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Purohit P, Barik D, Agasti S, Panda M, Meher BR. Evaluation of the inhibitory potency of anti-dengue phytocompounds against DENV-2 NS2B-NS3 protease: virtual screening, ADMET profiling and molecular dynamics simulation investigations. J Biomol Struct Dyn 2024; 42:2990-3009. [PMID: 37194462 DOI: 10.1080/07391102.2023.2212798] [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: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/18/2023]
Abstract
Dengue fever has been a worldwide concern, with 50-100 million new infections each year mainly due to five different serotypes of the Dengue virus (DENV). Designing a perfect anti-dengue agent that can inhibit all the serotypes by distinguishing antigenic differences is quite difficult. Previous anti-dengue researches have included chemical compounds screening against DENV enzymes. The ongoing analysis is meant for investigation of the plant-based compounds as antagonistic to DENV-2 focusing on the specific NS2B-NS3Pro target, a trypsin like serine protease that cuts the DENV polyprotein into separate proteins crucial for viral reproduction. Initially, a virtual library of more than 130 phytocompounds was prepared from previously published reports of plants with anti-dengue properties, which were then virtually screened and shortlisted against the WT, H51N and S135A mutant of DENV-2 NS2B-NS3Pro. The three top-most compounds were viewed as Gallocatechin (GAL), Flavokawain-C (FLV), and Isorhamnetin (ISO) showing docking scores of -5.8, -5.7, -5.7 kcal/mol for WT, -7.5, -6.8, -7.6 kcal/mol for the H51N, and -6.9, -6.5, -6.1 kcal/mol for the S135A mutant protease, respectively. 100 ns long MD simulations and MM-GBSA based free energy calculations were performed on the NS2B-NS3Pro complexes to witness the relative binding affinity of the compounds and favourable molecular interactions network. A comprehensive analysis of the study reveals some promising outcomes with ISO as the topmost compound with favourable pharmacokinetic properties for the WT and mutants (H51N and S135A) as well, suggesting as a novel anti-NS2B-NS3Pro agent with better adapting characters in both the mutants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Sidhartha Agasti
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha, India
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Ma Z, Xu J, Wang C, Liu Z, Zhu G. Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase. J Biomol Struct Dyn 2024:1-10. [PMID: 38263694 DOI: 10.1080/07391102.2024.2308781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/14/2024] [Indexed: 01/25/2024]
Abstract
Carbon nanotubes (CNTs) have potential prospects in disease treatment, so it is of great significance to study CNTs as the possible inhibitors of RNA-dependent RNA polymerase (RdRp). Through the way of using the RdRp of SARS-COV-2 as a model, five armchair single-walled carbon nanotubes (SWCNTs) (namely Dn, which stands for CNTs (n, m = n), n = 3-7) and RdRp have been selected to study the interactions by means of molecular docking and molecular dynamics simulation. After five SWCNT-RdRp complex systems have been subjected to the molecular dynamics simulations of 100 ns, and Molecular Mechanics Poisson - Boltzmann Surface Area (MMPBSA) has been used to calculate the binding free energy, it is found that the binding free energy of the D6 system (-189.541 kJ/mol) is significantly higher than that of the other four systems, and most of the amino acids with strong positive effects on binding are usually basic amino acids. What's more, in the further investigation of the specific interaction mechanism between CNT (6,6) and RdRp, it is revealed that the three amino acid residues LYS545, ARG553 and ARG555 located in the nucleoside triphosphate (NTP) entry channel all have strong effects. In addition, it is also observed that when ARG555 has been inserted into SWCNT, a stable structure will be formed, which will break the original NTP entry channel structure and inhibit virus replication. Therefore, it can be concluded that certain specific types of SWCNT, such as CNT (6,6), could be potential small molecule inhibitors in the treatment of coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zhaopeng Ma
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Jianqiang Xu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Chenchen Wang
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Zhicong Liu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
| | - Guanglai Zhu
- Anhui Province Key Laboratory of Optoelectronic Materials Science and Technology, School of Physics and Electronic Information, Anhui Normal University, Wuhu, China
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Hatta MHM, Matmin J, Malek NANN, Kamisan FH, Badruzzaman A, Batumalaie K, Ling Lee S, Abdul Wahab R. COVID‐19: Prevention, Detection, and Treatment by Using Carbon Nanotubes‐Based Materials. ChemistrySelect 2023. [DOI: 10.1002/slct.202204615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Mohd Hayrie Mohd Hatta
- Centre for Research and Development Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Juan Matmin
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Nik Ahmad Nizam Nik Malek
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Department of Biosciences, Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Farah Hidayah Kamisan
- Department of Biomedical Sciences Faculty of Health Sciences Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Aishah Badruzzaman
- Centre for Foundation, Language and General Studies Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences Faculty of Health Sciences Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Siew Ling Lee
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
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Functionalized carbon nanotubes as an alternative to traditional anti-HIV-1 protease inhibitors: An understanding towards Nano-medicine development through MD simulations. J Mol Graph Model 2022; 117:108280. [PMID: 35963109 DOI: 10.1016/j.jmgm.2022.108280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 01/14/2023]
Abstract
The Human Immunodeficiency Virus (HIV) has been the source of epidemic infection of AIDS for a longer period. One of the most difficult tasks is identifying novel medications that can help to decrease or control this global health hazard by overcoming drug resistance. In recent decades' nanoparticles are emerging as extremely relevant in drug delivery platforms. In the current study, the pristine (SWCNT) and hydroxyl functionalized (SWCNT-OH) versions of the SWCNT were investigated as inhibitors against the wild-type (WT) and three key mutants of HIV-1 protease (HIV-pr) (I50V, V82A, and I84V). Molecular docking of SWCNT in the catalytic domain and running all-atom MD simulations of all complexes are also part of this project. A thorough inspection of conformational dynamics from 50 ns trajectories reveals that both the pristine and SWCNT-OH can fit right to the pocket region of HIV-pr and govern flap dynamics. The binding affinity of the four HIV-pr-SWCNT/SWCNT-OH complexes was further investigated using MM-PBSA-dependent binding free energy studies. In most mutants and WT systems, SWCNT-OH was reported to bind proportionately many folds (kcal/mol) more than pristine SWCNTs. Hence, SWCNTs are possible HIV-pr inhibitors in terms of their stable existence in the pocket area, stronger binding to the protease, and regulation of flap dynamics in controlling the active site volume, which have vast potential for applications against drug resistance.
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Purohit P, Sahoo S, Panda M, Sahoo PS, Meher BR. Targeting the DENV NS2B-NS3 protease with active antiviral phytocompounds: structure-based virtual screening, molecular docking and molecular dynamics simulation studies. J Mol Model 2022; 28:365. [PMID: 36274116 PMCID: PMC9589672 DOI: 10.1007/s00894-022-05355-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/11/2022] [Indexed: 11/08/2022]
Abstract
Dengue fever has been a global health concern. Mitigation is a challenging problem due to non-availability of workable treatments. The most difficult objective is to design a perfect anti-dengue agent capable of inhibiting infections caused by all four serotypes. Various tactics have been employed in the past to discover dengue antivirals, including screening of chemical compounds against dengue virus enzymes. The objective of the current study is to investigate phytocompounds as anti-dengue remedies that target the non-structural 2B and non-structural 3 protease (NS2B-NS3pro), a possible therapeutic target for dengue fever. Initially, 300 + antiviral phytocompounds were collected from Duke's phytochemical and ethnobotanical database and 30 phytocompounds with anti-dengue properties were identified from previously reported studies, which were virtually screened against NS2B-NS3pro using molecular docking and toxicity evaluation. The top five most screened ligands were naringin, hesperidin, gossypol, maslinic acid and rhodiolin with binding affinities of - 8.7 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol, - 8.5 kcal/mol and - 8.1 kcal/mol, respectively. The finest docked compounds complexed with NS2B-NS3pro were subjected for molecular dynamics (MD) simulations and binding free energy estimations through molecular mechanics generalized born surface area-based calculations. The results of the study are intriguing in the context of computer-aided screening and the binding affinities of the phytocompounds, proposing maslinic acid (MAS) as a potent bioactive antiviral for the development of phytocompound-based anti-dengue agent.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Sthitaprajna Sahoo
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Partha Sarathi Sahoo
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, P.G. Department of Botany, Berhampur University, Berhampur, Odisha, 760007, India.
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Purohit P, Dash JJ, Muya JT, Meher BR. Molecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 M pro: an in silico approach towards drug repurposing. J Biomol Struct Dyn 2022; 41:3900-3913. [PMID: 35388744 DOI: 10.1080/07391102.2022.2059008] [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: 10/18/2022]
Abstract
SARS-CoV-2 Mpro is one of the most vital enzymes of the new coronavirus-2 (SARS-CoV-2) and is a crucial target for drug discovery. Unfortunately, there is not any potential drugs available to combat the action of SARS-CoV-2 Mpro. Based on the reports HIV-protease inhibitors can be applied against the SARS by targeting the SARS-CoV-1 Mpro, we have chosen few clinically trialed experimental and allophenylnorstatine (APNS) containing HIV-protease inhibitors (JE-2147, JE-533, KNI-227, KNI-272 & KNI-1931), to examine their binding affinities with SARS-CoV-2 Mpro and to assess their potential to check for a possible drug candidate against the protease. Here, we have chosen a methodology to understand the binding mechanism of these five inhibitors to SARS-CoV-2 Mpro by merging molecular docking, molecular dynamics (MD) simulation and MM-PBSA based free energy calculations. Our estimations disclose that JE-2147 is highly effective (ΔGBind = -28.31 kcal/mol) due to an increased favorable van der Waals (ΔEvdw) interactions and decreased solvation (ΔGsolv) energies between the inhibitor and viral protease. JE-2147 shows a higher level of interactions as compared to JE-533 (-6.85 kcal/mol), KNI-227 (-18.36 kcal/mol), KNI-272 (-15.69 kcal/mol) and KNI-1931 (-21.59 kcal/mol) against SARS-CoV-2 Mpro. Binding contributions of important residues (His41, Met49, Cys145, His164, Met165, Glu166, Pro168, Gln189, etc.) from the active site or near the active site regions with ≥1.0 kcal/mol suggest a potent binding of the inhibitors. It is anticipated that the current study of binding interactions of these APNS containing inhibitors can pitch some valuable insights to design the significantly effective anti-SARS-CoV-2 Mpro drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jiban Jyoti Dash
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Department of Chemistry, Hanyang University, Seoul, South Korea.,Faculté of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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de Carvalho Lima EN, Octaviano ALM, Piqueira JRC, Diaz RS, Justo JF. Coronavirus and Carbon Nanotubes: Seeking Immunological Relationships to Discover Immunotherapeutic Possibilities. Int J Nanomedicine 2022; 17:751-781. [PMID: 35241912 PMCID: PMC8887185 DOI: 10.2147/ijn.s341890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Since December 2019, the world has faced an unprecedented pandemic crisis due to a new coronavirus disease, coronavirus disease-2019 (COVID-19), which has instigated intensive studies on prevention and treatment possibilities. Here, we investigate the relationships between the immune activation induced by three coronaviruses associated with recent outbreaks, with special attention to SARS-CoV-2, the causative agent of COVID-19, and the immune activation induced by carbon nanotubes (CNTs) to understand the points of convergence in immune induction and modulation. Evidence suggests that CNTs are among the most promising materials for use as immunotherapeutic agents. Therefore, this investigation explores new possibilities of effective immunotherapies for COVID-19. This study aimed to raise interest and knowledge about the use of CNTs as immunotherapeutic agents in coronavirus treatment. Thus, we summarize the most important immunological aspects of various coronavirus infections and describe key advances and challenges in using CNTs as immunotherapeutic agents against viral infections and the activation of the immune response induced by CNTs, which can shed light on the immunotherapeutic possibilities of CNTs.
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Affiliation(s)
- Elidamar Nunes de Carvalho Lima
- Telecommunication and Control Engineering Department, Polytechnic School of the University of São Paulo, São Paulo, Brazil
- Infectious Diseases Division, Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
- Electronic Systems Engineering Department, Polytechnic School of the University of São Paulo, São Paulo, SP, CEP 05508-010, Brazil
| | - Ana Luiza Moraes Octaviano
- Telecommunication and Control Engineering Department, Polytechnic School of the University of São Paulo, São Paulo, Brazil
| | - José Roberto Castilho Piqueira
- Telecommunication and Control Engineering Department, Polytechnic School of the University of São Paulo, São Paulo, Brazil
| | - Ricardo Sobhie Diaz
- Infectious Diseases Division, Department of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - João Francisco Justo
- Electronic Systems Engineering Department, Polytechnic School of the University of São Paulo, São Paulo, SP, CEP 05508-010, Brazil
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Zhang YJ, Ding JN, Zhong H, Sun CP, Han JG. Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus. J Biol Phys 2017; 43:149-165. [PMID: 28110448 DOI: 10.1007/s10867-016-9440-5] [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: 09/05/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022] Open
Abstract
VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP. Interestingly, the sites and orientations of the SWCNT binding to the I295A mutant and K248A/I295A double mutants change significantly to accommodate the variation of the VP35 conformation. Moreover, the VDW can provide the major forces for affinity binding in all four systems.
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Affiliation(s)
- Yan-Jun Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
| | - Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
| | - Hui Zhong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
| | - Chang-Ping Sun
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.,Department of Physics, Linyi University, Shandong, 276000, People's Republic of China
| | - Ju-Guang Han
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China.
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AbrusAgglutinin, a type II ribosome inactivating protein inhibits Akt/PH domain to induce endoplasmic reticulum stress mediated autophagy-dependent cell death. Mol Carcinog 2016; 56:389-401. [DOI: 10.1002/mc.22502] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 04/26/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022]
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Esposito EX, Hopfinger AJ, Shao CY, Su BH, Chen SZ, Tseng YJ. Exploring possible mechanisms of action for the nanotoxicity and protein binding of decorated nanotubes: interpretation of physicochemical properties from optimal QSAR models. Toxicol Appl Pharmacol 2015. [PMID: 26200234 DOI: 10.1016/j.taap.2015.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Carbon nanotubes have become widely used in a variety of applications including biosensors and drug carriers. Therefore, the issue of carbon nanotube toxicity is increasingly an area of focus and concern. While previous studies have focused on the gross mechanisms of action relating to nanomaterials interacting with biological entities, this study proposes detailed mechanisms of action, relating to nanotoxicity, for a series of decorated (functionalized) carbon nanotube complexes based on previously reported QSAR models. Possible mechanisms of nanotoxicity for six endpoints (bovine serum albumin, carbonic anhydrase, chymotrypsin, hemoglobin along with cell viability and nitrogen oxide production) have been extracted from the corresponding optimized QSAR models. The molecular features relevant to each of the endpoint respective mechanism of action for the decorated nanotubes are also discussed. Based on the molecular information contained within the optimal QSAR models for each nanotoxicity endpoint, either the decorator attached to the nanotube is directly responsible for the expression of a particular activity, irrespective of the decorator's 3D-geometry and independent of the nanotube, or those decorators having structures that place the functional groups of the decorators as far as possible from the nanotube surface most strongly influence the biological activity. These molecular descriptors are further used to hypothesize specific interactions involved in the expression of each of the six biological endpoints.
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Affiliation(s)
- Emilio Xavier Esposito
- exeResearch, LLC, 32 University Drive, East Lansing, MI 48823, USA; The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045, USA.
| | - Anton J Hopfinger
- The Chem21 Group, Inc., 1780 Wilson Drive, Lake Forest, IL 60045, USA; College of Pharmacy MSC09 5360, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Chi-Yu Shao
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Bo-Han Su
- Department of Computer Science and Information Engineering, National Taiwan University, No. 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Sing-Zuo Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yufeng Jane Tseng
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan; Department of Computer Science and Information Engineering, National Taiwan University, No. 1 Sec. 4, Roosevelt Road, Taipei 106, Taiwan.
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Azamat J, Khataee A, Joo SW, Yin B. Removal of trihalomethanes from aqueous solution through armchair carbon nanotubes: A molecular dynamics study. J Mol Graph Model 2015; 57:70-5. [DOI: 10.1016/j.jmgm.2015.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 11/28/2022]
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Meher BR, Wang Y. Exploring the drug resistance of V32I and M46L mutant HIV-1 protease to inhibitor TMC114: flap dynamics and binding mechanism. J Mol Graph Model 2014; 56:60-73. [PMID: 25562662 DOI: 10.1016/j.jmgm.2014.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 10/14/2014] [Accepted: 11/07/2014] [Indexed: 12/22/2022]
Abstract
Inhibitors of HIV-1 protease (HIV-1-pr) generally only bind to the active site of the protease. However, for some mutants such as V32I and M46L the TMC114 can bind not only to the active cavity but also to the groove of the flexible flaps. Although the second binding site suggests the higher efficiency of the drug against HIV-1-pr, the drug resistance in HIV-1-pr due to mutations cannot be ignored, which prompts us to investigate the molecular mechanisms of drug resistance and behavior of double bound TMC114 (2T) to HIV-1-pr. The conformational dynamics of HIV-1-pr and the binding of TMC114 to the WT, V32I and M46L mutants were investigated with all-atom molecular dynamic (MD) simulation. The 20 ns MD simulation shows many fascinating effects of the inhibitor binding to the WT and mutant proteases. MM-PBSA calculations explain the binding free energies unfavorable for the M46L and V32I mutants as compared to the WT. For the single binding (1T) the less binding affinity can be attributed to the entropic loss for both V32I-1T and M46L-1T. Although the second binding of TMC114 with flap does increase binding energy for the mutants (V32I-2T and M46L-2T), the considerable entropy loss results in the lower binding Gibbs free energies. Thus, binding of TMC114 in the flap region does not help much in the total gain in binding affinity of the system, which was verified from this study and thereby validating experiments.
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Affiliation(s)
- Biswa Ranjan Meher
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA
| | - Yixuan Wang
- Computational Chemistry Laboratory, Department of Natural Sciences, Albany State University, Albany, GA 31705, USA.
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Yanamala N, Kagan VE, Shvedova AA. Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells. Adv Drug Deliv Rev 2013; 65:2070-7. [PMID: 23726945 DOI: 10.1016/j.addr.2013.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/06/2013] [Accepted: 05/23/2013] [Indexed: 12/11/2022]
Abstract
Over the past two decades, nanotechnology has emerged as a key player in various disciplines of science and technology. Some of the most exciting applications are in the field of biomedicine - for theranostics (for combined diagnostic and therapeutic purposes) as well as for exploration of biological systems. A detailed understanding of the molecular interactions between nanoparticles and biological nano-machinery - macromolecules, membranes, and intracellular organelles - is crucial for obtaining adequate information on mechanisms of action of nanomaterials as well as a perspective on the long term effects of these materials and their possible toxicological outcomes. This review focuses on the use of structure-based computational molecular modeling as a tool to understand and to predict the interactions between nanomaterials and nano-biosystems. We review major approaches and provide examples of computational analysis of the structural principles behind such interactions. A rationale on how nanoparticles of different sizes, shape, structure and chemical properties can affect the organization and functions of nano-machinery of cells is also presented.
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