Nanobiological studies on drug design using molecular mechanic method
Identifieur interne : 000543 ( Main/Exploration ); précédent : 000542; suivant : 000544Nanobiological studies on drug design using molecular mechanic method
Auteurs : Hooria Seyedhosseini Ghaheh [Iran] ; Maryam Mousavi [Iran] ; Mahmood Araghi [Iran] ; Reza Rasoolzadeh [Iran] ; Zahra Hosseini [Iran]Source :
- Advanced Biomedical Research [ 2277-9175 ] ; 2015.
Abstract
Influenza H1N1 is very important worldwide and point mutations that occur in the virus gene are a threat for the World Health Organization (WHO) and druggists, since they could make this virus resistant to the existing antibiotics. Influenza epidemics cause severe respiratory illness in 30 to 50 million people and kill 250,000 to 500,000 people worldwide every year. Nowadays, drug design is not done through trial and error because of its cost and waste of time; therefore bioinformatics studies is essential for designing drugs.
This paper, infolds a study on binding site of Neuraminidase (NA) enzyme, (that is very important in drug design) in 310K temperature and different dielectrics, for the best drug design. Information of NA enzyme was extracted from Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) websites. The new sequences of N1 were downloaded from the NCBI influenza virus sequence database. Drug binding sites were assimilated and homologized modeling using Argus lab 4.0, HyperChem 6.0 and Chem. D3 softwares. Their stability was assessed in different dielectrics and temperatures.
Measurements of potential energy (Kcal/mol) of binding sites of NA in different dielectrics and 310K temperature revealed that at time step size = 0 pSec drug binding sites have maximum energy level and at time step size = 100 pSec have maximum stability and minimum energy.
Drug binding sites are more dependent on dielectric constants rather than on temperature and the optimum dielectric constant is 39/78.
Url:
DOI: 10.4103/2277-9175.166642
PubMed: 26605248
PubMed Central: 4627179
Affiliations:
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type="main">Nanobiological studies on drug design using molecular mechanic method</title><author><name sortKey="Ghaheh, Hooria Seyedhosseini" sort="Ghaheh, Hooria Seyedhosseini" uniqKey="Ghaheh H" first="Hooria Seyedhosseini" last="Ghaheh">Hooria Seyedhosseini Ghaheh</name><affiliation wicri:level="1"><nlm:aff id="aff1">Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran</wicri:regionArea><wicri:noRegion>Tehran</wicri:noRegion></affiliation></author><author><name sortKey="Mousavi, Maryam" sort="Mousavi, Maryam" uniqKey="Mousavi M" first="Maryam" last="Mousavi">Maryam Mousavi</name><affiliation wicri:level="1"><nlm:aff id="aff2">Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Biology, Science and Research Branch, Islamic Azad University, Tehran</wicri:regionArea><wicri:noRegion>Tehran</wicri:noRegion></affiliation></author><author><name sortKey="Araghi, Mahmood" sort="Araghi, Mahmood" uniqKey="Araghi M" first="Mahmood" last="Araghi">Mahmood Araghi</name><affiliation wicri:level="1"><nlm:aff id="aff3">Department of Pathology, Amir-Momenin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Pathology, Amir-Momenin Hospital, Isfahan University of Medical Sciences, Isfahan</wicri:regionArea><wicri:noRegion>Isfahan</wicri:noRegion></affiliation></author><author><name sortKey="Rasoolzadeh, Reza" sort="Rasoolzadeh, Reza" uniqKey="Rasoolzadeh R" first="Reza" last="Rasoolzadeh">Reza Rasoolzadeh</name><affiliation wicri:level="1"><nlm:aff id="aff1">Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Young Researchers and Elites Club, Science and Research Branch, Islamic Azad University, Tehran</wicri:regionArea><wicri:noRegion>Tehran</wicri:noRegion></affiliation></author><author><name sortKey="Hosseini, Zahra" sort="Hosseini, Zahra" uniqKey="Hosseini Z" first="Zahra" last="Hosseini">Zahra Hosseini</name><affiliation wicri:level="1"><nlm:aff id="aff4">Department of Public Health, Isfahan University of Medical Sciences, Isfahan, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Public Health, Isfahan University of Medical Sciences, Isfahan</wicri:regionArea><wicri:noRegion>Isfahan</wicri:noRegion></affiliation></author></analytic><series><title level="j">Advanced Biomedical Research</title><idno type="ISSN">2277-9175</idno><idno type="eISSN">2277-9175</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="st1"><title>Background:</title><p>Influenza H1N1 is very important worldwide and point mutations that occur in the virus gene are a threat for the World Health Organization (WHO) and druggists, since they could make this virus resistant to the existing antibiotics. Influenza epidemics cause severe respiratory illness in 30 to 50 million people and kill 250,000 to 500,000 people worldwide every year. Nowadays, drug design is not done through trial and error because of its cost and waste of time; therefore bioinformatics studies is essential for designing drugs.</p></sec><sec id="st2"><title>Materials and Methods:</title><p>This paper, infolds a study on binding site of Neuraminidase (NA) enzyme, (that is very important in drug design) in 310K temperature and different dielectrics, for the best drug design. Information of NA enzyme was extracted from Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) websites. The new sequences of N1 were downloaded from the NCBI influenza virus sequence database. Drug binding sites were assimilated and homologized modeling using Argus lab 4.0, HyperChem 6.0 and Chem. D3 softwares. Their stability was assessed in different dielectrics and temperatures.</p></sec><sec id="st3"><title>Result:</title><p>Measurements of potential energy (Kcal/mol) of binding sites of NA in different dielectrics and 310K temperature revealed that at time step size = 0 pSec drug binding sites have maximum energy level and at time step size = 100 pSec have maximum stability and minimum energy.</p></sec><sec id="st4"><title>Conclusions:</title><p>Drug binding sites are more dependent on dielectric constants rather than on temperature and the optimum dielectric constant is 39/78.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, Cy" uniqKey="Chen C">CY Chen</name></author><author><name sortKey="Huang, Hj" uniqKey="Huang H">HJ Huang</name></author><author><name sortKey="Tsai, Fj" uniqKey="Tsai F">FJ Tsai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anh Nguyen, Tn" uniqKey="Anh Nguyen 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A">AR Khoshdel</name></author><author><name sortKey="Hosseini Shokouh, Sj" uniqKey="Hosseini Shokouh S">SJ Hosseini Shokouh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Treanor, Jj" uniqKey="Treanor J">JJ Treanor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Qi Shi Dua, Bd" uniqKey="Qi Shi Dua B">bd Qi-Shi Dua</name></author><author><name sortKey="Wang, Sq" uniqKey="Wang S">SQ Wang</name></author><author><name sortKey="Huang, Rb" uniqKey="Huang R">RB Huang</name></author><author><name sortKey="Chou, Kc" uniqKey="Chou K">KC Chou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Arias, Cf" uniqKey="Arias C">CF Arias</name></author><author><name sortKey="Escalera Zamudio, M" uniqKey="Escalera Zamudio M">M Escalera-Zamudio</name></author><author><name sortKey="Soto Del Rio, Ml" uniqKey="Soto Del Rio M">ML Soto-Del Rio</name></author><author><name sortKey="Cobian Guemes, Ag" uniqKey="Cobian Guemes A">AG Cobian-Guemes</name></author><author><name sortKey="Isa, P" uniqKey="Isa P">P Isa</name></author><author><name sortKey="Lopez, S" uniqKey="Lopez S">S Lopez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gong, J" uniqKey="Gong J">J Gong</name></author><author><name sortKey="Xu, W" uniqKey="Xu W">W Xu</name></author><author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Joseph, Nv" uniqKey="Joseph N">NV Joseph</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name></author><author><name sortKey="Zhu, X" uniqKey="Zhu X">X Zhu</name></author><author><name sortKey="Dwek, Ra" uniqKey="Dwek R">RA Dwek</name></author><author><name sortKey="Stevens, J" uniqKey="Stevens J">J Stevens</name></author><author><name sortKey="Wilson, Ia" uniqKey="Wilson I">IA Wilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bauer, K" uniqKey="Bauer K">K Bauer</name></author><author><name sortKey="Richter, M" uniqKey="Richter M">M Richter</name></author><author><name sortKey="Wutzler, P" uniqKey="Wutzler P">P Wutzler</name></author><author><name sortKey="Schmidtke, M" uniqKey="Schmidtke M">M Schmidtke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Masukawa, Km" uniqKey="Masukawa K">KM Masukawa</name></author><author><name sortKey="Kollman, Pa" uniqKey="Kollman P">PA Kollman</name></author><author><name sortKey="Kuntz, Id" uniqKey="Kuntz I">ID Kuntz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hong, Ak" uniqKey="Hong A">AK Hong</name></author><author><name sortKey="Peg, Ms" uniqKey="Peg M">MS Peg</name></author><author><name sortKey="Von, Im" uniqKey="Von I">IM von</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, Sq" uniqKey="Wang S">SQ Wang</name></author><author><name sortKey="Du, Qs" uniqKey="Du Q">QS Du</name></author><author><name sortKey="Huang, Rb" uniqKey="Huang R">RB Huang</name></author><author><name sortKey="Zhang, Dw" uniqKey="Zhang D">DW Zhang</name></author><author><name sortKey="Chou, Kc" uniqKey="Chou K">KC Chou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Okomo Adhiambo, M" uniqKey="Okomo Adhiambo M">M Okomo-Adhiambo</name></author><author><name sortKey="Nguyen, Ht" uniqKey="Nguyen H">HT Nguyen</name></author><author><name sortKey="Sleeman, K" uniqKey="Sleeman K">K Sleeman</name></author><author><name sortKey="Sheu, Tg" uniqKey="Sheu T">TG Sheu</name></author><author><name sortKey="Deyde, Vm" uniqKey="Deyde V">VM Deyde</name></author><author><name sortKey="Garten, Rj" uniqKey="Garten R">RJ Garten</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Baranovich, T" uniqKey="Baranovich T">T Baranovich</name></author><author><name sortKey="Saito, R" uniqKey="Saito R">R Saito</name></author><author><name sortKey="Suzuki, Y" uniqKey="Suzuki Y">Y Suzuki</name></author><author><name sortKey="Zaraket, H" uniqKey="Zaraket H">H Zaraket</name></author><author><name sortKey="Dapat, C" uniqKey="Dapat C">C Dapat</name></author><author><name sortKey="Caperig Dapat, I" uniqKey="Caperig Dapat I">I Caperig-Dapat</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Roschek B, Jr" uniqKey="Roschek B J">Jr Roschek B</name></author><author><name sortKey="Fink, Rc" uniqKey="Fink R">RC Fink</name></author><author><name sortKey="Mcmichael, Md" uniqKey="Mcmichael M">MD McMichael</name></author><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Alberte, Rs" uniqKey="Alberte R">RS Alberte</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mercader, Ag" uniqKey="Mercader A">AG 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Z" first="Zahra" last="Hosseini">Zahra Hosseini</name><name sortKey="Mousavi, Maryam" sort="Mousavi, Maryam" uniqKey="Mousavi M" first="Maryam" last="Mousavi">Maryam Mousavi</name><name sortKey="Rasoolzadeh, Reza" sort="Rasoolzadeh, Reza" uniqKey="Rasoolzadeh R" first="Reza" last="Rasoolzadeh">Reza Rasoolzadeh</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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