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Darvazi M, Ghorbani M, Ramazi S, Allahverdi A, Abdolmaleki P. A computational study of the R120G mutation in human αB-crystallin: implications for structural stability and functionality. J Biomol Struct Dyn 2024; 42:5788-5798. [PMID: 37354135 DOI: 10.1080/07391102.2023.2229434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
The eye is a vital organ in the visual system, which is composed of transparent vascular tissue. αB-crystallin, a significant protein found in the lens, plays a crucial role in our understanding of lens diseases. Mutations in the αB-crystallin protein can cause lens diseases, such as cataracts and myopathy. However, the molecular mechanism underlying the R120G mutation is not fully understood. In this study, we utilized molecular dynamics simulations to illustrate, in atomic detail, how the R120G mutation leads to the aggregation of αB-crystallin and scattering of light in the lens. Our findings show that the R120G mutation alters the dynamic and structural properties of the αB-crystallin protein. Specifically, this mutation causes the angle of the hairpin at the C-terminal to increase from 80° to 150°, while reducing the distance between the hydrophobic patches around residues 10 and 44-55 from 1.5 nm to 1 nm. In addition, our results showed that the mutation could disrupt the IPI motif - β4/β8 interaction. The disruption of this interaction could affect the αB-crystallin oligomerization and the chaperone activity of αB-crystallin protein. The exposed hydrophobic area at the IPI motif - β4/β8 could become the primary site for interprotein interactions, which are responsible for large-scale aggregation. We have demonstrated that, in wild-type αB-crystallin protein, salt bridges R120 and D109, R107 and D80 are formed. However, in the case of the R120G mutation, the salt bridges R120 and R109 are disrupted, and a new salt bridge with a different pattern is formed. In our study, it has been found that all of the changes associated with the R120G mutation are located at the interface of chains A and B, which could impact the multimerization of the αB-crystallin. Previous research on the K92-E99 residue has shown that a salt bridge in the dimer I can reduce the chaperone activity of the protein. Furthermore, the salt bridges R120 and D109, as well as R107 and D80 in dimer II, induce changes in the hydrophobic envelope of β-sheets in the α-crystallin domain (ACD). These changes could have an impact on the multimerization of the αB-crystallin, leading to disruption of the oligomer structure and aggregation. Moreover, the changes in the αB-crystallin resulting from the R120G mutation can lead to faulty interactions with other proteins, which can cause the aggregation of αB-crystallin with other proteins, such as desmin. These findings may provide new insights into the development of treatments for lens diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mona Darvazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Parviz Abdolmaleki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Ran X, Yu Y, Yang H, Tan X, Ran Z, Zhang R, Du G, Yang L. Handheld UV spectrophotometer device for detection of methamphetamine hydrochloride based on supramolecular sensing platform. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123499. [PMID: 37832445 DOI: 10.1016/j.saa.2023.123499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The realization of drug detection in drug-using crime sites can provide law enforcement officials with direct evidence. This research has developed and demonstrated an easy-to-use handheld sensor that can quickly detect methamphetamine (MA) in the field. The core of the handheld UV spectrophotometer device (HUVSD) is the STM32F103 series of single-chip micro-controller, which has a 32-bit microcontroller and two embedded 12-bit high-precision analog-to-digital converter (ADC) modules. Through Bluetooth-wireless transmission protocol, the spectral information can be displayed in the cell phone's app, and it is possible to visually determine whether the test sample contains methamphetamine hydrochloride substances based on the characteristic peak at 410 nm. The readily available and inexpensive inducible compound 3A and the phosphate pillar[5]arene@silver nanoparticle (PP5@AgNPs) colloidal solution were used as the reactants. The PP5@AgNPs colloidal solution and 3A were mixed and reacted at room temperature, and the color changed to gray-black. The color change was caused by the aggregation of AgNPs induced by the molecular recognition between the induction compound 3A and PP5 on the AgNPs surface. After continuing to add the drug MA, the color of the colloidal solution turned yellow again. This is due to the occurrence of competitive molecular recognition, and the interaction between PP5 and 3A/MA was investigated by molecular docking simulations. The HUVSD has high sensitivity, simple equipment, time-saving, color change visualization and suitable for on-site deployment. It only needs a Pasteur pipette, which has great potential to realize rapid on-site detection.
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Affiliation(s)
- Xin Ran
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China
| | - Yanbo Yu
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China
| | - Hongxing Yang
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China
| | - Xiaoping Tan
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China; College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, 408100, China.
| | - Zhiyong Ran
- Key Laboratory of Microsystems and Microstructures Manufacturing (Ministry of Education), School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China.
| | - Ruilin Zhang
- NHC Key Laboratory of Drug Addiction Medicine, School of Forensic Medicine, Kunming Medical University, Kunming 650500, China.
| | - Guanben Du
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China
| | - Long Yang
- Yunnan Province Key Lab of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming 650224, China
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Li H, Deng X, Zhang Z, Yang Z, Huang H, Ye X, Zhong L, Xu G, Liu R, Fang Y. Nitric oxide/paclitaxel micelles enhance anti-liver cancer effects and paclitaxel sensitivity by inducing ferroptosis, endoplasmic reticulum stress and pyroptosis. RSC Adv 2023; 13:31772-31784. [PMID: 37908648 PMCID: PMC10613954 DOI: 10.1039/d3ra04861f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
The objective of this study was to investigate the anticancer activities of biodegradable polymeric micelles composed of monomethoxy poly(ethylene glycol), polylactic acid, and nitric oxide (mPEG-PLA-NO) loaded with paclitaxel (PTX) as a nanomedicine delivery system. We aimed to compare the anticancer effects of these NO/PTX micelles with PTX alone and elucidate their mechanism of action. We evaluated the impact of NO/PTX and PTX on cell viability using Cell Counting Kit-8 (CCK8) assays conducted on the Bel-7402 liver cancer cell line. Additionally, we employed H22 xenografted mice to assess the in vivo tumor growth inhibitory activity of NO/PTX. To examine the cytotoxicity of NO/PTX, the intracellular levels of reactive oxygen species (ROS), and the expression of ferroptosis-related proteins, we conducted experiments in the presence of the ferroptosis inhibitor ferrostatin-1 (Fer-1) or the ROS inhibitor N-acetyl cysteine (NAC). Furthermore, we investigated the expression of endoplasmic reticulum stress (ERS) and apoptosis-associated proteins. Our results demonstrated that NO/PTX exhibited enhanced anticancer effects compared to PTX alone in both Bel-7402 cells and H22 xenografted mice. The addition of Fer-1 or NAC reduced the anticancer activity of NO/PTX, indicating the involvement of ferroptosis and ROS in its mechanism of action. Furthermore, NO/PTX modulated the expression of proteins related to ERS and apoptosis, indicating the activation of these cellular pathways. The anticancer effects of NO/PTX in liver cancer cells were mediated through the induction of ferroptosis, pyroptosis, ERS, and apoptosis-associated networks. Ferroptosis and pyroptosis were activated by treatment of NO/PTX at low concentration, whereas ERS was induced to trigger apoptosis at high concentration. The superior anti-tumor effect of NO/PTX may be attributed to the downregulation of a multidrug resistance transporter and the sensitization of cells to PTX chemotherapy. In summary, our study highlights the potential of mPEG-PLA-NO micelles loaded with PTX as a nanomedicine delivery system for liver cancer treatment. The observed enhancement in anticancer activity, combined with the modulation of key cellular pathways, provides valuable insights into the therapeutic potential of NO/PTX in overcoming resistance and improving treatment outcomes in liver cancer patients.
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Affiliation(s)
- Huilan Li
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine Nanchang 330006 China
| | - Xiaoyu Deng
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Ziwei Zhang
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Zunhua Yang
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Hesong Huang
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine Nanchang 330006 China
| | - Xide Ye
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Linyun Zhong
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Guoliang Xu
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Ronghua Liu
- College of Pharmacy, Jiangxi University of Chinese Medicine Nanchang 330004 China
| | - Yuanying Fang
- National Engineering Research Center for Manufacturing Technology of TCM Solid Preparation, Jiangxi University of Chinese Medicine Nanchang 330006 China
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Al-Warhi T, Almahli H, Maklad RM, Elsayed ZM, El Hassab MA, Alotaibi OJ, Aljaeed N, Ayyad RR, Ghabour HA, Eldehna WM, El-Ashrey MK. 1-Benzyl-5-bromo-3-hydrazonoindolin-2-ones as Novel Anticancer Agents: Synthesis, Biological Evaluation and Molecular Modeling Insights. Molecules 2023; 28:molecules28073203. [PMID: 37049966 PMCID: PMC10096524 DOI: 10.3390/molecules28073203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
Human health is experiencing several obstacles in the modern medical era, particularly cancer. As a result, the cancer therapeutic arsenal should be continually expanded with innovative small molecules that preferentially target tumour cells. In this study, we describe the development of two small molecule series (7a–d and 12a–e) based on the 1-benzyl-5-bromoindolin-2-one scaffold that connected through a hydrazone linker to a 4-arylthiazole (7a–d) or 4-methyl-5-(aryldiazenyl)thiazole (12a–e) moiety. The anticancer activity of all the reported indolin-2-one derivatives was assessed against breast (MCF-7) and lung (A-549) cancer cell lines. The 4-arylthiazole-bearing derivatives 7c and 7d revealed the best anticancer activity toward MCF-7 cells (IC50 = 7.17 ± 0.94 and 2.93 ± 0.47, respectively). Furthermore, the VEGFR-2 inhibitory activity for 7c and 7d was evaluated. Both molecules disclosed good inhibitory activity, and their IC50 values were equal to 0.728 µM and 0.503 µM, respectively. Additionally, the impacts of 7d on the cell cycle phases as well as on the levels of different apoptotic markers (caspase-3, caspase-9, Bax, and Bcl-2) were assessed. Molecular docking and dynamic simulations are carried out to explore the binding mode of 7d within the VEGFR-2 active site.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Raed M. Maklad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Zainab M. Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai 46612, Egypt
| | - Ohoud J. Alotaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nada Aljaeed
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Rezk R. Ayyad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Hazem A. Ghabour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City 11829, Egypt
| | - Mohamed K. El-Ashrey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elini St., Cairo 11562, Egypt
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Shi M, He J, Xu M, Lin X, Liu H, Jiang T, Yi Z. Interactions between polycyclic musks and human lactoferrin: Multi-spectroscopic methods and docking simulation. J Mol Recognit 2023; 36:e3005. [PMID: 36573888 DOI: 10.1002/jmr.3005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8-hexamethylcyclopenta-γ-2-benzopyrane; HHCB) and Tonalide (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene; AHTN) are "pseudo-persistent" pollutants that can cause DNA damage, endocrine disruption, organ toxicity, and reproductive toxicity in humans. HHCB and AHTN are readily enriched in breast milk, so exposure of infants to HHCB and AHTN is of concern. Here, the molecular mechanisms through which HHCB and AHTN interact with human lactoferrin (HLF) are investigated using computational simulations and spectroscopic methods to identify indirectly how HHCB and AHTN may harm infants. Molecular docking and kinetic simulation studies indicated that HHCB and AHTN can interact with and alter the secondary HLF structure. The fluorescence quenching of HLF by HHCB, AHTN was static with the forming of HLF-HHCB, HLF-AHTN complex, and accompanied by non-radiative energy transfer and that 1:1 complexes form through interaction forces. Time-resolved fluorescence spectroscopy indicated that binding to small molecules does not markedly change the HLF fluorescence lifetime. Three-dimensional fluorescence spectroscopy indicated that HHCB and AHTN alter the peptide chain backbone structure of HLF. Ultraviolet-visible absorption spectroscopy, simultaneous fluorescence spectroscopy, Fourier-transform infrared spectroscopy, and circular dichroism spectroscopy indicated that HHCB and AHTN change the secondary HLF conformation. Antimicrobial activity experiments indicated that polycyclic musks decrease lactoferrin activity and interact with HLF. These results improve our understanding of the mechanisms involved in the toxicities of polycyclic musks bound to HLF at the molecular level and provide theoretical support for mother-and-child health risk assessments.
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Affiliation(s)
- Mengjie Shi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Jinfeng He
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Minhua Xu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Xiaolian Lin
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China
| | - Hongyan Liu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China.,South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, People's Republic of China
| | - Tiemin Jiang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China.,South Asia Branch of National Engineering Center of Dairy for Maternal and Child Health, Guilin University of Technology, Guilin, People's Republic of China
| | - Zhongsheng Yi
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, People's Republic of China
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Computational Approaches to the Rational Design of Tubulin-Targeting Agents. Biomolecules 2023; 13:biom13020285. [PMID: 36830654 PMCID: PMC9952983 DOI: 10.3390/biom13020285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.
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Chen J, Liu Z, Yang R, Liu M, Feng H, Li N, Jin M, Zhang M, Shui L. A liquid crystal-based biosensor for detection of insulin driven by conformational change of an aptamer at aqueous-liquid crystal interface. J Colloid Interface Sci 2022; 628:215-222. [DOI: 10.1016/j.jcis.2022.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 11/28/2022]
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Jiang W, Cai G, Hu P, Wang Y. Personalized medicine of non-gene-specific chemotherapies for non-small cell lung cancer. Acta Pharm Sin B 2021; 11:3406-3416. [PMID: 34900526 PMCID: PMC8642451 DOI: 10.1016/j.apsb.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
Non-small cell lung cancer is recognized as the deadliest cancer across the globe. In some areas, it is more common in women than even breast and cervical cancer. Its rise, vaulted by smoking habits and increasing air pollution, has garnered much attention and resource in the medical field. The first lung cancer treatments were developed more than half a century ago. Unfortunately, many of the earlier chemotherapies often did more harm than good, especially when they were used to treat genetically unsuitable patients. With the introduction of personalized medicine, physicians are increasingly aware of when, how, and in whom, to use certain anti-cancer agents. Drugs such as tyrosine kinase inhibitors, anaplastic lymphoma kinase inhibitors, and monoclonal antibodies possess limited utility because they target specific oncogenic mutations, but other drugs that target mechanisms universal to all cancers do not. In this review, we discuss many of these non-oncogene-targeting anti-cancer agents including DNA replication inhibitors (i.e., alkylating agents and topoisomerase inhibitors) and cytoskeletal function inhibitors to highlight their application in the setting of personalized medicine as well as their limitations and resistance factors.
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Affiliation(s)
| | - Guiqing Cai
- Quest Diagnostics, San Juan Capistrano, CA 92675, USA
| | - Peter Hu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Srivastava M, Mittal L, Kumari A, Asthana S. Molecular Dynamics Simulations Reveal the Interaction Fingerprint of Remdesivir Triphosphate Pivotal in Allosteric Regulation of SARS-CoV-2 RdRp. Front Mol Biosci 2021; 8:639614. [PMID: 34490343 PMCID: PMC8417884 DOI: 10.3389/fmolb.2021.639614] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/24/2021] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic has now strengthened its hold on human health and coronavirus' lethal existence does not seem to be going away soon. In this regard, the optimization of reported information for understanding the mechanistic insights that facilitate the discovery towards new therapeutics is an unmet need. Remdesivir (RDV) is established to inhibit RNA-dependent RNA polymerase (RdRp) in distinct viral families including Ebola and SARS-CoV-2. Therefore, its derivatives have the potential to become a broad-spectrum antiviral agent effective against many other RNA viruses. In this study, we performed comparative analysis of RDV, RMP (RDV monophosphate), and RTP (RDV triphosphate) to undermine the inhibition mechanism caused by RTP as it is a metabolically active form of RDV. The MD results indicated that RTP rearranges itself from its initial RMP-pose at the catalytic site towards NTP entry site, however, RMP stays at the catalytic site. The thermodynamic profiling and free-energy analysis revealed that a stable pose of RTP at NTP entrance site seems critical to modulate the inhibition as its binding strength improved more than its initial RMP-pose obtained from docking at the catalytic site. We found that RTP not only occupies the residues K545, R553, and R555, essential to escorting NTP towards the catalytic site, but also interacts with other residues D618, P620, K621, R624, K798, and R836 that contribute significantly to its stability. From the interaction fingerprinting it is revealed that the RTP interact with basic and conserved residues that are detrimental for the RdRp activity, therefore it possibly perturbed the catalytic site and blocked the NTP entrance site considerably. Overall, we are highlighting the RTP binding pose and key residues that render the SARS-CoV-2 RdRp inactive, paving crucial insights towards the discovery of potent inhibitors.
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Affiliation(s)
| | | | | | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Mou K, Abdalla M, Wei DQ, Khan MT, Lodhi MS, Darwish DB, Sharaf M, Tu X. Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. INFORMATICS IN MEDICINE UNLOCKED 2021; 25:100675. [PMID: 34337139 PMCID: PMC8314890 DOI: 10.1016/j.imu.2021.100675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
Structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are potential drug targets due to their role in the virus life cycle. The envelope (E) protein is one of the structural proteins; plays a critical role in virulency. However, the emergence of mutations oftenly leads to drug resistance and may also play a vital role in virus stabilization and evolution. In this study, we aimed to identify mutations in E proteins that affect the protein stability. About 0.3 million complete whole genome sequences were analyzed to screen mutations in E protein. All these mutations were subjected to stability prediction using the DynaMut server. The most common mutations that were detected at the C-terminal domain, Ser68Phe, Pro71Ser, and Leu73Phe, were examined through molecular dynamics (MD) simulations for a 100ns period. The sequence analysis shows the existence of 259 mutations in E protein. Interestingly, 16 of them were detected in the DFLV amino acid (aa) motif (aa72-aa75) that binds the host PALS1 protein. The results of root mean square deviation, fluctuations, radius of gyration, and free energy landscape show that Ser68Phe, Pro71Ser, and Leu73Phe are exhibiting a more stabilizing effect. However, a more comprehensive experimental study may be required to see the effect on virus pathogenicity. Potential antiviral drugs, and vaccines may be developed used after screening the genomic variations for better management of SARS-CoV-2 infections.
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Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing, China
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Doaa B Darwish
- Department of Biology, Faculty of Science, University of Tabuk, 71491, Saudi Arabia
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, PR China
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
| | - Xudong Tu
- Chongqing Medical and Pharmaceutical College, Chongqing, China
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Kumari A, Mittal L, Srivastava M, Asthana S. Binding mode characterization of 13b in the monomeric and dimeric states of SARS-CoV-2 main protease using molecular dynamics simulations. J Biomol Struct Dyn 2021; 40:9287-9305. [PMID: 34029506 DOI: 10.1080/07391102.2021.1927844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The main protease, Mpro/3CLpro, plays an essential role in processing polyproteins translated from viral RNA to produce functional viral proteins and therefore serve as an attractive target for discovering COVID-19 therapeutics. The availability of both monomer and dimer crystal bound with a common ligand, '13b' (α-ketoamide inhibitor), opened up opportunities to understand the Mpro mechanism of action. A comparative analysis of both forms of Mpro was carried out to elucidate the binding site architectural differences in the presence and absence of '13b'. Molecular dynamics simulations suggest that the presence of '13b' enhances the stability of Mpro than the unbound APO form. The N- and C- terminals of both the protomers stabilize each other, and making it's interface essential for the active form of Mpro. In comparison to monomer, the relatively high affinity of '13b' is gained in dimer pocket due to the high stability of the pocket by the interaction of S1 residue of chain B with residues F140, E166 and H172 of chain A, which is absent in monomer. The comprehensive essential dynamics, protein structure network analysis and thermodynamic profiling highlight the hot-spots, pivotal in molecular recognition process at protein-ligand and protein-protein interaction levels, cross-validated through computational alanine scanning study. A comparative description of '13b' binding mechanism in both forms illustrates valuable insights into the inhibition mechanism and the selection of critical residues suitable for the structure-based approaches for the identification of more potent Mpro inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
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12
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Cui K, Chen JH, Zou YF, Zhang SY, Wu B, Jing K, Li LW, Xia L, Sun C, Dong YL. Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. Technol Cancer Res Treat 2021; 20:1533033821990368. [PMID: 34018447 PMCID: PMC8142016 DOI: 10.1177/1533033821990368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common clinical intracranial malignancy worldwide, and the most common supratentorial tumor in adults. GBM mainly causes damage to the brain tissue, which can be fatal. This research explored potential gene targets for the diagnosis and treatment of GBM using bioinformatic technology. METHODS Public data from patients with GBM and controls were downloaded from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified by Gene Expression Profiling Interactive Analysis (GEPIA) and Gene Expression Omnibus 2R (GEO2R). Construction of the protein-protein interaction network and the identification of a significant module were performed. Subsequently, hub genes were identified, and their expression was examined and compared by real-time quantitative (RT-q)PCR between patients with GBM and controls. RESULTS GSE122498 (GPL570 platform), GSE104291 (GPL570 platform), GSE78703_DMSO (GPL15207 platform), and GSE78703_LXR (GPL15207 platform) datasets were obtained from the GEO. A total of 130 DEGs and 10 hub genes were identified by GEPIA and GEO2R between patients with GBM and controls. Of these, strong connections were identified in correlation analysis between CCNB1, CDC6, KIF23, and KIF20A. RT-qPCR showed that all 4 of these genes were expressed at significantly higher levels in patients with GBM compared with controls. CONCLUSIONS The hub genes CCNB1, CDC6, KIF23, and KIF20A are potential biomarkers for the diagnosis and treatment of GBM.
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Affiliation(s)
- Kai Cui
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, 12 Health Road, Shijiazhuang, Hebei, 050011, People's Republic of China
| | - Jin-Hui Chen
- Department of Neurosurgery, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518033, People's Republic of China
| | - Yang-Fan Zou
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Shu-Yuan Zhang
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Bing Wu
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Kai Jing
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Li-Weng Li
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Liang Xia
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Caixing Sun
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, People's Republic of China.,Department of Neurosurgery, Zhejiang Cancer Hospital, Hangzhou 310022, People's Republic of China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou 310022, People's Republic of China
| | - Ya-Lan Dong
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, 12 Health Road, Shijiazhuang, Hebei, 050011, People's Republic of China
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13
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Wilson CJ, Chang M, Karttunen M, Choy WY. KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability. Int J Mol Sci 2021; 22:5408. [PMID: 34065616 PMCID: PMC8161161 DOI: 10.3390/ijms22105408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/30/2022] Open
Abstract
We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant's mode of action.
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Affiliation(s)
- Carter J. Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
- Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5C1, Canada; (C.J.W.); (M.C.)
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14
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Al-Khafaji K, Taskin Tok T. Molecular dynamics simulation, free energy landscape and binding free energy computations in exploration the anti-invasive activity of amygdalin against metastasis. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 195:105660. [PMID: 32726718 DOI: 10.1016/j.cmpb.2020.105660] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVE Historically, amygdalin has been used as alternative medicine or in vitro and in vivo studies, but no single study exists which discusses the structural mechanism of amygdalin at a molecular level. This paper inquiries into the inhibitory actions of amygdalin on the selected targets: AKT1, FAK, and ILK, which are regulators for various mediated signaling pathways, and are associated with cell adhesion, migration, and differentiation. In order to get details at the molecular level of amygdalin's inhibitory activities against chosen proteins, molecular modeling and simulation techniques including double docking, molecular dynamics simulation, free energy landscape analysis, and binding free energy calculation were exerted. METHODS To get molecular level details of amygdalin inhibitory effects against the relevant proteins; here the utilized tools are the following: the double docking, molecular dynamics simulation, free energy landscape analysis, g_mmpbsa, and interaction entropy were used to evaluate the inhibitory activity against targeted proteins. RESULTS The computational calculations revealed that amygdalin inhibits the selected targets via block the ATP-binding pocket of AKT1, FAK, and ILK by forming stable hydrogen bonds. Moreover, free energy landscape, FEL exposed that amygdalin stabilized the global conformations of both FAK and ILK proteins to the minimum global energy besides it reduced the essential dynamics of FAK and ILK proteins. MMPBSA computations provided further evidence for amygdalin's stability inside the ATP-binding pocket of AKT1, FAK, and ILK with a binding free energy of 45.067, -13.033, 13.109 kJ/mol, respectively. The binding free energies are lastly consistent with the hydrogen bonding and pairs within 0.35 nm results. The decomposition of binding energy shows the pivotal amino acid residues responsible for the stability of amygdalin's interactions inside the ATP-binding sites by forming hydrogen bonds. CONCLUSIONS Before this work, it was enigmatic to make predictions about how amygdalin inhibits metastasis of cancer. But the computational results contribute in several ways to our understanding of amygdalin activity and provide a basic insight into the activity of amygdalin as a multi-target drug in the metastasis and invasion of cancer.
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Affiliation(s)
- Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, 27310 Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, 27310 Gaziantep, Turkey; Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, 27310 Gaziantep, Turkey.
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15
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Ali A, Khan MT, Khan A, Ali S, Chinnasamy S, Akhtar K, Shafiq A, Wei DQ. Pyrazinamide resistance of novel mutations in pncA and their dynamic behavior. RSC Adv 2020; 10:35565-35573. [PMID: 35515677 PMCID: PMC9056903 DOI: 10.1039/d0ra06072k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
Pyrazinamide (PZA) is one of the essential anti-mycobacterium drugs, active against non-replicating Mycobacterium tuberculosis (MTB) isolates. PZA is converted into its active state, called pyrazinoic acid (POA), by action of pncA encoding pyrazinamidase (PZase). In the majority of PZA-resistance isolates, pncA harbored mutations in the coding region. In our recent report, we detected a number of novel variants in PZA-resistance (PZAR) MTB isolates, whose resistance mechanisms were yet to be determined. Here we performed several analyses to unveil the PZAR mechanism of R123P, T76P, G150A, and H71R mutants (MTs) through molecular dynamics (MD) simulations. In brief, culture positive MTB isolates were subjected to PZA susceptibility tests using the WHO recommended concentration of PZA (100 μg ml−1). The PZAR samples were screened for mutations in pncA along sensitive isolates through polymerase chain reactions and sequencing. A large number of variants (GeneBank accession no. MH461111), including R123P, T76P, G150A, and H71R, have been spotted in more than 70% of isolates. However, the mechanism of PZAR for mutants (MTs) R123P, T76P, G150A, and H71R was unknown. For the MTs and native PZase structures (WT), thermodynamic properties were compared using molecular dynamics simulations for 100 ns. The MTs structural activity was compared to the WT. Folding effect and pocket volume variations have been detected when comparing between WT and MTs. Geometric matching further confirmed the effect of R123P, T76P, G150A, and H71R mutations on PZase dynamics, making them vulnerable for activating the pro-drug into POA. This study offers a better understanding for management of PZAR TB. The results may be used as alternative diagnostic tools to infer PZA resistance at a structural dynamics level. We performed several analyses to unveil the pyrazinamide-resistance mechanism of R123P, T76P, G150A, and H71R mutants through molecular dynamics simulations.![]()
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Affiliation(s)
- Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology Pakistan
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Sajid Ali
- Quaid-i-Azam University Islamabad, Provincial Tuberculosis Reference Laboratory Hayatabad Medical Complex Peshawar Pakistan
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Khalid Akhtar
- National University of Science and Technology Pakistan
| | - Athar Shafiq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573.,Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District Shenzhen Guangdong 518055 China
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16
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Zhu J, Qi R, Liu Y, Zhao L, Han W. Mechanistic Insights into the Effect of Ligands on Structural Stability and Selectivity of Sulfotransferase 2A1 (SULT2A1). ACS OMEGA 2019; 4:22021-22034. [PMID: 31891082 PMCID: PMC6933797 DOI: 10.1021/acsomega.9b03136] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/14/2019] [Indexed: 05/04/2023]
Abstract
Cytosolic sulfotransferases (SULTs) acting as phase II metabolic enzymes can be used in the sulfonation of small molecules by transferring a sulfonate group from the unique co-factor 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the substrates. In the present study, molecular dynamics (MD) simulations and ensemble docking study were employed to theoretically characterize the mechanism for the effect of co-factor (PAP) and ligands (LCA, raloxifene, α-hydroxytamoxifen, ouabain, and 3'-phosphoadenylyl sulfate) on structural stability and selectivity of SULT2A1 from the perspective of the dynamic behavior of SULT2A1 structures. Structural stability and network analyses indicated that the cooperation between PAP and LCA may enhance the thermal stability and compact communication in enzymes. During the MD simulations, the obviously rigid region and inward displacement were detected in the active-site cap (loop16) of the conformation containing PAP, which may be responsible for the significant changes in substrate accessibility and catalytic activity. The smaller substrates such as LCA could bind stably to the active pocket in the presence of PAP. However, the substrates or inhibitors with a large spatial structure needed to bind to the open conformation (without PAP) prior to PAPS binding.
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17
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Dash R, Ali MC, Dash N, Azad MAK, Hosen SMZ, Hannan MA, Moon IS. Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding. Int J Mol Sci 2019; 20:ijms20246256. [PMID: 31835852 PMCID: PMC6969939 DOI: 10.3390/ijms20246256] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/16/2022] Open
Abstract
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 (R213H) is responsible for inefficient enzymatic activity and associated with cancer progression. To characterize the detailed functional consequences of this mutation behind the loss-of-function of SULT1A1, the present study deployed molecular dynamics simulation to get insights into changes in the conformation and binding energy. The dynamics scenario of SULT1A1 in both wild and mutated types as well as with and without ligand showed that R213H induced local conformational changes, especially in the substrate-binding loop rather than impairing overall stability of the protein structure. The higher conformational changes were observed in the loop3 (residues, 235-263), turning loop conformation to A-helix and B-bridge, which ultimately disrupted the plasticity of the active site. This alteration reduced the binding site volume and hydrophobicity to decrease the binding affinity of the enzyme to substrates, which was highlighted by the MM-PBSA binding energy analysis. These findings highlight the key insights of structural consequences caused by R213H mutation, which would enrich the understanding regarding the role of SULT1A1 mutation in cancer development and also xenobiotics management to individuals in the different treatment stages.
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Affiliation(s)
- Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
| | - Md Chayan Ali
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Nayan Dash
- Department of Computer Science and Engineering, BGC Trust University, Bangladesh, Chittagong 4381, Bangladesh
| | - Md Abul Kalam Azad
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - S M Zahid Hosen
- Pancreatic Research Group, South Western Sydney Clinical School, University of New South Wales, and Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Il Soo Moon
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Korea
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18
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Sun Y, Xia Z, Zhao Q, Zheng B, Zhang M, Ying Y. Insights Into the Resistance Mechanisms of Inhibitors to FLT3 F691L Mutation via an Integrated Computational Approach. Front Pharmacol 2019; 10:1050. [PMID: 31619996 PMCID: PMC6763581 DOI: 10.3389/fphar.2019.01050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/19/2019] [Indexed: 11/26/2022] Open
Abstract
Research has shown that FMS-like tyrosine kinase 3 (FLT3) may be a vital drug target for acute myeloid leukemia (AML). However, even though the clinically relevant F691L gatekeeper mutation conferred resistance to current FLT3 drug quizartinib, PLX3397 remained unaffected. In this study, the protein–ligand interactions between FLT3 kinase domain (wild-type or F691L) and quizartinib or PLX3397 were compared via an integrated computational approach. The classical molecular dynamics (MD) simulations in conjunction with dynamic cross-correlation (DCC) analysis, solvent-accessible surface area (SASA), and free energy calculations indicated that the resistant mutation may induce the conformational change of αC-helix and A-loop of the FLT3 protein. The major variations were controlled by the electrostatic interaction and SASA, which were allosterically regulated by residues Glu-661 and Asp-829. When FLT3-F691L was bound to quizartinib, a large conformational change was observed via combination of accelerated MD simulations (aMDs), principal component analysis (PCA), and free energy landscape (FEL) calculations. The umbrella sampling (US) simulations were applied to investigate the dissociation processes of the quizartinib or PLX3397 from FLT3-WT and FLT3-F691L. The calculated results suggested that PLX3397 had similar dissociation processes from both FLT3-WT and FLT3-F691L, but quizartinib dissociated more easily from FLT3-F691L than from FLT3-WT. Thus, reduced residence time was responsible for the FLT3-F691L resistance to inhibitors. These findings indicated that both the conformational changes of αC-helix and A-loop and the drug residence time should be considered in the design of drugs so that rational decisions can be made to overcome resistance to FLT3-F691L.
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Affiliation(s)
- Yunfeng Sun
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Zhongni Xia
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Qinqin Zhao
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Bei Zheng
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Meiling Zhang
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Yin Ying
- Department of Pharmacy, Tongde Hospital of Zhejiang Province, Hangzhou, China
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19
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Srivastava G, Darokar MP, Sharma A. Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation. J Biomol Struct Dyn 2019; 38:3411-3431. [PMID: 31448694 DOI: 10.1080/07391102.2019.1659854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Pyrazinamide (PZA), a crucial component of anti-TB therapy, is a prodrug. PZA interacts with PncA protein to be converted into its functional form i.e. pyrazinoic acid (POA). It has unique feature to kill dormant tubercle bacilli of acidic environment. Although significance of pH environment in PZA activation has been investigated in several of previous studies, insight into the significant atomistic variations in the interaction pattern of PZA with PncA, at different pH environments, are still required to be explored. On the other hand, continuously emerging PncA mutants, associated with PZA resistance, have also become a serious threat for global TB control program. Therefore, the current study was designed to understand the role of pH environment in the PZA activation and to explore the PZA resistance mechanism in various PncA mutants. The study included various in silico experiments like molecular docking, MD simulation, binding free energy estimation, PCA and FEL. In our study, we have found pH-3 and pH-5 environment as a highly significant environment for PZA activation. It was found that protonation or deprotonation of PZA activation site (PAS) residues, majorly K48, D56, K96 and E107, resulted in rearrangement of the PAS according to the pH conditions. It has also been observed that positioning of PZA binding near to Fe2+ and residues of catalytic triad (i.e. D8, K96 and C138) also play a very crucial role in the activation of PZA. The overall insight from the current study may help to develop new therapeutics against PncA mutated PZA resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M P Darokar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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20
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Simulation-based protein engineering of R. erythropolis FMN oxidoreductase (DszD). Heliyon 2019; 5:e02193. [PMID: 31428711 PMCID: PMC6695286 DOI: 10.1016/j.heliyon.2019.e02193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
The sulfur contents of fossil fuels have negative impacts on the environment and human health. The bio-catalytic desulfurization strategies and the biological refinement of fossil fuels are a cost-effective process compared to classical chemistry desulfurization. Rhodococcus erythropolis IGTS8 is able to metabolize the organic sulfur compound by the unique genes cluster (i.e. DszA, B, C and D genes) in the 4S metabolic pathway. The dszD gene codes a key enzyme for sulfur reduction in the gene cluster. In this study, the structure of the DszD enzyme was predicted and then the key residues toward FMN binding were identified which were Thr62, Ser63, Asn77, and Ala79. To investigate the effect of manipulation in key residues on the enzymatic activity of the DszD, different mutations were performed on key residues. The molecular docking simulation showed that A79I and A79N mutants have the lowest binding free energies compared to the wild-type enzyme in binding with FMN substrate. A 50 ns molecular dynamics (MD) simulation performed using GROMACS software. The RMSD and RMSF analysis showed that two mutants are more stable than the wild-type enzyme during MD simulation. The binding free energies between FMN substrate and complexes were calculated and analyzed by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) method. The experimental results showed that the enzyme activity for the oxidoreductase process toward biodesulfurization increased 1.9 and 2.3 fold for A79I and A79N mutants, respectively.
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21
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Liu WS, Wang RR, Sun YZ, Li WY, Li HL, Liu CL, Ma Y, Wang RL. Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation. J Cell Biochem 2019; 120:17015-17029. [PMID: 31125141 DOI: 10.1002/jcb.28963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/03/2019] [Accepted: 03/15/2019] [Indexed: 01/02/2023]
Abstract
Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.
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Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Khan MT, Khan A, Rehman AU, Wang Y, Akhtar K, Malik SI, Wei DQ. Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. Sci Rep 2019; 9:7482. [PMID: 31097767 PMCID: PMC6522564 DOI: 10.1038/s41598-019-44013-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/29/2019] [Indexed: 02/04/2023] Open
Abstract
Resistance to key first-line drugs is a major hurdle to achieve the global end tuberculosis (TB) targets. A prodrug, pyrazinamide (PZA) is the only drug, effective in latent TB, recommended in drug resistance and susceptible Mycobacterium tuberculosis (MTB) isolates. The prodrug conversion into active form, pyrazinoic acid (POA), required the activity of pncA gene encoded pyrazinamidase (PZase). Although pncA mutations have been commonly associated with PZA resistance but a small number of resistance cases have been associated with mutationss in RpsA protein. Here in this study a total of 69 PZA resistance isolates have been sequenced for pncA mutations. However, samples that were found PZA resistant but pncA wild type (pncAWT), have been sequenced for rpsA and panD genes mutation. We repeated a drug susceptibility testing according to the WHO guidelines on 18 pncAWT MTB isolates. The rpsA and panD genes were sequenced. Out of total 69 PZA resistant isolates, 51 harbored 36 mutations in pncA gene (GeneBank Accession No. MH46111) while, fifteen different mutations including seven novel, were detected in the fourth S1 domain of RpsA known as C-terminal (MtRpsACTD) end. We did not detect any mutations in panD gene. Among the rpsA mutations, we investigated the molecular mechanism of resistance behind mutations, D342N, D343N, A344P, and I351F, present in the MtRpsACTD through molecular dynamic simulations (MD). WT showed a good drug binding affinity as compared to mutants (MTs), D342N, D343N, A344P, and I351F. Binding pocket volume, stability, and fluctuations have been altered whereas the total energy, protein folding, and geometric shape analysis further explored a significant variation between WT and MTs. In conclusion, mutations in MtRpsACTD might be involved to alter the RpsA activity, resulting in drug resistance. Such molecular mechanism behind resistance may provide a better insight into the resistance mechanism to achieve the global TB control targets.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Abbas Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Ashfaq Ur Rehman
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Wang
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Khalid Akhtar
- National University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China.
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Khan MT, Junaid M, Mao X, Wang Y, Hussain A, Malik SI, Wei DQ. Pyrazinamide resistance and mutations L19R, R140H, and E144K in Pyrazinamidase of Mycobacterium tuberculosis. J Cell Biochem 2019; 120:7154-7166. [PMID: 30485476 DOI: 10.1002/jcb.27989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
Pyrazinamide (PZA) is an important component of first-line antituberculosis drugs activated by Mycobacterium tuberculosis pyrazinamidase (PZase) into its active form pyrazinoic acid. Mutations in the pncA gene have been recognized as the major cause of PZA resistance. We detected some novel mutations, Leucine19Arginine (L19R), Arginine140Histidine (R140H), and Glutamic acid144 Lysine (E144K), in the pncA gene of PZA-resistant isolates in our wet lab PZA drug susceptibility testing and sequencing. As the molecular mechanism of resistance of these variants has not been reported earlier, we have performed multiple analyses to unveil different mechanisms of resistance because of PZase mutations L19R, R140H, and E144K. The mutants and native PZase structures were subjected to comprehensive computational molecular dynamics (MD) simulations at 100 nanoseconds in apo and drug-bound form. Mutants and native PZase binding pocket were compared to observe the consequence of mutations on the binding pocket size. Hydrogen bonding, Gibbs free energy, and natural ligand Fe +2 effect were also analyzed between native and mutants. A significant variation between native and mutant PZase structure activity was observed. The native PZase protein docking score was found to be the maximum, showing strong binding affinity in comparison with mutants. MD simulations explored the effect of the variants on the biological function of PZase. Hydrogen bonding, metal ion Fe +2 deviation, and fluctuation also seemed to be affected because of the mutations L19R, R140H, and E144K. The variants L19R, R140H, and E144K play a significant role in PZA resistance, altering the overall activity of native PZase, including metal ion Fe +2 displacement and free energy. This study offers valuable evidence for better management of drug-resistant tuberculosis.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.,Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Mao
- Department of Bioinformatics and Biostatistics, Qianweichang College, Shanghai University, Shanghai, China
| | - Yanjie Wang
- Department of Computer Science, College of Computer Science and Information Tech, Henan Normal University, Xixiang, China
| | - Abid Hussain
- Department of Pharmaceutics, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Srivastava G, Tripathi S, Kumar A, Sharma A. Molecular insight into multiple RpoB clinical mutants of Mycobacterium tuberculosis: An attempt to probe structural variations in rifampicin binding site underlying drug resistance. Int J Biol Macromol 2018; 120:2200-2214. [DOI: 10.1016/j.ijbiomac.2018.06.184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022]
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25
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Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations. PLoS One 2018; 13:e0207234. [PMID: 30444912 PMCID: PMC6239307 DOI: 10.1371/journal.pone.0207234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023] Open
Abstract
Adenosine deaminase (ADA) catalyzes the deamination of adenosine, which is important in purine metabolism. ADA is ubiquitous to almost all human tissues, and ADA abnormalities have been reported in various diseases, including rheumatoid arthritis. ADA can be divided into two conformations based on the inhibitor that it binds to: open and closed forms. Here, we chose three ligands, namely, FR117016 (FR0), FR221647 (FR2) (open form), and HDPR (PRH, closed form), to investigate the inhibition mechanism of ADA and its effect on ADA through molecular dynamics simulations. In open forms, Egap and electrostatic potential (ESP) indicated that electron transfer might occur more easily in FR0 than in FR2. Binding free energy and hydrogen bond occupation revealed that the ADA-FR0 complex had a more stable structure than ADA-FR2. The probability of residues Pro159 to Lys171 of ADA-FR0 and ADA-FR2 to form a helix moderately increased compared with that in nonligated ADA. In comparison with FR0 and FR2 PRH could maintain ADA in a closed form to inhibit the function of ADA. The α7 helix (residues Thr57 to Ala73) of ADA in the closed form was mostly unfastened because of the effect of PRH. The number of H bonds and the relative superiority of the binding free energy indicated that the binding strength of PRH to ADA was significantly lower than that of an open inhibitor, thereby supporting the comparison of the inhibitory activities of the three ligands. Alanine scanning results showed that His17, Gly184, Asp295, and Asp296 exerted the greatest effects on protein energy, suggesting that they played crucial roles in binding to inhibitors. This study served as a theoretical basis for the development of new ADA inhibitors.
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Khan MT, Rehaman AU, Junaid M, Malik SI, Wei DQ. Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance. Comput Struct Biotechnol J 2018; 16:379-387. [PMID: 30402208 PMCID: PMC6205349 DOI: 10.1016/j.csbj.2018.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis drugs which is converted into active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoded, pyrazinamidase (PZase). Mutations in pncA are detected in >70% of PZA resistant isolates but, noticeably, not in all. In this study, we selected 18 PZA-resistant but wild type pncA (pncAWT) MTB isolates. Drug susceptibility testing (DST) of all the isolates were repeated at the critical concentration of PZA drug. All these PZA-resistance but pncAWT isolates were subjected to RpsA sequencing. Fifteen different mutations were identified in eleven isolates, where seven were present in a conserved region including, Ser324Phe, Glu325Lys, Gly341Arg. As the molecular mechanism of resistance behind these variants has not been reported earlier, we have performed multiple analysis to unveil the mechanisms of resistance behind mutations S324F, E325K, and G341R. The mutant and wild type RpsA structures were subjected to comprehensive computational molecular dynamic simulations at 50 ns. Root mean square deviation (RMSD), Root mean square fluctuation (RMSF), and Gibbs free energy of mutants were analyzed in comparison with wild type. Docking score of wild type-RpsA has been found to be maximum, showing a strong binding affinity in comparison with mutants. Pocket volume, RMSD and RMSF have also been found to be altered, whereas total energy, folding effect (radius of gyration) and shape complimentarily analysis showed that variants S324F, E325K, and G341R have been playing a significant role behind PZA-resistance. The study offers valuable information for better management of drug resistance tuberculosis.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Ashfaq Ur Rehaman
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Muhammad Junaid
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
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Zhu J, Li Y, Wang J, Yu Z, Liu Y, Tong Y, Han W. Adaptive Steered Molecular Dynamics Combined With Protein Structure Networks Revealing the Mechanism of Y68I/G109P Mutations That Enhance the Catalytic Activity of D-psicose 3-Epimerase From Clostridium Bolteae. Front Chem 2018; 6:437. [PMID: 30320068 PMCID: PMC6166005 DOI: 10.3389/fchem.2018.00437] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/03/2018] [Indexed: 12/19/2022] Open
Abstract
The scarcity, richness, and other important physiological functions of D-psicose make it crucial to increase the yield of D-psicose. The production of D-psicose can be accomplished by D-psicose 3-epimerase (DPEase) from Clostridium bolteae (CbDPEase) catalyzing the substrate D-fructose. Although the catalytic efficiency of the CbDPEase has been raised via using the site-directed mutagenesis (Y68I/G109P) technique, structure-activity relationship in the wild-type CbDPEase and Y68I/G109P mutant is currently poorly understood. In our study, a battery of molecular modeling methods [homology modeling, adaptive steered molecular dynamics (ASMD) simulations, and Molecular Mechanics/Generalized Born Surface Area (MM-GB/SA)], combined with protein structure networks, were employed to theoretically characterize the reasons for the differences in the abilities of the D-fructose catalyzed by the wild-type CbDPEase and Y68I/G109P mutant. Protein structure networks demonstrated that site-directed mutagenesis enhanced the connectivity between D-fructose and CbDPEase, leading to the increased catalytic efficiency mediated by the functional residues with high betweenness. During the dissociation of the D-fructose from the Y68I/G109P mutant, planes of benzene rings of F248 and W114 could be continuously parallel to the stretching direction of D-fructose. It made the tunnel have an open state and resulted in the stable donor-π interactions between D-fructose and the benzene rings around 18Å. The stronger substrate-protein interactions were detected in the Y68I/G109P mutant, instead of in the wild-type CbDPEase, which were consistent with the binding free energy and Potential Mean of Force (PMF) results. The theoretical results illustrated the reasons that Y68I/G109P mutations increased the catalytic efficiency of CbDPEase and could be provided the new clue for further DPEase engineering.
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Affiliation(s)
- Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Yi Li
- COFCO (Jilin) Bio-Chemical Technology Co., Ltd, Changchun, China
| | - Jinzhi Wang
- COFCO (Jilin) Bio-Chemical Technology Co., Ltd, Changchun, China
| | - Zhengfei Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Ye Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Yi Tong
- COFCO (Jilin) Bio-Chemical Technology Co., Ltd, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
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28
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Wei Y, Yi Z, Xu J, Yang W, Yang L, Liu H. Study on the binding characteristics of hydroxylated polybrominated diphenyl ethers and thyroid transporters using the multispectral technique and computational simulation. J Biomol Struct Dyn 2018; 37:1402-1413. [DOI: 10.1080/07391102.2018.1461134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Yuchen Wei
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Zhongsheng Yi
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Jie Xu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Wu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Lulu Yang
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
| | - Hongyan Liu
- Guangxi Colleges and Universities Key Laboratory of Food Safety and Detection, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin 541004, China
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29
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Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. J Comput Aided Mol Des 2018. [DOI: 10.1007/s10822-018-0109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Hemmat M, Castle BT, Odde DJ. Microtubule dynamics: moving toward a multi-scale approach. Curr Opin Cell Biol 2018; 50:8-13. [PMID: 29351860 PMCID: PMC5911414 DOI: 10.1016/j.ceb.2017.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/12/2017] [Accepted: 12/23/2017] [Indexed: 12/17/2022]
Abstract
Microtubule self-assembly dynamics serve to facilitate many vital cellular functions, such as chromosome segregation during mitosis and synaptic plasticity. However, the detailed atomistic basis of assembly dynamics has remained an unresolved puzzle. A key challenge is connecting together the vast range of relevant length-time scales, events happening at time scales ranging from nanoseconds, such as tubulin molecular interactions (Å-nm), to minutes-hours, such as the cellular response to microtubule dynamics during mitotic progression (μm). At the same time, microtubule interactions with associated proteins and binding agents, such as anti-cancer drugs, can strongly affect this dynamic process through atomic-level mechanisms that remain to be elucidated. New high-resolution technologies for investigating these interactions, including cryo-electron microscopy (EM) techniques and total internal reflection fluorescence (TIRF) microscopy, are yielding important new insights. Here, we focus on recent studies of microtubule dynamics, both theoretical and experimental, and how these findings shed new light on this complex phenomenon across length-time scales, from Å to μm and from nanoseconds to minutes.
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Affiliation(s)
- Mahya Hemmat
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian T Castle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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Kumar A, Srivastava G, Negi AS, Sharma A. Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β. J Biomol Struct Dyn 2018; 37:275-290. [DOI: 10.1080/07391102.2018.1426043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Arvind S. Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
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Sun C, Zhu L, Zhang C, Song C, Wang C, Zhang M, Xie Y, Schaefer HF. Conformers, properties, and docking mechanism of the anticancer drug docetaxel: DFT and molecular dynamics studies. J Comput Chem 2018; 39:889-900. [DOI: 10.1002/jcc.25165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Chuancai Sun
- School of Biomedical Engineering and TechnologyTianjin Medical University, No.22 Qi xiang tai Road, Heping DistrictTianjin300070 China
| | - Lijuan Zhu
- School of Biomedical Engineering and TechnologyTianjin Medical University, No.22 Qi xiang tai Road, Heping DistrictTianjin300070 China
| | - Chao Zhang
- School of Biomedical Engineering and TechnologyTianjin Medical University, No.22 Qi xiang tai Road, Heping DistrictTianjin300070 China
| | - Ce Song
- Hefei National Laboratory of Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefei Anhui230026 China
- Department of Theoretical Chemistry and Biology, School of BiotechnologyRoyal Institute of TechnologyStockholmSE‐10691 Sweden
| | - Cuihong Wang
- School of ScienceTianjin Chengjian UniversityTianjin300384 China
| | - Meiling Zhang
- School of Biomedical Engineering and TechnologyTianjin Medical University, No.22 Qi xiang tai Road, Heping DistrictTianjin300070 China
| | - Yaoming Xie
- Center for Computational Quantum ChemistryUniversity of GeorgiaAthens Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Quantum ChemistryUniversity of GeorgiaAthens Georgia 30602
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Li HL, Ma Y, Zheng CJ, Jin WY, Liu WS, Wang RL. Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study. J Biomol Struct Dyn 2017; 36:3856-3868. [PMID: 29125030 DOI: 10.1080/07391102.2017.1402709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Noonan syndrome (NS) is a common autosomal dominant congenital disorder which could cause the congenital cardiopathy and cancer predisposition. Previous studies reported that the knock-in mouse models of the mutant D61G of SHP2 exhibited the major features of NS, which demonstrated that the mutation D61G of SHP2 could cause NS. To explore the effect of D61G mutation on SHP2 and explain the high activity of the mutant, molecular dynamic simulations were performed on wild type (WT) of SHP2 and the mutated SHP2-D61G, respectively. The principal component analysis and dynamic cross-correlation mapping, associated with secondary structure, showed that the D61G mutation affected the motions of two regions (residues Asn 58-Thr 59 and Val 460-His 462) in SHP2 from β to turn. Moreover, the residue interaction networks analysis, the hydrogen bond occupancy analysis and the binding free energies were calculated to gain detailed insight into the influence of the mutant D61G on the two regions, revealing that the major differences between SHP2-WT and SHP2-D61G were the different interactions between Gly 61 and Gly 462, Gly 61 and Ala 461, Gln 506 and Ile 463, Gly 61 and Asn 58, Ile 463 and Thr 466, Gly 462 and Cys 459. Consequently, our findings here may provide knowledge to understand the increased activity of SHP2 caused by the mutant D61G.
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Key Words
- CHD, congenital heart defects
- D61G
- DCCM, dynamic cross-correlation mapping
- DSPP, Definition of Secondary Structure of Proteins
- H bond, hydrogen bond
- MD, molecular dynamic
- MM-PBSA, molecular mechanics Poisson Boltzmann surface area
- NS, Noonan syndrome
- PCA, principal component analysis
- PTPN11, tyrosine protein phosphatase non-receptor type 11
- RINs, residue interaction networks
- RMSD, root-mean-square deviation
- RMSF, root-mean-square fluctuation
- SH2, Src-homology 2
- SHP2
- SHP2, protein tyrosine phosphatase-2
- SPC, single-point charge
- VDW, Van der Waals
- WT, wild type
- molecular dynamic simulation
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Affiliation(s)
- Hong-Lian Li
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Ying Ma
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Chang-Jie Zheng
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Wen-Yan Jin
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Wen-Shan Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Run-Ling Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
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Kayık G, Tüzün NŞ, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K + channel. J Mol Graph Model 2017; 77:399-412. [DOI: 10.1016/j.jmgm.2017.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022]
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35
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Zhu J, Lv Y, Han X, Xu D, Han W. Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations. Sci Rep 2017; 7:12439. [PMID: 28963484 PMCID: PMC5622063 DOI: 10.1038/s41598-017-12031-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/01/2017] [Indexed: 01/24/2023] Open
Abstract
ADP-ribosylhydrolases (ARH1, ARH2 and ARH3) are a family of enzymes to catalyze ADP-ribosylation, a reversible and covalent post-translational modification (PTM). There are four phosphorylated sites (Tyr-4, Tyr-19, Tyr-20, and Tyr-205) in ARH1. To explore the structural changes and functional impact induced by phosphorylation, molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations were performed for the phosphorylated and non-phosphorylated ARH1 with the ligands. MD simulations results indicate that: (1) Glu-25 is more frequently in the α helix group in the phosphorylated state with the adenosine-5-diphosphate-ribosylarginine (ADP-RA) complex (51.56%) than that of the non-phosphorylated state(2.12%); (2) Ser-124 and Ser-264 become less flexible in the phosphorylated state with ADP-RA complex, which helps two residues form hydrogen bonds with ADP-RA; and (3) Tyr-211 is also less flexible in the phosphorylated state with ADP-RA complex, which helps stabilize the cation-π interaction of Y211-R119. All these changes facilitate ADP-RA to bind ARH1. In addition, according to the crystal structure of adenosine-5-diphosphate-ribose (ADP-ribose) in complex with non-phosphorylated and phosphorylated ARH1, the possible unbinding pathways of ADP-ribose from non-phosphorylated and phosphorylated ARH1 were explored respectively using SMD simulations. Our results show that phosphorylated ARH1 has more ordered structures than the non-phosphorylated type.
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Affiliation(s)
- Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Yishuo Lv
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Xiaosong Han
- Department of Electric Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA
- College of Computer Science and Technology Jilin University, 2699 Qianjin Street, Changchun, 130012, China
| | - Dong Xu
- Department of Electric Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.
- College of Computer Science and Technology Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun, 130012, China.
- Department of Electric Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65211, USA.
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Srivastava G, Tripathi S, Kumar A, Sharma A. Molecular investigation of active binding site of isoniazid (INH) and insight into resistance mechanism of S315T-MtKatG in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2017; 105:18-27. [DOI: 10.1016/j.tube.2017.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/19/2022]
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Zúñiga MA, Alderete JB, Jaña GA, Jiménez VA. Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis. J Comput Aided Mol Des 2017; 31:643-652. [DOI: 10.1007/s10822-017-0029-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/28/2017] [Indexed: 01/27/2023]
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Tian Y, Yu Y, Shen Y, Wan H, Chang S, Zhang T, Wan S, Zhang J. Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK. J Chem Inf Model 2017; 57:977-987. [PMID: 28318251 DOI: 10.1021/acs.jcim.7b00019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ROS1 and ALK are promising targets of anticancer drugs for non-small-cell lung cancer. Since they have 49% amide acid sequence homology in the kinases domain and 77% identity at the ATP binding area, some ALK inhibitors also showed some significant responses for ROS1 in the clinical trial, such as the type-I binding inhibitor crizotinib and PF-06463922. As a newly therapeutic target, the selective ROS1 inhibitor is relatively rare. Moreover, the molecular basis for the selectivity of ROS1 versus ALK still remains unclear. In order to disclose the binding preference toward ROS1 over ALK and to aid the design of selective ROS1 inhibitors, the specific interactions and difference of conformational changes in the dual and selective ROS1/ALK inhibitors systems were investigated by molecular dynamics (MD) simulation and principle component analysis (PCA) in our work. Afterward, binding free energies (MM/GBSA) and binding free energies decomposition analysis indicated that the dominating effect of Van der Waals interaction drives the specific binding process of the type-I inhibitor, and residues of the P-loop and the DFG motif would play an important role in selectivity. On the basis of the modeling results, the new designed compound 14c was verified as a selective ROS1 inhibitor versus ALK, and SMU-B was a dual ROS1/ALK inhibitor by the kinase inhibitory study. These results are expected to facilitate the discovery and rational design of novel and specific ROS1 inhibitors.
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Affiliation(s)
- Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yonghuan Yu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yudong Shen
- College of Food Sciences, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou, 213001, People's Republic of China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
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Karuppasamy R, Verma K, Sequeira VM, Basavanna LN, Veerappapillai S. An Integrative Drug Repurposing Pipeline: Switching Viral Drugs to Breast Cancer. J Cell Biochem 2017; 118:1412-1422. [PMID: 27859674 DOI: 10.1002/jcb.25799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/15/2016] [Indexed: 11/07/2022]
Abstract
The growing incidence rate of breast cancer, coupled with cellular chemotherapeutic resistance, has made this disease one of the most prevalent cancers among women worldwide. Despite the recent efforts to understand the underlying cause of the resistance due to mutation, there are no feasible tactics to overcome this bottleneck. This issue could be addressed by the concept of polypharmacology-disguising drugs present in the pharmacopeia for novel purposes (drug repurposing). Of note, we have proposed a multi-modal computational drug-repositioning stratagem to predict drugs possessing anti-proliferative effect. Our results suggest that Ombitasvir, a Hepatitis C NS5B polymerase inhibitor, could be "repurposed" for the control and prevention of beta-tubulin-driven breast cancers. J. Cell. Biochem. 118: 1412-1422, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Kanika Verma
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Velin Marita Sequeira
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Lokapriya Nandan Basavanna
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Shanthi Veerappapillai
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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