useful scaffold types for the chemical inhibition of ROP18 or alternative conformations to develop new anti-toxoplasmosis drug leads. Electronic supplementary material The online version of this article (10.1186/s13071-019-3341-y) contains supplementary material, which is available to authorized users.
Collapse
|
4
|
Malvacio I, Cuzzolin A, Sturlese M, Vera DMA, Moyano EL, Moro S. Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors. J Enzyme Inhib Med Chem 2017; 33:171-183. [PMID: 29210298 PMCID: PMC6010083 DOI: 10.1080/14756366.2017.1404592] [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] [Indexed: 12/30/2022] Open
Abstract
The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 H-pyrazolo[4,3-c]quinolin-3-one (PQ) was evaluated by in-vitro and in-silico approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds 4e2 and 4h2 have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.
Collapse
Affiliation(s)
- Ivana Malvacio
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina.,b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Alberto Cuzzolin
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Mattia Sturlese
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - D Mariano A Vera
- c Department of Chemistry, QUIAMM-INBIOTEC, School of Exact and Natural Sciences , National University of Mar del Plata , Mar del Plata , Buenos Aires , Argentina
| | - E Laura Moyano
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina
| | - Stefano Moro
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| |
Collapse
|
5
|
Ruan Z, Katiyar S, Kannan N. Computational and Experimental Characterization of Patient Derived Mutations Reveal an Unusual Mode of Regulatory Spine Assembly and Drug Sensitivity in EGFR Kinase. Biochemistry 2017; 56:22-32. [PMID: 27936599 PMCID: PMC5508873 DOI: 10.1021/acs.biochem.6b00572] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The catalytic activation of protein kinases requires precise positioning of key conserved catalytic and regulatory motifs in the kinase core. The Regulatory Spine (RS) is one such structural motif that is dynamically assembled upon kinase activation. The RS is also a mutational hotspot in cancers; however, the mechanisms by which cancer mutations impact RS assembly and kinase activity are not fully understood. In this study, through mutational analysis of patient derived mutations in the RS of EGFR kinase, we identify an activating mutation, M766T, at the RS3 position. RS3 is located in the regulatory αC-helix, and a series of mutations at the RS3 position suggest a strong correlation between the amino acid type present at the RS3 position and ligand (EGF) independent EGFR activation. Small polar amino acids increase ligand independent activity, while large aromatic amino acids decrease kinase activity. M766T relies on the canonical asymmetric dimer for full activation. Molecular modeling and molecular dynamics simulations of WT and mutant EGFR suggest a model in which M766T activates the kinase domain by disrupting conserved autoinhibitory interactions between M766 and hydrophobic residues in the activation segment. In addition, a water mediated hydrogen bond network between T766, the conserved K745-E762 salt bridge, and the backbone amide of the DFG motif is identified as a key determinant of M766T-mediated activation. M766T is resistant to FDA approved EGFR inhibitors such as gefitinib and erlotinib, and computational estimation of ligand binding free energy identifies key residues associated with drug sensitivity. In sum, our studies suggest an unusual mode of RS assembly and oncogenic EGFR activation, and provide new clues for the design of allosteric protein kinase inhibitors.
Collapse
Affiliation(s)
- Zheng Ruan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Samiksha Katiyar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
6
|
Nasief NN, Said AM, Hangauer D. Modulating hydrogen-bond basicity within the context of protein-ligand binding: A case study with thrombin inhibitors that reveals a dominating role for desolvation. Eur J Med Chem 2017; 125:975-991. [DOI: 10.1016/j.ejmech.2016.09.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/10/2016] [Accepted: 09/12/2016] [Indexed: 01/14/2023]
|
7
|
Dube D, Tiwari P, Kaur P. The hunt for antimitotic agents: an overview of structure-based design strategies. Expert Opin Drug Discov 2016; 11:579-97. [PMID: 27077683 DOI: 10.1080/17460441.2016.1174689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Structure-based drug discovery offers a rational approach for the design and development of novel anti-mitotic agents which target specific proteins involved in mitosis. This strategy has paved the way for development of a new generation of chemotypes which selectively interfere with the target proteins. The interference of these anti-mitotic targets implicated in diverse stages of mitotic cell cycle progression culminates in cancer cell apoptosis. AREAS COVERED This review covers the various mitotic inhibitors developed against validated mitotic checkpoint protein targets using structure-based design and optimization strategies. The protein-ligand interactions and the insights gained from these studies, culminating in the development of more potent and selective inhibitors, have been presented. EXPERT OPINION The advent of structure-based drug design coupled with advances in X-ray crystallography has revolutionized the discovery of candidate lead molecules. The structural insights gleaned from the co-complex protein-drug interactions have provided a new dimension in the design of anti-mitotic molecules to develop drugs with a higher selectivity and specificity profile. Targeting non-catalytic domains has provided an alternate approach to address cross-reactivity and broad selectivity among kinase inhibitors. The elucidation of structures of emerging mitotic drug targets has opened avenues for the design of inhibitors that target cancer.
Collapse
Affiliation(s)
- D Dube
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Tiwari
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Kaur
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| |
Collapse
|
8
|
Maisanaba S, Hercog K, Filipic M, Jos Á, Zegura B. Genotoxic potential of montmorillonite clay mineral and alteration in the expression of genes involved in toxicity mechanisms in the human hepatoma cell line HepG2. JOURNAL OF HAZARDOUS MATERIALS 2016; 304:425-433. [PMID: 26599662 DOI: 10.1016/j.jhazmat.2015.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/29/2015] [Accepted: 10/11/2015] [Indexed: 06/05/2023]
Abstract
Montmorillonite, also known as Cloisite(®)Na(+) (CNa(+)), is a natural clay with a wide range of well-documented and novel applications, such as pharmaceutical products or food packaging. Although considered a low toxic product, the expected increased exposure to CNa(+) arises concern on the potential consequences on human and environmental health especially as its genotoxicity has scarcely been investigated so far. Thus, we investigated, for the first time, the influence of non-cytotoxic concentrations of CNa(+) (15.65, 31.25 and 62.5 μg/mL) on genomic instability of human hepatoma cell line (HepG2) by determining the formation of micronuclei (MNi), nucleoplasmic bridges (NPBs) and nuclear buds (NBUDs) with the Cytokinesis block micronucleus cytome assay. Further on we studied the influence of CNa(+) on the expression of several genes involved in toxicity mechanisms using the real-time quantitative PCR. The results showed that CNa(+) increased the number of MNi, while the numbers of NBUDs and NPBs were not affected. In addition it deregulated genes in all the groups studied, mainly after longer time of exposure. These findings provide the evidence that CNa(+) is potentially genotoxic. Therefore further studies that will elucidate the molecular mechanisms involved in toxic activity of CNa(+) are needed for hazard identification and human safety assessment.
Collapse
Affiliation(s)
- Sara Maisanaba
- Area of Toxicology, Faculty of Pharmacy, University of Sevilla, Profesor García González no. 2, 41012 Seville, Spain.
| | - Klara Hercog
- National Institute of Biology, Department for Genetic Toxicology and Cancer Biology, Vecna pot 111, 1000 Ljubljana, Slovenia
| | - Metka Filipic
- National Institute of Biology, Department for Genetic Toxicology and Cancer Biology, Vecna pot 111, 1000 Ljubljana, Slovenia
| | - Ángeles Jos
- Area of Toxicology, Faculty of Pharmacy, University of Sevilla, Profesor García González no. 2, 41012 Seville, Spain
| | - Bojana Zegura
- National Institute of Biology, Department for Genetic Toxicology and Cancer Biology, Vecna pot 111, 1000 Ljubljana, Slovenia
| |
Collapse
|
9
|
Cuzzolin A, Sturlese M, Malvacio I, Ciancetta A, Moro S. DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations. Molecules 2015; 20:9977-93. [PMID: 26035098 PMCID: PMC6272630 DOI: 10.3390/molecules20069977] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/05/2015] [Accepted: 05/21/2015] [Indexed: 11/17/2022] Open
Abstract
Virtual screening (VS) is a computational methodology that streamlines the drug discovery process by reducing costs and required resources through the in silico identification of potential drug candidates. Structure-based VS (SBVS) exploits knowledge about the three-dimensional (3D) structure of protein targets and uses the docking methodology as search engine for novel hits. The success of a SBVS campaign strongly depends upon the accuracy of the docking protocol used to select the candidates from large chemical libraries. The identification of suitable protocols is therefore a crucial step in the setup of SBVS experiments. Carrying out extensive benchmark studies, however, is usually a tangled task that requires users' proficiency in handling different file formats and philosophies at the basis of the plethora of existing software packages. We present here DockBench 1.0, a platform available free of charge that eases the pipeline by automating the entire procedure, from docking benchmark to VS setups. In its current implementation, DockBench 1.0 handles seven docking software packages and offers the possibility to test up to seventeen different protocols. The main features of our platform are presented here and the results of the benchmark study of human Checkpoint kinase 1 (hChk1) are discussed as validation test.
Collapse
Affiliation(s)
- Alberto Cuzzolin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Ivana Malvacio
- INFIQC-Organic Chemistry Department, School of Chemical Sciences, National University of Cordoba, Cordoba, CP 5000, Argentine.
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova 35131, Italy.
| |
Collapse
|
10
|
Kramer C, Fuchs JE, Liedl KR. Strong nonadditivity as a key structure-activity relationship feature: distinguishing structural changes from assay artifacts. J Chem Inf Model 2015; 55:483-94. [PMID: 25760829 PMCID: PMC4372821 DOI: 10.1021/acs.jcim.5b00018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nonadditivity
in protein–ligand affinity data represents
highly instructive structure–activity relationship (SAR) features
that indicate structural changes and have the potential to guide rational
drug design. At the same time, nonadditivity is a challenge for both
basic SAR analysis as well as many ligand-based data analysis techniques
such as Free-Wilson Analysis and Matched Molecular Pair analysis,
since linear substituent contribution models inherently assume additivity
and thus do not work in such cases. While structural causes for nonadditivity
have been analyzed anecdotally, no systematic approaches to interpret
and use nonadditivity prospectively have been developed yet. In this
contribution, we lay the statistical framework for systematic analysis
of nonadditivity in a SAR series. First, we develop a general metric
to quantify nonadditivity. Then, we demonstrate the non-negligible
impact of experimental uncertainty that creates apparent nonadditivity,
and we introduce techniques to handle experimental uncertainty. Finally,
we analyze public SAR data sets for strong nonadditivity and use recourse
to the original publications and available X-ray structures to find
structural explanations for the nonadditivity observed. We find that
all cases of strong nonadditivity (ΔΔpKi and ΔΔpIC50 > 2.0 log units)
with sufficient structural information to generate reasonable hypothesis
involve changes in binding mode. With the appropriate statistical
basis, nonadditivity analysis offers a variety of new attempts for
various areas in computer-aided drug design, including the validation
of scoring functions and free energy perturbation approaches, binding
pocket classification, and novel features in SAR analysis tools.
Collapse
Affiliation(s)
- Christian Kramer
- †Department of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| | - Julian E Fuchs
- †Department of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.,‡Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Klaus R Liedl
- †Department of Theoretical Chemistry, Faculty for Chemistry and Pharmacy, Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria
| |
Collapse
|
11
|
Eldebss TMA, Gomha SM, Abdulla MM, Arafa RK. Novel pyrrole derivatives as selective CHK1 inhibitors: design, regioselective synthesis and molecular modeling. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00560k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
3D binding interactions of 7a (magenta-colored carbons) and the co-crystallized ligand (cyan-colored carbons) with the active site amino acids of CHK1.
Collapse
Affiliation(s)
- Taha M. A. Eldebss
- Department of Chemistry
- Faculty of Science
- Cairo University
- Giza 12613
- Egypt
| | - Sobhi M. Gomha
- Department of Chemistry
- Faculty of Science
- Cairo University
- Giza 12613
- Egypt
| | | | - Reem K. Arafa
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Cairo University
- 11562 Giza
- Egypt
| |
Collapse
|
12
|
Lv M, Ma S, Tian Y, Zhang X, Lv W, Zhai H. Computational studies on the binding mechanism between triazolone inhibitors and Chk1 by molecular docking and molecular dynamics. MOLECULAR BIOSYSTEMS 2014; 11:275-86. [PMID: 25372494 DOI: 10.1039/c4mb00449c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chk1, a serine/threonine protein kinase that participates in transducing DNA damage signals, is an attractive target due to its involvement in tumor initiation and progression. As a novel Chk1 inhibitor, the triazolone's bioactivity mechanism is not clear. In this study, we carried out an integrated computational study that combines molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations to identify the key factors necessary for the bioactivities. With the aim of discerning the structural features that affect the inhibitory activity of triazolones, MK-8776, a Chk1 inhibitor that reached the clinical stage, was also used as a reference for simulations. A comparative analysis of the triazolone inhibitors at the molecular level offers valuable insight into the structural and energetic properties. A general feature is that all the studied inhibitors bind in the pocket characterized by residues Leu14, Val22, Ala35, Glu84, Tyr85, Cys86, and Leu136 of Chk1. Moreover, introducing hydrophobic groups into triazolone inhibitors is favorable for binding to Chk1, which is corroborated by residue Leu136 with a relatively large difference in the contribution between MK-8776 and five triazolones to the total binding free energies. A hydrogen bond between the polar hydrogen atoms at R1 and Cys86 can facilitate proper placement of the inhibitor in the binding pocket of Chk1 that favors binding. However, the introduction of hydrophilic groups into the R2 position diminishes binding affinity. The information provided by this research is of benefit for further rational design of novel promising inhibitors of Chk1.
Collapse
Affiliation(s)
- Min Lv
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu Province, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
13
|
Liu YC, Zhang R, Wu QY, Chen Q, Yang GF. Recent Developments in the Synthesis and Applications of Isatins. ORG PREP PROCED INT 2014. [DOI: 10.1080/00304948.2014.922378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
14
|
Matthews TP, Jones AM, Collins I. Structure-based design, discovery and development of checkpoint kinase inhibitors as potential anticancer therapies. Expert Opin Drug Discov 2013; 8:621-40. [PMID: 23594139 DOI: 10.1517/17460441.2013.788496] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Checkpoint kinase (CHK) inhibitors offer the promise of enhancing the effectiveness of widely prescribed cancer chemotherapies and radiotherapy by inhibiting the DNA damage response, as well as the potential for single agent efficacy. AREAS COVERED This article surveys structural insights into the checkpoint kinases CHK1 and CHK2 that have been exploited to enhance the selectivity and potency of small molecule inhibitors. Furthermore, the authors review the use of mechanistic cellular assays to guide the optimisation of inhibitors. Finally, the authors discuss the status of the current clinical candidates and emerging new clinical contexts for CHK1 and CHK2 inhibitors, including the prospects for single agent efficacy. EXPERT OPINION Protein-bound water molecules play key roles in structural features that can be targeted to gain high selectivity for either enzyme. The results of early phase clinical trials of checkpoint inhibitors have been mixed, but significant progress has been made in testing the combination of CHK1 inhibitors with genotoxic chemotherapy. Second-generation CHK1 inhibitors are likely to benefit from increased selectivity and oral bioavailability. While the optimum therapeutic context for CHK2 inhibition remains unclear, the emergence of single agent preclinical efficacy for CHK1 inhibitors in specific tumour types exhibiting constitutive replication stress represents exciting progress in exploring the therapeutic potential of these agents.
Collapse
Affiliation(s)
- Thomas P Matthews
- Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, London SM2 5NG, UK
| | | | | |
Collapse
|
15
|
Sławiński J, Żołnowska B, Orlewska C, Chojnacki J. Synthesis and molecular structure of novel 2-(alkylthio)-4-chloro- N-(4,5-dihydro-5-oxo-1 H-1,2,4-triazol-3-yl)-5-methylbenzenesulfonamides with potential anticancer activity. MONATSHEFTE FUR CHEMIE 2012; 143:1705-1718. [PMID: 26166861 PMCID: PMC4495025 DOI: 10.1007/s00706-012-0849-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 08/22/2012] [Indexed: 11/26/2022]
Abstract
ABSTRACT A series of novel 4-chloro-N-(4,5-dihydro-5-oxo-1-R2-1H-1,2,4-triazol-3-yl)-5-methyl-2-(R1-methylthio)benzenesulfonamide derivatives have been synthesized as potential anticancer agents. The in vitro antitumor activity of some compounds was evaluated in the US National Cancer Institute (NCI) against the NCI-60 cell line panel. The most prominent compound showed remarkable activity against 13 human tumor cell lines representing lung, colon, CNS, melanoma, ovarian, renal, prostate, and breast at low micromolar GI50 level in the range of 1.9-3.0 μM. GRAPHICAL ABSTRACT
Collapse
Affiliation(s)
- Jarosław Sławiński
- Department of Organic Chemistry, Medical University of Gdańsk, Gen. J. Hallera Str. 107, 80416 Gdańsk, Poland
| | - Beata Żołnowska
- Department of Organic Chemistry, Medical University of Gdańsk, Gen. J. Hallera Str. 107, 80416 Gdańsk, Poland
| | - Czesława Orlewska
- Department of Organic Chemistry, Medical University of Gdańsk, Gen. J. Hallera Str. 107, 80416 Gdańsk, Poland
| | - Jarosław Chojnacki
- Department of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80233 Gdańsk, Poland
| |
Collapse
|