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Matevosyan M, Harutyunyan V, Abelyan N, Khachatryan H, Tirosyan I, Gabrielyan Y, Sahakyan V, Gevorgyan S, Arakelov V, Arakelov G, Zakaryan H. Design of new chemical entities targeting both native and H275Y mutant influenza a virus by deep reinforcement learning. J Biomol Struct Dyn 2023; 41:10798-10812. [PMID: 36541127 DOI: 10.1080/07391102.2022.2158936] [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: 08/02/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Influenza virus remains a major public health challenge due to its high morbidity and mortality and seasonal surge. Although antiviral drugs against the influenza virus are widely used as a first-line defense, the virus undergoes rapid genetic changes, resulting in the emergence of drug-resistant strains. Thus, new antiviral drugs that can outwit resistant strains are of significant importance. Herein, we used deep reinforcement learning (RL) algorithm to design new chemical entities (NCEs) that are able to bind to the native and H275Y mutant (oseltamivir-resistant) neuraminidases (NAs) of influenza A virus with better binding energy than oseltamivir. We generated more than 66211 NCEs, which were prioritized based on the filtering rules, structural alerts, and synthetic accessibility. Then, 18 NCEs with better MM/PBSA scores than oseltamivir were further analyzed in molecular dynamics (MD) simulations conducted for 100 ns. The MD experiments showed that 8 NCEs formed very stable complexes with the binding pocket of both native and H275Y mutant NAs of H1N1. Furthermore, most NCEs demonstrated much better binding affinity to group 2 (N2, N3, and N9) and influenza B virus NAs than oseltamivir. Although all 8 NCEs have non-sialic acid-like structures, they showed a similar binding mode as oseltamivir, indicating that it is possible to find new scaffolds with better binding and antiviral properties than sialic acid-like inhibitors. In conclusion, we have designed potential compounds as antiviral candidates for further synthesis and testing against wild and mutant influenza virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Vahram Arakelov
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
| | - Grigor Arakelov
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
| | - Hovakim Zakaryan
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
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2
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Reddy Peddi S, Kundenapally R, Kanth Sivan S, Somadi G, Manga V. A pragmatic pharmacophore informatics strategy to discover new potent inhibitors against pim-3. Struct Chem 2022. [DOI: 10.1007/s11224-022-01949-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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3
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Zhang W, Xu H, Guan S, Wang C, Dong G. Frequency and distribution of H1N1 influenza A viruses with oseltamivir-resistant mutations worldwide before and after the 2009 pandemic. J Med Virol 2022; 94:4406-4416. [PMID: 35585032 DOI: 10.1002/jmv.27870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/06/2022]
Abstract
H1N1 influenza has brought serious threats to people's health and a high socio-economic burden to society. Oseltamivir, a kind of neuraminidase (NA) inhibitor, is the second-generation specific drug that is broadly used currently. However, H1N1 influenza viruses have exhibited oseltamivir resistance in the past decades, which might be a hidden danger. To understand the frequency and distribution laws of oseltamivir-resistant viruses, we conducted a thorough and deep analysis of the available NA protein sequences of H1N1 influenza viruses worldwide from 1918 to 2020. The differences and similarities before and after 2009 were also considered since the dominant viruses changed in this period. Results showed that 3.76% of H1N1 viruses harbored oseltamivir resistance currently. Among various significative mutations, H274Y had the highest frequency of 3.30%, while the frequencies of the other mutations were far below this whether before or after 2009. The oseltamivir resistance was mainly found in three hosts, human, swine, and avian. Different mutation sites could exhibit different distributions in each host. Our results showed that the resistance level reached a peak during the 2007-2008 influenza season and then quickly decreased in 2009. The resistance also displayed a global distribution. The densely populated countries usually had a high resistance level. However, frequent significative mutations were also found in some small countries. Our findings indicated the necessity of monitoring oseltamivir resistance around the world. The study could provide a unique perspective towards the cognition of viruses and facilitate the future study of both pandemic and drug development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weixu Zhang
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Hefeng Xu
- Department of Developmental Cell Biology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Shuxuan Guan
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Chengmin Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangdong Province, Guangzhou, 510260, China
| | - Guoying Dong
- College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
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4
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Yu Y, Qin HJ, Shi XX, Song JQ, Zhou JP, Yu P, Fan ZC, Zhong M, Yang Y. Thiosialoside-decorated polymers use a two-step mechanism to inhibit both early and late stages of influenza virus infection. Eur J Med Chem 2020; 199:112357. [DOI: 10.1016/j.ejmech.2020.112357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022]
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5
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Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J Comput Aided Mol Des 2019; 34:27-37. [PMID: 31773463 DOI: 10.1007/s10822-019-00251-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
Influenza epidemics are responsible for an average of 3-5 millions of severe cases and up to 500,000 deaths around the world. One of flu pandemic types is influenza A(H1N1)pdm09 virus (pdm09H1N1). Oseltamivir is the antiviral drug used to treat influenza targeting at neuraminidase (NA) located on the viral surface. Influenza virus undergoes high mutation rates and leads to drug resistance, and thus the development of more efficient drugs is required. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. The obtained results in terms of binding free energy and intermolecular interactions in the ligand-protein interface showed that the oseltamivir could not be well accommodated in the binding pocket of both NA mutants and the 150-loop moves out from oseltamivir as an "open" state. A greater number of water molecules accessible to the binding pocket could disrupt the oseltamivir binding with NA target as seen be high mobility of oseltamivir at the active site. Additionally, our finding could guide to the design and development of novel NA inhibitor drugs.
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6
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James N, Shanthi V, Ramanathan K. Density Functional Theory and Molecular Simulation Studies for Prioritizing Anaplastic Lymphoma Kinase Inhibitors. Appl Biochem Biotechnol 2019; 190:1127-1146. [PMID: 31712989 DOI: 10.1007/s12010-019-03156-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022]
Abstract
Targeting anaplastic lymphoma kinase (ALK) is one of the important treatment strategies for the treatment of non-small cell lung cancer (NSCLC). In the present perspective, multidimensional approaches were used for the identification of ALK inhibitors. Initially, an e-pharmacophore model was generated using the PHASE algorithm and was used as a 3D query to screen 468,200 molecules of ASINEX database. Prior to the screening process, the model was evaluated for its significance and the ability to differentiate actives from inactives, using enrichment analysis. Subsequently, the hierarchical docking protocol and binding free energy calculations were instigated using GLIDE algorithm and Prime module, respectively. Further, the pharmacokinetic/pharmacodynamics (PK/PD) properties and toxicities of the hit compounds were envisaged respectively using QikProp program, Osiris explorer, and Protox-II algorithm. These approaches retrieved two hits namely BAS 00137817 and BAS 00680055 with acceptable absorption, distribution, metabolism, excretion and toxicity (ADMET) properties and higher affinity towards ALK protein. Additionally, density functional theory calculations and molecular dynamics simulations were performed to validate the inhibitory activity of the lead compounds. It is noteworthy to mention that all the hits constitute of particular scaffolds which play a major role in the downregulation of some ALK-positive lung cancer pathways. We speculate that the outcomes of this research are of substantial prominence in the rational designing of novel and efficacious ALK inhibitors.
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Affiliation(s)
- Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - V Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - K Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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7
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Rohini K, Roy R, Ramanathan K, Shanthi V. E-pharmacophore hypothesis strategy to discover potent inhibitor for influenza treatment. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The surface protein of Influenza virus, Neuraminidase (NA), is believed to play a critical role in the release of new viral particle and thus spreads infection. It has been recognized as a valid drug target for anti-influenza therapy. Despite the number of available approved drugs for the influenza infection treatment, the emergence of resistant variants with novel mutations are the foremost challenges for the currently used NA inhibitors. Thus, the current investigation was carried out to ascertain potent inhibitors using computational strategies such as e-pharmacophore based virtual screening and docking approach. A three-dimensional e-pharmacophore hypothesis was generated based on the chemical features of complexes of the drugs and NA protein using PHASE module of Schrödinger suite. The generated hypothesis consisted of one hydrogen bond acceptor (A), two hydrogen bond donors (D), one negatively charged group (N) and one aromatic ring (R), ADDNR. The hypothesis was further evaluated for its integrity using enrichment analysis and used to filter out molecules with similar pharmacophoric features from approved, investigational and experimental subsets of DrugBank and ZINC database. In addition, ligand filtration was performed to curb down the molecules to an efficient collection of hit molecules by using Lipinski “rule of five and ADME analysis by using Qikprop module. Overall, the results from our analysis suggest that compound lisinopril and formoterol could serve as potent antiviral compounds for the treatment of influenza A virus infection. It is worth mentioning that the results correlate well with literature evidences.
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Affiliation(s)
- K. Rohini
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Roosha Roy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - K. Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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8
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Synthesis and Evaluation of Novel Cholestanoheterocyclic Steroids as Anticancer Agents. Appl Biochem Biotechnol 2019; 188:635-662. [DOI: 10.1007/s12010-018-02943-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/26/2018] [Indexed: 11/26/2022]
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9
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Ligand-Based Pharmacophore Screening Strategy: a Pragmatic Approach for Targeting HER Proteins. Appl Biochem Biotechnol 2018; 186:85-108. [PMID: 29508211 DOI: 10.1007/s12010-018-2724-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
Targeting ErbB family of receptors is an important therapeutic option, because of its essential role in the broad spectrum of human cancers, including non-small cell lung cancer (NSCLC). Therefore, in the present work, considerable effort has been made to develop an inhibitor against HER family proteins, by combining the use of pharmacophore modelling, docking scoring functions, and ADME property analysis. Initially, a five-point pharmacophore model was developed using known HER family inhibitors. The generated model was then used as a query to screen a total of 468,880 compounds of three databases namely ZINC, ASINEX, and DrugBank. Subsequently, docking analysis was carried out to obtain hit molecules that could inhibit the HER receptors. Further, analysis of GLIDE scores and ADME properties resulted in one hit namely BAS01025917 with higher glide scores, increased CNS involvement, and good pharmaceutically relevant properties than reference ligand, afatinib. Furthermore, the inhibitory activity of the lead compounds was validated by performing molecular dynamic simulations. Of note, BAS01025917 was found to possess scaffolds with a broad spectrum of antitumor activity. We believe that this novel hit molecule can be further exploited for the development of a pan-HER inhibitor with low toxicity and greater potential.
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10
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Kannan S, Kolandaivel P. The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. J Biomol Struct Dyn 2017; 36:4255-4269. [PMID: 29199545 DOI: 10.1080/07391102.2017.1413422] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oseltamivir (Tamiflu) is the most accepted antiviral drug that targets the neuraminidase (NA) protein to inhibit the viral release from the host cell. Few H1N1 influenza strains with the H274Y mutation creates drug resistance to oseltamivir. In this study, we report that flavonoid cyanidin-3-sambubiocide (C3S) compound acts as a potential inhibitor against H274Y mutation. The drug resistance mechanism and inhibitory activity of C3S and oseltamivir against wild-type (WT) and H274Y mutant-type (MT) have been studied and compared based on the results of molecular docking, molecular dynamics, and quantum chemical methods. Oseltamivir has been found less binding affinity with MT. C3S has more binding affinity with WT and MT proteins. From the dynamical study, the 150th loop of the MT protein has found more deformation than WT. A single H274Y mutation induces the conformational changes in the 150th loop which leads to produce more resistance to oseltamivir. The 150th cavity is more attractive target for C3S to stop the conformational changes in the MT, than 430th cavity of NA protein. The C3S is stabilized with MT by more number of hydrogen bonds than oseltamivir. The electrostatic interaction energy shows a stronger C3S binding with MT and this compound may be more effective against oseltamivir-resistant virus strains.
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Affiliation(s)
- S Kannan
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore , India
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11
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Drug Design for ALK-Positive NSCLC: an Integrated Pharmacophore-Based 3D QSAR and Virtual Screening Strategy. Appl Biochem Biotechnol 2017; 185:289-315. [DOI: 10.1007/s12010-017-2650-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/26/2017] [Indexed: 12/27/2022]
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12
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Discovery of Potent Neuraminidase Inhibitors Using a Combination of Pharmacophore-Based Virtual Screening and Molecular Simulation Approach. Appl Biochem Biotechnol 2017; 184:1421-1440. [DOI: 10.1007/s12010-017-2625-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/02/2017] [Indexed: 01/20/2023]
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13
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Yusuf M, Mohamed N, Mohamad S, Janezic D, Damodaran KV, Wahab HA. H274Y’s Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. J Chem Inf Model 2016; 56:82-100. [DOI: 10.1021/acs.jcim.5b00331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muhammad Yusuf
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Nornisah Mohamed
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Suriyati Mohamad
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
- School
of Biological Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Dusanka Janezic
- Faculty
of Mathematics, Natural Sciences and Information Technologies, University of Primorska, SI-6000 Koper, Slovenia
| | - K. V. Damodaran
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Habibah A. Wahab
- Pharmaceutical
Design and Simulation (PhDS) Laboratory, School of Pharmaceutical
Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
- Malaysian
Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Halaman Bukit Gambir, 11900 Bayan Lepas, Pulau Pinang, Malaysia
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14
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Singh A, Soliman ME. Understanding the cross-resistance of oseltamivir to H1N1 and H5N1 influenza A neuraminidase mutations using multidimensional computational analyses. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:4137-54. [PMID: 26257512 PMCID: PMC4527369 DOI: 10.2147/dddt.s81934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study embarks on a comprehensive description of the conformational contributions to resistance of neuraminidase (N1) in H1N1 and H5N1 to oseltamivir, using comparative multiple molecular dynamic simulations. The available data with regard to elucidation of the mechanism of resistance as a result of mutations in H1N1 and H5N1 neuraminidases is not well established. Enhanced post-dynamic analysis, such as principal component analysis, solvent accessible surface area, free binding energy calculations, and radius of gyration were performed to gain a precise insight into the binding mode and origin of resistance of oseltamivir in H1N1 and H5N1 mutants. Three significant features reflecting resistance in the presence of mutations H274Y and I222K, of the protein complexed with the inhibitor are: reduced flexibility of the α-carbon backbone; an improved ΔEele of ~15 (kcal/mol) for H1N1 coupled with an increase in ΔGsol (~13 kcal/mol) from wild-type to mutation; a low binding affinity in comparison with the wild-type of ~2 (kcal/mol) and ~7 (kcal/mol) with respect to each mutation for the H5N1 systems; and reduced hydrophobicity of the overall surface structure due to an impaired hydrogen bonding network. We believe the results of this study will ultimately provide a useful insight into the structural landscape of neuraminidase-associated binding of oseltamivir. Furthermore, the results can be used in the design and development of potent inhibitors of neuraminidases.
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Affiliation(s)
- Ashona Singh
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
| | - Mahmoud E Soliman
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
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15
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Preethi B, Shanthi V, Ramanathan K. Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques. Appl Biochem Biotechnol 2015. [DOI: 10.1007/s12010-015-1760-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Guan Y, Sun H, Pan P, Li Y, Li D, Hou T. Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations. MOLECULAR BIOSYSTEMS 2015. [DOI: 10.1039/c5mb00394f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Mutations at a number of key positions (Ala156, Asp168 and Arg155) of the HCV NS3/4A protease can induce medium to high resistance to MK5172.
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Affiliation(s)
- Yan Guan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
- Institute of Functional Nano & Soft Materials (FUNSOM)
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
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17
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Analysis of hepatitis B virus drug-resistant mutation (M204V) using molecular dynamics simulation techniques. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0471-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Karthick V, Ramanathan K. Insight into the oseltamivir resistance R292K mutation in H5N1 influenza virus: a molecular docking and molecular dynamics approach. Cell Biochem Biophys 2014; 68:291-9. [PMID: 23794010 DOI: 10.1007/s12013-013-9709-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
H5N1 is a subtype of the influenza A virus that can cause disease in humans and many other animal species. Oseltamivir (Tamiflu) is a potent and selective antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase (NA), a flu protein responsible for the release and spread of the progeny virions. However, oseltamivir resistance has become a critical problem. In particular, influenza strains with a R292K NA mutation are highly resistant to the oseltamivir. Though the biological functions of the mutations have previously been characterized, the structural basis behind the reduced catalytic activity and reduced protein level is not clear. In this study, molecular docking and molecular dynamics (MD) approach were employed to investigate the structural and dynamical effects throughout the protein structure and specifically, at the drug-binding pocket. Furthermore, potential of mean force was analyzed using explicit solvent MD simulations with the umbrella sampling method to explore the free energy of binding. It is believed that this study provides valuable guidance for the resistance management of oseltamivir and designing of more potent antiviral inhibitor.
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Affiliation(s)
- V Karthick
- Bioinformatics Division, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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19
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Tan H, Wei K, Bao J, Zhou X. In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. MOLECULAR BIOSYSTEMS 2014; 9:2764-74. [PMID: 24056678 DOI: 10.1039/c3mb70253g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It was recently reported that an I223R/H275Y double mutant of neuraminidase (NA) creates a multidrug-resistant form of the pandemic influenza A (H1N1) virus. However, a comprehensive understanding of the molecular mechanisms is still lacking. We conducted a systematic in silico study to explore the structural basis underlying this multidrug resistance. By molecular docking analyses and molecular dynamics (MD) simulations, we compared various biochemical and biophysical properties of the wild type, the I223R single mutant and the I223R/H275Y double mutant NA with two inhibitors, zanamivir (ZMR) and oseltamivir (G39). The binding free energy of oseltamivir with all types of NA was substantially lower than its zanamivir counterpart. On the other hand, the binding free energy of each inhibitor with wild type NA was generally higher than that with mutant NAs. MD simulation outcomes exemplify distinct patterns for oseltamivir and zanamivir with all types of NA. In particular, the stronger resistance of the double mutant NA relative to the wild and single mutant types can be ascribed to the overall looser but locally more compact structure of the former. Specifically, as a whole the double mutant NA adapts to the larger gyration radius and greater distance between charged atom groups, which is contrary to the pattern in the local binding site region. The enhanced resistance of all types of NA to oseltamivir rather than zanamivir might be accounted for similarly. We expect these findings to provide significant insights into improving inhibitors for the multidrug-resistant neuraminidase of H1N1 influenza viruses.
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Affiliation(s)
- Hua Tan
- College of Global Change and Earth System Science, Beijing Normal University, Beijing 100875, P. R. China.
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20
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Karthick V, Ramanathan K, Shanthi V, Rajasekaran R. Identification of potential inhibitors of H5N1 influenza A virus neuraminidase by ligand-based virtual screening approach. Cell Biochem Biophys 2014; 66:657-69. [PMID: 23306969 DOI: 10.1007/s12013-012-9510-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The neuraminidase (NA) of the influenza virus is the target of antiviral drug, oseltamivir. Recently, cases were reported that influenza virus becoming resistant to oseltamivir, necessitating the development of new long-acting antiviral compounds. In this report, a novel class of lead molecule with potential NA inhibitory activity was identified using a combination of virtual screening (VS), molecular docking, and molecular dynamic approach. The PubChem database was used to perform the VS analysis by employing oseltamivir as query. Subsequently, the data reduction was carried out by employing molecular docking study. Furthermore, the screened lead molecules were analyzed with respect to the Lipinski rule of five, drug-likeness, toxicity profiles, and other physico-chemical properties of drugs by suitable software program. Final screening was carried out by normal mode analysis and molecular dynamic simulation approach. The result indicates that CID 25145634, deuterium-enriched oseltamivir, become a promising lead compound and be effective in treating oseltamivir sensitive as well as resistant influenza virus strains.
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Affiliation(s)
- V Karthick
- Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Neuraminidase amino acids 149 and 347 determine the infectivity and oseltamivir sensitivity of pandemic influenza A/H1N1 (2009) and avian influenza A/H5N1. Virus Res 2013; 175:128-33. [PMID: 23639424 DOI: 10.1016/j.virusres.2013.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/21/2013] [Accepted: 04/22/2013] [Indexed: 11/22/2022]
Abstract
Pandemic influenza A/H1N1 (2009) and avian influenza A/H5N1 neuraminidase (NA) differ at two critical residues, positions 149 and 347. Recombinant influenza A viruses were constructed in which these two residues in pandemic influenza A/H1N1 (2009) NA were changed to the corresponding amino acids of avian influenza A/H5N1 NA, and vice versa. Recombinant viruses bearing N1 NA with the oseltamivir resistance mutation H274Y in combination with mutations at residues 149 and 347 were also constructed. Recombinant viruses grew normally in allantoic fluid and were subsequently studied for viral infectivity (TCID50), substrate binding (Km) and sensitivity to oseltamivir (Ki). The data demonstrated that infectivity of mutant viruses in Madin Darby canine kidney cells was comparable to, or even greater than, the infectivity of the parental viruses harboring wild-type N1 NA. Furthermore, mutations at NA residues 149 and 347 altered Km and Ki values, and thus modulated oseltamivir sensitivity. Although these mutants have yet to be observed among natural isolates, the minimal costs to the growth of recombinant viruses indicate their possible viability. Reassortment between pandemic influenza A/H1N1 (2009) and avian influenza A/H5N1 viruses may therefore generate new influenza A viruses with increased infectivity and oseltamivir resistance, and continued surveillance will be crucial for public health preparedness.
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Karthick V, Ramanathan K. Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. SPRINGERPLUS 2013; 2:115. [PMID: 23638404 PMCID: PMC3636431 DOI: 10.1186/2193-1801-2-115] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 03/08/2013] [Indexed: 11/10/2022]
Abstract
The neuraminidase (NA) of the influenza virus is the target of antiviral drug, oseltamivir. Recently, cases are reported that Influenza virus becoming resistant to oseltamivir, necessitating the development of new long-acting antiviral compounds. Most importantly, H274Y mutation in neuraminidase exhibits high levels of resistance to oseltamivir. In this report, a novel class of lead molecule with potential NA inhibitory activity was found from the traditional Chinese medicine database (TCMD) using virtual screening approach. Initially ADME properties of the lead compounds were analyzed with respect to the Lipinski rule of five. Subsequently, the data reduction was carried out by employing molecular docking study. Final validation was done by means of molecular dynamic simulations. The toxicity profiles for the screened compound were also analyzed. The result indicates that neoglucobrassicin (a compound derived from TCMD) become a promising lead compound and be effective in treating oseltamivir-resistant influenza virus strains.
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Affiliation(s)
- Vasudevan Karthick
- Bioinformatics Division, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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Tolentino-Lopez L, Segura-Cabrera A, Reyes-Loyola P, Zimic M, Quiliano M, Briz V, Muñoz-Fernández A, Rodríguez-Pérez M, Ilizaliturri-Flores I, Correa-Basurto J. Outside-binding site mutations modify the active site's shapes in neuraminidase from influenza A H1N1. Biopolymers 2012; 99:10-21. [DOI: 10.1002/bip.22130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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