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Mtetwa LM, Salifu EY, Omolo CA, Soliman ME, Faya M. Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights. Comput Biol Chem 2023; 105:107909. [PMID: 37418952 DOI: 10.1016/j.compbiolchem.2023.107909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/09/2023]
Abstract
To date, Cancer remains a global threat due to its impact on growing life expectancy. With the many efforts and methods of combating the disease, complete success remains a challenge owing to several limitations including cancer cells developing resistance through mutations, off-target effect of some cancer drugs resulting in toxicities, among many others. Aberrant DNA methylation is understood to be the primary reason for improper gene silence, which can result in neoplastic transformation, carcinogenesis, and tumour progression. DNA methyltransferase B (DNMT3B) enzyme is considered a potential target for the treatment of several cancers due to its important role in DNA methylation. However, only a few DNMT3B inhibitors have been reported to date. Herein, in silico molecular recognition techniques such as Molecular docking, Pharmacophore-based virtual screen and MD simulation were employed to identify potential inhibitors of DNMT3B that can halt aberrancy in DNA methylation. Findings initially identified 878 hit compounds based on a designed pharmacophore model from the reference compound Hypericin. Molecular docking was used to rank the hits by testing their efficiency when bound to the target enzyme and the top three (3) selected. All three (3) of the top hits showed excellent pharmacokinetic properties but two (2) (Zinc33330198 and Zinc77235130) were identified to be non-toxic. Molecular dynamic simulation of the final two hits showed good stability, flexibility, and structural rigidity of the compounds on DNMT3B. Finally, thermodynamic energy estimations show both compounds had favourable free energies comprising - 26.04 kcal/mol for Zinc77235130 and - 15.73 kcal/mol for Zinc33330198. Amongst the final two hits, Zinc77235130 showed consistency in favourable results across all the tested parameters and was thus selected as the lead compound for further experimental validation. The identification of this lead compound will form important basis for the inhibition of aberrant DNA methylation in cancer therapy.
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Affiliation(s)
- Lusanda M Mtetwa
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Elliasu Y Salifu
- West African Centre for Computational Analysis, Accra, Ghana; Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; School of Pharmacy and Health Sciences, United States International University of Africa, Nairobi, Kenya
| | - Mahmoud E Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mbuso Faya
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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2
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Rehman HM, Sajjad M, Ali MA, Gul R, Irfan M, Naveed M, Bhinder MA, Ghani MU, Hussain N, Said ASA, Al Haddad AHI, Saleem M. Identification of NS2B-NS3 Protease Inhibitors for Therapeutic Application in ZIKV Infection: A Pharmacophore-Based High-Throughput Virtual Screening and MD Simulations Approaches. Vaccines (Basel) 2023; 11:vaccines11010131. [PMID: 36679976 PMCID: PMC9862652 DOI: 10.3390/vaccines11010131] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) pandemic and its implication in congenital malformations and severe neurological disorders had created serious threats to global health. ZIKV is a mosquito-borne flavivirus which spread rapidly and infect a large number of people in a shorter time-span. Due to the lack of effective therapeutics, this had become paramount urgency to discover effective drug molecules to encounter the viral infection. Various anti-ZIKV drug discovery efforts during the past several years had been unsuccessful to develop an effective cure. The NS2B-NS3 protein was reported as an attractive therapeutic target for inhibiting viral proliferation, due to its central role in viral replication and maturation of non-structural viral proteins. Therefore, the current in silico drug exploration aimed to identify the novel inhibitors of Zika NS2B-NS3 protease by implementing an e-pharmacophore-based high-throughput virtual screening. A 3D e-pharmacophore model was generated based on the five-featured (ADPRR) pharmacophore hypothesis. Subsequently, the predicted model is further subjected to the high-throughput virtual screening to reveal top hit molecules from the various small molecule databases. Initial hits were examined in terms of binding free energies and ADME properties to identify the candidate hit exhibiting a favourable pharmacokinetic profile. Eventually, molecular dynamic (MD) simulations studies were conducted to evaluate the binding stability of the hit molecule inside the receptor cavity. The findings of the in silico analysis manifested affirmative evidence for three hit molecules with -64.28, -55.15 and -50.16 kcal/mol binding free energies, as potent inhibitors of Zika NS2B-NS3 protease. Hence, these molecules holds the promising potential to serve as a prospective candidates to design effective drugs against ZIKV and related viral infections.
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Affiliation(s)
- Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Muhammad Akhtar Ali
- School of Biological Sciences, University of the Punjab, Quaid e Azam Campus, Lahore 54590, Punjab, Pakistan
| | - Roquyya Gul
- Faculty of Life Sciences, Gulab Devi Educational Complex, Lahore 54590, Punjab, Pakistan
| | - Muhammad Irfan
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Lahore 54600, Punjab, Pakistan
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab Lahore, Lahore 54590, Punjab, Pakistan
| | - Munir Ahmad Bhinder
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore 54590, Punjab, Pakistan
| | - Muhammad Usman Ghani
- Center for Applied Molecular Biology, University of the Punjab, Lahore 54590, Punjab, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
| | - Amira S. A. Said
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi 112612, United Arab Emirates
- Department of Clinical Pharmacy, College of Pharmacy, Al Ain University, Al Ain 64141, United Arab Emirates
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni Suef University, Beni Suef 62521, Egypt
| | - Amal H. I. Al Haddad
- Chief Operations Office, Sheikh Shakhbout Medical City (SSMC) in Partnership with Mayo Clinic, Abu Dhabi 11001, United Arab Emirates
| | - Mahjabeen Saleem
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Punjab, Pakistan
- School of Medical Lab Technology, Minhaj University Lahore, Lahore 54770, Punjab, Pakistan
- Correspondence:
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Naseem S, Shafiq Z, Taslimi P, Hussain S, Taskin-Tok T, Kisa D, Saeed A, Temirak A, Tahir MN, Rauf K, El-Gokha A. Synthesis and evaluation of novel xanthene-based thiazoles as potential antidiabetic agents. Arch Pharm (Weinheim) 2023; 356:e2200356. [PMID: 36220614 DOI: 10.1002/ardp.202200356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 01/04/2023]
Abstract
A series of xanthene-based thiazoles was synthesized and characterized by different scpectroscopic methods, i.e. Proton nuclear magnetic resonance (1 H NMR), carbon nuclear magnetic resonance (13 C NMR), infrared spectroscopy, carbon hydrogen nitrogen analysis, and X-ray crystallography. The inhibition potencies of 18 newly synthesized thiazole derivatives were investigated on the activities of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), α-amylase (α-Amy), and α-glycosidase (α-Gly) enzymes in accordance with their antidiabetic and anticholinesterase ability. The synthesized compounds have the highest inhibition potential against the enzymes at low nanomolar concentrations. Among the 18 newly synthesized molecules, 3b and 3p were superior to the known commercial inhibitors of the enzymes and have a much more effective inhibitory potential, with IC50 : 2.37 and 1.07 nM for AChE, 0.98 and 0.59 nM for BChE, 56.47 and 61.34 nM for α-Gly, and 152.48 and 124.84 nM for α-Amy, respectively. Finally, the optimized 18 compounds were subjected to molecular docking to describe the interaction between thiazole derivatives and AChE, BChE, α-Amy, and α-Gly enzymes in which important interactions were monitored with amino acid residues of each target enzyme.
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Affiliation(s)
- Saira Naseem
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan.,Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey.,Department of Chemistry, Faculty of Science, Istinye University, Istanbul, Turkey
| | - Saghir Hussain
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | - Dursun Kisa
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ahmed Temirak
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo, Egypt
| | - Muhammad N Tahir
- Department of Physics, University of Sargodha, Sargodha, Pakistan
| | - Khawar Rauf
- Department of Chemistry, Govt. Post-Graduate Gordon College, Rawalpindi, Pakistan
| | - Ahmed El-Gokha
- Chemistry Department, Faculty of Science, Menoufia University, Menoufia, Egypt
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Muhammad S, Saba A, Khera RA, Al-Sehemi AG, Algarni H, Iqbal J, Alshahrani MY, Chaudhry AR. Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2072840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Afsheen Saba
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Rasheed Ahmad Khera
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Abdullah. G. Al-Sehemi
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - H. Algarni
- Department of Physics, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Javed Iqbal
- Department of Chemistry, College of Science, University of Agriculture, Faisalabad, Pakistan
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
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5
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Fukui T, Soda K, Takao K, Rikiyama T. Extracellular Spermine Activates DNA Methyltransferase 3A and 3B. Int J Mol Sci 2019; 20:E1254. [PMID: 30871110 PMCID: PMC6429523 DOI: 10.3390/ijms20051254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/09/2019] [Indexed: 01/10/2023] Open
Abstract
We first demonstrated that long-term increased polyamine (spermine, spermidine, putrescine) intake elevated blood spermine levels in mice and humans, and lifelong consumption of polyamine-rich chow inhibited aging-associated increase in aberrant DNA methylation, inhibited aging-associated pathological changes, and extend lifespan of mouse. Because gene methylation status is closely associated with aging-associated conditions and polyamine metabolism is closely associated with regulation of gene methylation, we investigated the effects of extracellular spermine supplementation on substrate concentrations and enzyme activities involved in gene methylation. Jurkat cells and human mammary epithelial cells were cultured with spermine and/or D,L-alpha-difluoromethylornithine (DFMO), an inhibitor of ornithine decarboxylase. Spermine supplementation inhibited enzymatic activities of adenosylmethionine decarboxylase in both cells. The ratio of decarboxylated S-adenosylmethionine to S-adenosyl-L-methionine increased by DFMO and decreased by spermine. In Jurkat cells cultured with DFMO, the protein levels of DNA methyltransferases (DNMTs) 1, 3A and 3B were not changed, however the activity of the three enzymes markedly decreased. The protein levels of these enzymes were not changed by addition of spermine, DNMT 3A and especially 3B were activated. We show that changes in polyamine metabolism dramatically affect substrate concentrations and activities of enzymes involved in gene methylation.
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Affiliation(s)
- Taro Fukui
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama-city, Saitama 330-8503, Japan.
| | - Kuniyasu Soda
- Cardiovascular Research Institute, Saitama Medical Center, Jichi Medical University, Saitama-city, Saitama 330-8503, Japan.
| | - Koichi Takao
- Laboratory of Cellular Physiology, Department of Clinical Dietetics & Human Nutrition, Faculty of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan.
| | - Toshiki Rikiyama
- Department of Surgery, Saitama Medical Center, Jichi Medical University, Saitama-city, Saitama 330-8503, Japan.
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Rohini K, Agarwal P, Preethi B, Shanthi V, Ramanathan K. Exploring the Lead Compounds for Zika Virus NS2B-NS3 Protein: an e-Pharmacophore-Based Approach. Appl Biochem Biotechnol 2018; 187:194-210. [PMID: 29911269 DOI: 10.1007/s12010-018-2814-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/05/2018] [Indexed: 12/19/2022]
Abstract
The rapid spread of the Zika virus and its association with the abnormal brain development constitute a global health emergency. With a continuing spread of the mosquito vector, the exposure is expected to accelerate in the coming years. Despite number of efforts, there is still no proper vaccine or medicine to combat this virus. Of note, the NS2B-NS3 protein is proven to be the potential target for the Zika virus therapeutics. Hence, e-pharmacophore-based drug design strategy was employed to identify potent inhibitors of NS2B-NS3 protein from ASINEX database consisting of 467,802 molecules. A 3D e-pharmacophore model was generated using PHASE module of Schrödinger Suite. The generated model consists of one hydrogen bond acceptor (A), two hydrogen bond donors (D), and two aromatic rings (R), ADDRR. The model was further evaluated for its ability to screen actives using enrichment analysis. Subsequently, high-throughput virtual screening protocol was employed, and the resultant hit molecules were also examined for its binding free energies and ADME properties using Prime MM-GBSA and Qikprop module of Schrodinger packages, respectively. Finally, the screened hit molecule was subjected to molecular dynamics simulation to examine its stability. Overall, the results from our analysis suggest that compound BAS 19192837 could be a potent inhibitor for the NS2B-NS3 protein of the Zika virus. It is also noteworthy to mention that our results are in good agreement with literature evidences. We hope that this result is of immense importance in designing potential drug molecules to combat the spread of Zika virus in the near future.
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Affiliation(s)
- K Rohini
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - Pratika Agarwal
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - B Preethi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India
| | - K Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamilnadu, 632014, India.
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Chen Q, Niu X, Li N. Exploring the natural chemiome to target interleukin-6 receptor (IL-6R) cytokines: an atomic scale investigation for novel rheumatoid arthritis drug discovery. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902017000317256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | - Nana Li
- Huazhong Agricultural University, China
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8
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Yan S, Zhang L, Wang S, Wu T, Gong Z. Inhibition of the Ras/Raf/extracellular signal-regulated kinase 1/2 signaling pathway by compounds of natural origin for possible treatment of spinal cord injury: An in silico approach. Exp Ther Med 2018; 15:2860-2868. [PMID: 29456689 PMCID: PMC5795380 DOI: 10.3892/etm.2018.5734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023] Open
Abstract
Spinal cord injury (SCI) is a severe disease associated with permanent neurological deficit. Recent studies in the treatment of SCI have demonstrated that the Ras/Raf/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway serves an important role in the disease etiology, and that upregulation of this signaling pathway is associated with the development of SCI. In the present study, inhibition of Ras protein was employed in order to downregulate the Ras/Raf/ERK1/2 signaling pathway using compounds of natural origin from the Interbioscreen natural compound database. To the best of our knowledge, this is the first study using a chemical-computational approach in order to identify novel small molecule inhibitors for Ras. A database of ~50,000 compounds was selected for virtual screening, setting a free energy binding bias of −7 kcal/mol to limit the number of compounds. The subset of compounds generated by virtual screening was further limited by subjecting these to the Lipinski's rule of five parameters. A total of five shortlisted compounds were subjected to molecular docking simulation. The compounds were docked into the GTP binding site of Ras, and the inhibition of this site was examined as a promising strategy for the downregulation of Ras/Raf/ERK1/2 signaling pathway. The compounds bound to the GTP binding site through hydrogen bonds and hydrophobic interactions. The identified lead compound was then subjected to molecular dynamics simulation, and the results revealed that GLY60 in the GTP binding site of Ras protein was the optimal binding site during a 100 nsec run.
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Affiliation(s)
- Shilei Yan
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Li Zhang
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Shuai Wang
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Tianhao Wu
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Zhixin Gong
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
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Tumhom S, Krusong K, Pongsawasdi P. Y418 in 410s loop is required for high transglucosylation activity and large-ring cyclodextrin production of amylomaltase from Corynebacterium glutamicum. Biochem Biophys Res Commun 2017; 488:516-521. [PMID: 28522291 DOI: 10.1016/j.bbrc.2017.05.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/14/2017] [Indexed: 01/10/2023]
Abstract
Amylomaltase catalyzes α-1,4 glucosyl transfer reaction to yield linear or cyclic oligosaccharide products. The aim of this work is to investigate functional roles of 410s loop unique to amylomaltase from Corynebacterium glutamicum (CgAM). Site-directed mutagenesis of Y418, the residue at the loop tip, was performed. Y418A/S/D/R/W/F - CgAMs were characterized and compared to the wild-type (WT). A significant decrease in starch transglucosylation, disproportionation and cyclization activities was observed. Specificity for G3 substrate in disproportionation reaction was not changed; however, Y418F showed an increase in preference for longer oligosaccharides G5 to G7. The catalytic efficiency of Y418 mutated CgAMs, except for Y418F, was significantly lower (up to 8- and 12- fold for the W and R mutants, respectively) than that of WT. The change was in the kcat, not the Km values which were around 16-20 mM. The profile of large-ring cyclodextrin (LR-CD) product was different; the principal product of Y418A/D/S was shifted to the larger size (CD36-CD40) while that of the WT and Y418F peaked at CD29-CD33. The product yield was reduced especially in W and R mutants. Hence Y418 in 410s loop of CgAM not only contributes to transglucosylation activities but also controls the amount and size of LR-CD products through the proposed hydrophobic stacking interaction and the suitable distance of loop channel for substrate entering. This is the first report to show the effect of the loop tip residue on LR-CD product formation.
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Affiliation(s)
- Suthipapun Tumhom
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kuakarun Krusong
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piamsook Pongsawasdi
- Starch and Cyclodextrin Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Zang SZ, Yang YR, Zhao SS, Li YX, Gao XY, Zhong CL. In silico insight into EGFR treatment in patients with lung carcinoma and T790M mutations. Exp Ther Med 2017; 13:1735-1740. [PMID: 28565760 PMCID: PMC5443239 DOI: 10.3892/etm.2017.4168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/19/2016] [Indexed: 01/16/2023] Open
Abstract
The T790M mutational basis of treatment failure, following treatment via alteration of the epidermal growth factor receptor (EGFR) pathway, is a well-known anomaly in patients with non-small cell lung cancer (NSCLC). The T790M mutation activates the kinase domain, causing tyrosine kinase inhibitors, such as gefitinib, to elicit little or no response. To overcome this acquired resistance in NSCLC cells, the present study utilized a structure-based drug designing method to identify a novel lead compound. An in-house traditional Chinese medicinal compound database was used and following initial virtual screening, pre-absorption, distribution, metabolism and excretion/Tox and automated docking analyses, nardosinon was selected as the most appropriate candidate for further analysis. Two NSCLC cell lines, PC9GR4 and H2347, were used to test nardosinon and the results were compared with gefitinib. Results from an initial cell death assay revealed that nardosinon was able to induce cell death in NSCLC cells with and without the T790M mutation. These findings suggest that nardosinon may be an effective pharmacological compound for NSCLC treatment, including T790M EGFR mutant NSCLC cells.
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Affiliation(s)
- Shu-Zhi Zang
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Yan-Rong Yang
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Sha-Sha Zhao
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Yun-Xia Li
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Xin-Yuan Gao
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
| | - Chun-Lei Zhong
- Department of Respiration, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453100, P.R. China
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Ramatenki V, Dumpati R, Vadija R, Vellanki S, Potlapally SR, Rondla R, Vuruputuri U. Identification of New Lead Molecules Against UBE2NL Enzyme for Cancer Therapy. Appl Biochem Biotechnol 2017; 182:1497-1517. [DOI: 10.1007/s12010-017-2414-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/16/2017] [Indexed: 11/30/2022]
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Patel TN, Roy S, Ravi R. Gastric cancer and related epigenetic alterations. Ecancermedicalscience 2017; 11:714. [PMID: 28144288 PMCID: PMC5243136 DOI: 10.3332/ecancer.2017.714] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer, a malignant and highly proliferative condition, has significantly affected a large population around the globe and is known to be caused by various factors including genetic, epigenetic, and environmental influences. Though the global trend of these cancers is declining, an increase in its frequency is still a threat because of changing lifestyles and dietary habits. However, genetic and epigenetic alterations related to gastric cancers also have an equivalent contribution towards carcinogenic development. DNA methylation is one of the major forms of epigenetic modification which plays a significant role in gastric carcinogenesis. Methylation leads to inactivation of some of the most important genes like DNA repair genes, cell cycle regulators, apoptotic genes, transcriptional regulators, and signalling pathway regulators; which subsequently cause uncontrolled proliferation of cells. Mutations in these genes can be used as suitable prognostic markers for early diagnosis of the disease, since late diagnosis of gastric cancers has a huge negative impact on overall patient survival. In this review, we focus on the important epigenetic mutations that contribute to the development of gastric cancer and the molecular pathogenesis underlying each of them. Methylation, acetylation, and histone modifications play an integral role in the onset of genomic instability, one of the many contributory factors to gastric cancer. This article also covers the constraints of incomplete knowledge of epigenetic factors influencing gastric cancer, thus throwing light on our understanding of the disease.
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Affiliation(s)
- Trupti N Patel
- Department of Medical Biotechnology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Soumyadipta Roy
- Department of Medical Biotechnology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Revathi Ravi
- Department of Medical Biotechnology, VIT University, Vellore 632014, Tamil Nadu, India
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Amin A, Chikan NA, Mokhdomi TA, Bukhari S, Koul AM, Shah BA, Gharemirshamlu FR, Wafai AH, Qadri A, Qadri RA. Irigenin, a novel lead from Western Himalayan chemiome inhibits Fibronectin-Extra Domain A induced metastasis in Lung cancer cells. Sci Rep 2016; 6:37151. [PMID: 27849000 PMCID: PMC5111083 DOI: 10.1038/srep37151] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 02/08/2023] Open
Abstract
Several lines of evidence indicate that Fibronectin Extra Domain A (EDA) promotes metastatic capacity of tumor cells by engaging cell surface α9β1 integrins. This interaction mediated by the C-C loop of EDA activates pro-oncogenic signaling pathways leading to epithelial to mesenchymal transition (EMT) of tumor cells, thus signifying its importance in control of metastatic progression. In this context the present study was designed to explore the active compounds from selected ethno-medicinal plants of western Himalayan region for targeting EDA of Fibronectin in lung carcinoma cells. Structure based informatics for drug designing and screening was employed to generate a lead compound(s) feed that were conformationally and energetically viable. Out of 120 compounds selected, Irigenin showed best binding-affinity with C-C loop of EDA. Irigenin specifically targeted α9β1 and α4β1 integrin binding sites on EDA comprising LEU46, PHE47, PRO48, GLU58, LEU59 and GLN60 in its C-C loop as evaluated by energy decomposition per residue of Irigenin–EDA complex. In-vitro cell motility assays complemented with EDA knock-in and knockdown assays distinctively demonstrated that Irigenin prevents metastatic capacity of lung cancer cells by selectively blocking EDA. The results presented thus project Irigenin as a lead compound to overcome Fibronectin EDA induced metastatic progression in lung carcinoma cells.
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Affiliation(s)
- Asif Amin
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India.,Hybridoma Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Naveed Anjum Chikan
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India.,Aaidah Life Sciences Pvt. Ltd., New Delhi, 110025, India
| | - Taseem A Mokhdomi
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India
| | - Shoiab Bukhari
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India.,Molecular Reproduction, Development &Genetics Lab, Indian Institute of Science, Bangalore, 560 012, India
| | - Aabid M Koul
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India
| | - Basit Amin Shah
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India
| | | | - Asrar H Wafai
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India
| | - Ayub Qadri
- Hybridoma Laboratory, National Institute of Immunology, New Delhi, 110067, India
| | - Raies A Qadri
- Department of Biotechnology, University of Kashmir, Srinagar (J and K), 190006, India
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Fatima S, Sen P, Sneha P, Priyadoss CG. Hydrophobic Interaction Between Domain I of Albumin and B Chain of Detemir May Support Myristate-Dependent Detemir-Albumin Binding. Appl Biochem Biotechnol 2016; 182:82-96. [DOI: 10.1007/s12010-016-2312-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/30/2016] [Indexed: 01/01/2023]
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15
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Zhao GF, Huang ZA, Du XK, Yang ML, Huang DD, Zhang S. Molecular docking studies of Traditional Chinese Medicinal compounds against known protein targets to treat non-small cell lung carcinomas. Mol Med Rep 2016; 14:1132-8. [PMID: 27279494 PMCID: PMC4940108 DOI: 10.3892/mmr.2016.5350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 03/07/2016] [Indexed: 01/09/2023] Open
Abstract
In silico drug design using virtual screening, absorption, distribution, metabolism and excretion (ADME)/Tox data analysis, automated docking and molecular dynamics simulations for the determination of lead compounds for further in vitro analysis is a cost effective strategy. The present study used this strategy to discover novel lead compounds from an in-house database of Traditional Chinese Medicinal (TCM) compounds against epithelial growth factor receptor (EGFR) protein for targeting non-small cell lung cancer (NSCLC). After virtual screening of an initial dataset of 2,242 TCM compounds, leads were identified based on binding energy and ADME/Tox data and subjected to automated docking followed by molecular dynamics simulation. Triptolide, a top compound identified by this vigorous in silico screening, was then tested in vitro on the H2347 cell line carrying wild-type EGFR, revealing an anti-proliferative potency similar to that of known drugs against NSCLC.
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Affiliation(s)
| | - Zuo-An Huang
- Department of Stem Cell Laboratory, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, P.R. China
| | | | | | - Dan-Dan Huang
- Department of Stem Cell Laboratory, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, P.R. China
| | - Shun Zhang
- Department of Stem Cell Laboratory, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, P.R. China
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16
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Zhao FL, Yang GH, Xiang S, Gao DD, Zeng C. In silico analysis of the effect of mutation on epidermal growth factor receptor in non-small-cell lung carcinoma: from mutational analysis to drug designing. J Biomol Struct Dyn 2016; 35:427-434. [PMID: 26813338 DOI: 10.1080/07391102.2016.1146165] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Fu-Li Zhao
- The First Department of Oncology Subject, Center Hospital of Zhumadian in Henan, Zhumadian, Henan 463000, P.R. China
| | - Guang-Hua Yang
- The First Department of Oncology Subject, Center Hospital of Zhumadian in Henan, Zhumadian, Henan 463000, P.R. China
| | - Sen Xiang
- The First Department of Oncology Subject, Center Hospital of Zhumadian in Henan, Zhumadian, Henan 463000, P.R. China
| | - Dong-Dong Gao
- The First Department of Oncology Subject, Center Hospital of Zhumadian in Henan, Zhumadian, Henan 463000, P.R. China
| | - Chen Zeng
- The First Department of Oncology Subject, Center Hospital of Zhumadian in Henan, Zhumadian, Henan 463000, P.R. China
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Wang N, Wang Z, Wang Y, Xie X, Shen J, Peng C, You J, Peng F, Tang H, Guan X, Chen J. Dietary compound isoliquiritigenin prevents mammary carcinogenesis by inhibiting breast cancer stem cells through WIF1 demethylation. Oncotarget 2016; 6:9854-76. [PMID: 25918249 PMCID: PMC4496402 DOI: 10.18632/oncotarget.3396] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/15/2015] [Indexed: 02/07/2023] Open
Abstract
Breast cancer stem cells (CSCs) are considered as the root of mammary tumorigenesis. Previous studies have demonstrated that ISL efficiently limited the activities of breast CSCs. However, the cancer prevention activities of ISL and its precise molecular mechanisms remain largely unknown. Here, we report a novel function of ISL as a natural demethylation agent targeting WIF1 to prevent breast cancer. ISL administration suppressed in vivo breast cancer initiation and progression, accompanied by reduced CSC-like populations. A global gene expression profile assay further identified WIF1 as the main response gene of ISL treatment, accompanied by the simultaneous downregulation of β-catenin signaling and G0/G1 phase arrest in breast CSCs. In addition, WIF1 inhibition significantly relieved the CSC-limiting effects of ISL and methylation analysis further revealed that ISL enhanced WIF1 gene expression via promoting the demethylation of its promoter, which was closely correlated with the inhibition of DNMT1 methyltransferase. Molecular docking analysis finally revealed that ISL could stably dock into the catalytic domain of DNMT1. Taken together, our findings not only provide preclinical evidence to demonstrate the use of ISL as a dietary supplement to inhibit mammary carcinogenesis but also shed novel light on WIF1 as an epigenetic target for breast cancer prevention.
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Affiliation(s)
- Neng Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Zhiyu Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong.,Department of Mammary Disease, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Yu Wang
- Department of Pharmacology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jiangang Shen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Cheng Peng
- School of Pharmaceutical Science, Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China
| | - Jieshu You
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Fu Peng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Xinyuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Jianping Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong.,School of Pharmaceutical Science, Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China
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18
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From covalent bonds to eco-physiological pharmacology of secondary plant metabolites. Biochem Pharmacol 2015; 98:269-77. [DOI: 10.1016/j.bcp.2015.07.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 07/30/2015] [Indexed: 01/08/2023]
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Abstract
Oral squamous cell carcinoma (OSCC) is a multistep process which is modulated by several endogenous and environmental factors. Epigenetic changes have been found to be equally responsible for OSCC as genetic changes. A plethora of genes showing hypermethylation have been discovered in OSCC. Since these changes are reversible, a lot of emphasis is on using the natural compounds for their ability to cause demethylation which could lead to reactivation of the inactivated tumor suppressor genes. This review encompasses the promoter hypermethylation of tumor suppressor genes in OSCC and its possible reversal using natural compounds. In addition, new compounds which could be screened for their demethylating ability have also been proposed.
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20
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Abstract
In today's world, the pursuit of a novel anti-cancer agent remains top priority because of the fact that the global burden of this malady is continuously increasing. Our work is no different from others in searching for new therapeutic solutions. To achieve this, we are looking into Epigenetics, the phenomenon governed by hypermethylation and hypomethylation of tumor suppressor genes and oncogenes, respectively. Our target for this study is an important intermediary methyl-CpG binding protein named kaiso. In our study, we have used the X-ray crystallographic structure of Kaiso for virtual screening and molecular dynamics simulations to study the binding modes of possible inhibitors. The C2H2 domain comprising LYS539 was used for screening the inter bio screen Database having 48,531 natural compounds. Our approach of using computer-aided drug designing methods helped us to remove the execrable compounds and narrowed our focus on a selected few for molecular simulation studies. The top ranked compound (chem. ID 28127) exhibited the highest binding affinity and was also found to be stable throughout the 20 ns timeframe. This compound is therefore a good starting point for developing strong inhibitors.
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Affiliation(s)
- Naveed Anjum Chikan
- a Medical Biotechnology Division, School of Bio Sciences and Technology , VIT University , Vellore 632014 , Tamilnadu , India
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