1
|
Kodchakorn K, Kongtawelert P. Molecular dynamics study on the strengthening behavior of Delta and Omicron SARS-CoV-2 spike RBD improved receptor-binding affinity. PLoS One 2022; 17:e0277745. [PMID: 36395151 PMCID: PMC9671323 DOI: 10.1371/journal.pone.0277745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic caused by a virus that can be transmitted from human to human via air droplets has changed the quality of life and economic systems all over the world. The viral DNA has mutated naturally over time leading to the diversity of coronavirus victims which has posed a serious threat to human security on a massive scale. The current variants have developed in a dominant way and are considered "Variants of Concern" by the World Health Organization (WHO). In this work, Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants were obtained to evaluate whether naturally occurring mutations have strengthened viral infectivity. We apply reliable in silico structural dynamics and energetic frameworks of the mutated S-RBD protein for ACE2-binding to analyze and compare the structural information related to the wild-type. In particular, the hotspot residues at Q493, Q498, and N501 on the S-RBD protein were determined as contributing factors to the employment stability of the relevant binding interface. The L452R mutation induces an increment of the hydrogen bonds formed by changing the Q493 environment for ACE2 binding. Moreover, the Q493K exchange in Omicron enables the formation of two additional salt bridges, leading to a strong binding affinity by increased electrostatic interaction energy. These results could be used in proposing concrete informative data for a structure-based design engaged in finding better therapeutics against novel variants.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Prachya Kongtawelert
- Thailand Excellence Center for Tissue Engineering and Stem Cells, Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- * E-mail:
| |
Collapse
|
2
|
Pekel H, Guzel M, Sensoy O. Mechanistic insight into impact of phosphorylation on the enzymatic steps of farnesyltransferase. Protein Sci 2022; 31:e4414. [PMID: 36173156 PMCID: PMC9601885 DOI: 10.1002/pro.4414] [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: 02/22/2022] [Revised: 05/27/2022] [Accepted: 06/21/2022] [Indexed: 11/08/2022]
Abstract
Farnesyltransferase (FTase) is a heterodimeric enzyme, which catalyzes covalent attachment of the farnesyl group to target proteins, thus coordinating their trafficking in the cell. FTase has been demonstrated to be highly expressed in cancer and neurological diseases; hence considered as a hot target for therapeutic purposes. However, due to the nonspecific inhibition, there has been only one inhibitor that could be translated into the clinic. Importantly, it has been shown that phosphorylation of the α-subunit of FTase increases the activity of the enzyme in certain diseases. As such, understanding the impact of phosphorylation on dynamics of FTase provides a basis for targeting a specific state of the enzyme that emerges under pathological conditions. To this end, we performed 18 μs molecular dynamics (MD) simulations using complexes of (non)-phosphorylated FTase that are representatives of the farnesylation reaction. We demonstrated that phosphorylation modulated the catalytic site by rearranging interactions between farnesyl pyrophosphate (FPP)/peptide substrate, catalytic Zn2+ ion/coordinating residues and hot-spot residues at the interface of the subunits, all of which led to the stabilization of the substrate and facilitation of the release of the product, thus collectively expediting the reaction rate. Importantly, we also identified a likely allosteric pocket on the phosphorylated FTase, which might be used for specific targeting of the enzyme. To the best of our knowledge, this is the first study that systematically examines the impact of phosphorylation on the enzymatic reaction steps, hence opens up new avenues for drug discovery studies that focus on targeting phosphorylated FTase.
Collapse
Affiliation(s)
- Hanife Pekel
- Department of Pharmacy ServicesVocational School of Health Services, Istanbul Medipol UniversityIstanbulTurkey
- Regenerative and Restorative Medicine Research Center (REMER)Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Mustafa Guzel
- Department of Medical Pharmacology/International School of MedicineIstanbul Medipol UniversityIstanbulTurkey
- Center of Drug Discovery and DevelopmentResearch Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
| | - Ozge Sensoy
- Regenerative and Restorative Medicine Research Center (REMER)Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol UniversityIstanbulTurkey
- Department of Computer Engineering/School of Engineering and Natural SciencesIstanbul Medipol UniversityIstanbulTurkey
| |
Collapse
|
3
|
Kodchakorn K, Chokepaichitkool T, Kongtawelert P. Mutational scanning of spike RBD protein for enhanced ACE2 affinity emerging Southeast Asia in the late transmission phase. Sci Rep 2022; 12:5896. [PMID: 35393512 PMCID: PMC8989122 DOI: 10.1038/s41598-022-09999-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 03/31/2022] [Indexed: 12/11/2022] Open
Abstract
The COVID-19 pandemic has changed the quality of life and economic systems all over the world, as the virus can be transmitted from human to human via air-droplets. Since the SARS-CoV-2 virus was first identified in 2019, the virus has naturally mutated over time. Southeast Asia is one of the areas in the world that has implemented various procedures and measures to slow down the disease outbreaks. The first cluster of COVID-19 was identified from the tourist-travel history, and then the diversity of coronavirus victims has posed a serious issue of human security on a massive scale. To evaluate whether or not naturally occurring mutations have strengthened the infectivity of SARS-CoV-2, we computed in silico the structural dynamics of the RBD-spike protein mutation enhancing ACE2-binding. When considering emerging variations in Southeast Asia, 14 dominant mutations were analyzed by applying the structural and energetic characterization using MD simulations. The ones in the RBD region displayed higher affinity to ACE2 due to the improved interfacial stability of the RBD β-strand surrounding the ACE2 across salt bridge hotspots. The binding hotspots and structurally conserved conformational-epitopes have been identified, which are deleterious for RBD mutation and ACE2 binding. We present an interactive visualization to facilitate the development of effective neutralizing agents for vaccination, prevention and treatment.
Collapse
Affiliation(s)
- Kanchanok Kodchakorn
- Department of Biochemistry, Faculty of Medicine, Thailand Excellence Center for Tissue Engineering and Stem Cells, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tawan Chokepaichitkool
- Department of Biochemistry, Faculty of Medicine, Thailand Excellence Center for Tissue Engineering and Stem Cells, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prachya Kongtawelert
- Department of Biochemistry, Faculty of Medicine, Thailand Excellence Center for Tissue Engineering and Stem Cells, Chiang Mai University, Chiang Mai, 50200, Thailand.
| |
Collapse
|
4
|
Vieira TF, Magalhães RP, Simões M, Sousa SF. Drug Repurposing Targeting Pseudomonas aeruginosa MvfR Using Docking, Virtual Screening, Molecular Dynamics, and Free-Energy Calculations. Antibiotics (Basel) 2022; 11:185. [PMID: 35203788 PMCID: PMC8868191 DOI: 10.3390/antibiotics11020185] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium responsible for acute and chronic infections in planktonic state or in biofilms. The sessile structures are known to confer physical stability, increase virulence, and work as a protective armor against antimicrobial compounds. P. aeruginosa can control the expression of genes, population density, and biofilm formation through a process called quorum sensing (QS), a rather complex and hierarchical system of communication. A recent strategy to try and overcome bacterial resistance is to target QS proteins. In this study, a combined multi-level computational approach was applied to find possible inhibitors against P. aeruginosa QS regulator protein MvfR, also known as PqsR, using a database of approved FDA drugs, as a repurposing strategy. Fifteen compounds were identified as highly promising putative MvfR inhibitors. On those 15 MvfR ligand complexes, molecular dynamic simulations and MM/GBSA free-energy calculations were performed to confirm the docking predictions and elucidate on the mode of interaction. Ultimately, the five compounds that presented better binding free energies of association than the reference molecules (a known antagonist, M64 and a natural inducer, 2-nonyl-4-hydroxyquinoline) were highlighted as very promising MvfR inhibitors.
Collapse
Affiliation(s)
- Tatiana F. Vieira
- UCIBIO/REQUIMTE, BioSIM, Departamento de Medicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (T.F.V.); (R.P.M.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Rita P. Magalhães
- UCIBIO/REQUIMTE, BioSIM, Departamento de Medicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (T.F.V.); (R.P.M.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Manuel Simões
- LEPABE Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal;
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Medicina, Faculdade de Medicina da Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal; (T.F.V.); (R.P.M.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| |
Collapse
|
5
|
Coelho CMM, Pereira R, Vieira TF, Teixeira CM, Fernandes MJG, Rodrigues ARO, Pereira DM, Sousa S, Gil Fortes A, Castanheira EMS, T Gonçalves MS. Synthesis, computational and nanoencapsulation studies on eugenol-derived insecticides. NEW J CHEM 2022. [DOI: 10.1039/d2nj01893d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new set of alkoxy alcohols were synthesised by reaction of eugenol oxirane with aliphatic and aromatic alcohols. These eugenol derivatives were evaluated against their effect upon the viability of...
Collapse
|
6
|
Pereira RB, Pinto NFS, Fernandes MJG, Vieira TF, Rodrigues ARO, Pereira DM, Sousa SF, Castanheira EMS, Fortes AG, Gonçalves MST. Amino Alcohols from Eugenol as Potential Semisynthetic Insecticides: Chemical, Biological, and Computational Insights. Molecules 2021; 26:molecules26216616. [PMID: 34771025 PMCID: PMC8587747 DOI: 10.3390/molecules26216616] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
A series of β-amino alcohols were prepared by the reaction of eugenol epoxide with aliphatic and aromatic amine nucleophiles. The synthesized compounds were fully characterized and evaluated as potential insecticides through the assessment of their biological activity against Sf9 insect cells, compared with a commercial synthetic pesticide (chlorpyrifos, CHPY). Three derivatives bearing a terminal benzene ring, either substituted or unsubstituted, were identified as the most potent molecules, two of them displaying higher toxicity to insect cells than CHPY. In addition, the most promising molecules were able to increase the activity of serine proteases (caspases) pivotal to apoptosis and were more toxic to insect cells than human cells. Structure-based inverted virtual screening and molecular dynamics simulations demonstrate that these molecules likely target acetylcholinesterase and/or the insect odorant-binding proteins and are able to form stable complexes with these proteins. Encapsulation assays in liposomes of DMPG and DPPC/DMPG (1:1) were performed for the most active compound, and high encapsulation efficiencies were obtained. A thermosensitive formulation was achieved with the compound release being more efficient at higher temperatures.
Collapse
Affiliation(s)
- Renato B. Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.B.P.); (D.M.P.)
| | - Nuno F. S. Pinto
- Centre of Chemistry, Department of Chemistry, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (N.F.S.P.); (M.J.G.F.); (A.G.F.)
| | - Maria José G. Fernandes
- Centre of Chemistry, Department of Chemistry, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (N.F.S.P.); (M.J.G.F.); (A.G.F.)
| | - Tatiana F. Vieira
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (T.F.V.); (S.F.S.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM—Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Ana Rita O. Rodrigues
- Centre of Physics of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (A.R.O.R.); (E.M.S.C.)
| | - David M. Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.B.P.); (D.M.P.)
| | - Sérgio F. Sousa
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; (T.F.V.); (S.F.S.)
- UCIBIO—Applied Molecular Biosciences Unit, BioSIM—Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Elisabete M. S. Castanheira
- Centre of Physics of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (A.R.O.R.); (E.M.S.C.)
| | - A. Gil Fortes
- Centre of Chemistry, Department of Chemistry, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (N.F.S.P.); (M.J.G.F.); (A.G.F.)
| | - M. Sameiro T. Gonçalves
- Centre of Chemistry, Department of Chemistry, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal; (N.F.S.P.); (M.J.G.F.); (A.G.F.)
- Correspondence: ; Tel.: +351-253-604-372
| |
Collapse
|
7
|
Natal CM, Fernandes MJG, Pinto NFS, Pereira RB, Vieira TF, Rodrigues ARO, Pereira DM, Sousa SF, Fortes AG, Castanheira EMS, T Gonçalves MS. New carvacrol and thymol derivatives as potential insecticides: synthesis, biological activity, computational studies and nanoencapsulation. RSC Adv 2021; 11:34024-34035. [PMID: 35497284 PMCID: PMC9042360 DOI: 10.1039/d1ra05616f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
New compounds with potential insecticide activity were synthesized by structural modifications performed in the monoterpenoid phenolic moieties of carvacrol and thymol, resulting in a set of derivatives with the ether function containing the propyl, chloropropyl or hydroxypropyl chains, as well as a bicyclic ether with an unsaturated chain containing a carboxylic acid terminal. In addition, an analogue of carvacrol and thymol isomers bearing methoxyl, 1-hydroxyethyl and (3-chlorobenzoyl)oxy, instead of the three original methyl groups, was also synthesized. Several structural changes that resulted in diminished insecticide activity have been identified, but two significantly active molecules have been synthesized, one of them being less toxic to human cells than the naturally-derived starting materials. Structure-based inverted virtual screening and molecular dynamics simulations demonstrate that these active molecules likely target the insect odorant binding proteins and/or acetylcholinesterase and are able to form stable complexes. For the most promising compounds, nanoencapsulation assays were carried out in liposomes of egg phosphatidylcholine/cholesterol (7 : 3) prepared by both thin film hydration and ethanolic injection methods. The compound-loaded liposomes were generally monodisperse and with sizes smaller than or around 200 nm. The thin film hydration method allowed high encapsulation efficiencies (above 85%) for both compounds and a delayed release, while for the systems prepared by ethanolic injection the encapsulation efficiency is lower than 50%, but the release is almost complete in two days.
Collapse
Affiliation(s)
- Carolina M Natal
- Centre of Chemistry, Department of Chemistry, University of Minho Campus of Gualtar 4710-057 Braga Portugal
| | - Maria José G Fernandes
- Centre of Chemistry, Department of Chemistry, University of Minho Campus of Gualtar 4710-057 Braga Portugal
| | - Nuno F S Pinto
- Centre of Chemistry, Department of Chemistry, University of Minho Campus of Gualtar 4710-057 Braga Portugal
| | - Renato B Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto R. Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Tatiana F Vieira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto 4200-319 Porto Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto 4200-319 Porto Portugal
| | - Ana Rita O Rodrigues
- Centre of Physics of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus of Gualtar 4710-057 Braga Portugal
| | - David M Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto R. Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto 4200-319 Porto Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto 4200-319 Porto Portugal
| | - A Gil Fortes
- Centre of Chemistry, Department of Chemistry, University of Minho Campus of Gualtar 4710-057 Braga Portugal
| | - Elisabete M S Castanheira
- Centre of Physics of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus of Gualtar 4710-057 Braga Portugal
| | - M Sameiro T Gonçalves
- Centre of Chemistry, Department of Chemistry, University of Minho Campus of Gualtar 4710-057 Braga Portugal
| |
Collapse
|
8
|
Ghufran M, Rehman AU, Shah M, Ayaz M, Ng HL, Wadood A. In-silico design of peptide inhibitors of K-Ras target in cancer disease. J Biomol Struct Dyn 2019; 38:5488-5499. [DOI: 10.1080/07391102.2019.1704880] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, South Korea
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Pakistan
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| |
Collapse
|
9
|
Isa DM, Chin SP, Chong WL, Zain SM, Rahman NA, Lee VS. Dynamics and binding interactions of peptide inhibitors of dengue virus entry. J Biol Phys 2019; 45:63-76. [PMID: 30680580 DOI: 10.1007/s10867-018-9515-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023] Open
Abstract
In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potentially modified further to be active against all dengue strains. Molecular docking was performed using AutoDock Vina and the best-ranked peptide-domain III complex was further explored using molecular dynamics simulations. Molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) was used to calculate the relative binding free energies and to locate the key residues of peptide-protein interactions. The predicted binding affinity correlated well with the previous experimental studies. DET4 outperformed DET2 and is oriented within the binding site through favorable vdW and electrostatic interactions. Pairwise residue decomposition analysis has revealed several key residues that contribute to the binding of these peptides. Residues in DET2 interact relatively lesser with the domain III compared to DET4. Dynamic cross-correlation analysis showed that both the DET2 and DET4 trigger different dynamic patterns on the domain III. Correlated motions were seen between the residue pairs of DET4 and the binding site while binding of DET2 results in anti-correlated motion on the binding site. This work showcases the use of computational study in elucidating and explaining the experiment observation on an atomic level.
Collapse
Affiliation(s)
- Diyana Mohd Isa
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wei Lim Chong
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sharifuddin M Zain
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| |
Collapse
|
10
|
Satish L, Millan S, Bera K, Mohapatra S, Sahoo H. A spectroscopic and molecular dynamics simulation approach towards the stabilizing effect of ammonium-based ionic liquids on bovine serum albumin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02900d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Experimental and theoretical evidence in support of the stabilizing effect of ammonium-based ionic liquids on thermal unfolding/refolding of bovine serum albumin is provided in this article.
Collapse
Affiliation(s)
- Lakkoji Satish
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Sabera Millan
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Krishnendu Bera
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Sujata Mohapatra
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Harekrushna Sahoo
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| |
Collapse
|
11
|
Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1578-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
12
|
Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery. J Enzyme Inhib Med Chem 2016; 31:1428-42. [PMID: 26887913 DOI: 10.3109/14756366.2016.1144593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10 ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein-ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or π-π) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained from PLIF analysis. The pharmacophore models have 3-4 pharmacophore contours consist of acceptor and metal ligation (Acc & ML), hydrophobic (HydA) and extended acceptor (Acc2) features with the radius ranging between 1-3 Å for Acc & ML and 1-2 Å for HydA. The excluded volumes of the pharmacophore contours radius are between 1-2 Å. Further, the distance between the interacting groups, root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radial distribution function (RDF) analysis were performed for the MD-simulated proteins using PTRAJ module. The generated pharmacophore models were used to screen a set of natural compounds and database compounds to select significant HITs. We conclude that the developed pharmacophore model can be a significant model for the identification of HITs as FTase inhibitors.
Collapse
Affiliation(s)
- N S Hari Narayana Moorthy
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Sergio F Sousa
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Maria J Ramos
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Pedro A Fernandes
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| |
Collapse
|
13
|
|
14
|
Janssen FFBJ, Peters LCJM, Schlebos PPJ, Smits JMM, de Gelder R, Rowan AE. Uncorrelated Dynamical Processes in Tetranuclear Carboxylate Clusters Studied by Variable-Temperature 1H NMR Spectroscopy. Inorg Chem 2013; 52:13004-13. [DOI: 10.1021/ic401522v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Femke F. B. J. Janssen
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Laurens C. J. M. Peters
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul P. J. Schlebos
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jan M. M. Smits
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - René de Gelder
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alan E. Rowan
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
15
|
Marcial B, Sousa S, Santos HD, Ramos M. Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs). J Biomol Struct Dyn 2013; 32:1907-18. [DOI: 10.1080/07391102.2013.842186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
16
|
Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif. J Mol Model 2012; 19:673-88. [DOI: 10.1007/s00894-012-1590-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
|
17
|
Yang Y, Wang B, Ucisik MN, Cui G, Fierke CA, Merz KM. Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS. J Am Chem Soc 2012; 134:820-3. [PMID: 22206225 DOI: 10.1021/ja209650h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes farnesylation of a variety of peptide substrates. (3)H α-secondary kinetic isotope effect (α-SKIE) measurements of two peptide substrates, CVIM and CVLS, are significantly different and have been proposed to reflect a rate-limiting S(N)2-like transition state with dissociative characteristics for CVIM, while, due to the absence of an isotope effect, CVLS was proposed to have a rate-limiting peptide conformational change. Potential of mean force quantum mechanical/molecular mechanical studies coupled with umbrella sampling techniques were performed to further probe this mechanistic dichotomy. We observe the experimentally proposed transition state (TS) for CVIM but find that CVLS has a symmetric S(N)2 TS, which is also consistent with the absence of a (3)H α-SKIE. These calculations demonstrate facile substrate-dependent alterations in the transition state structure catalyzed by FTase.
Collapse
Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
| | | | | | | | | | | |
Collapse
|
18
|
Sousa SF, Fernandes PA, Ramos MJ. Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers. Phys Chem Chem Phys 2012; 14:12431-41. [DOI: 10.1039/c2cp41180f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
19
|
Perez MAS, Sousa SF, Oliveira EFT, Fernandes PA, Ramos MJ. Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis. J Phys Chem B 2011; 115:15339-54. [DOI: 10.1021/jp205481y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marta A. S. Perez
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Eduardo F. T. Oliveira
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| |
Collapse
|
20
|
Narayana Moorthy NSH, Sousa SF, Ramos MJ, Fernandes PA. In Silico–Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects. ACTA ACUST UNITED AC 2011; 16:1037-46. [DOI: 10.1177/1087057111414899] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the present investigation, the authors have performed an in silico–based analysis on a series of arylthiophene derivatives for the determination of their structural features responsible for farnesyltransferase (FTase) inhibitory activity, hERG blocking activity, and toxicity by quantitative structure–activity relationship and pharmacophore analysis techniques. The statistically significant models derived through multiple linear regression analysis were validated by different validation methods. The applicability of the descriptors contributed in the selected models show that the polar and polarizable properties on the van der Waals (vdW) surface area of the molecules are important for the FTase inhibitory and hERG blocking activities, while being detrimental for the toxicity of the molecules. It is interesting to note that the topological properties, molecular flexibility, and connectivity of the molecules are positively correlated to all the activities (FTase inhibition, hERG blocking, and toxicity). This implies that the flexibility of the molecules is the common feature for interaction in all targets, whereas the presence of polar groups on the molecular surface (vdW) is a determinant for the favorable (FTase inhibition) or unwanted effect (hERG blocking and toxicity) of the molecules. The pharmacophore analysis of the molecules demonstrated that the aromatic/hydrophobicity and polarizability features are important pharmacophore contours favorable for these activities.
Collapse
Affiliation(s)
| | - Sergio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
21
|
Yang Y, Chakravorty DK, Merz KM. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry 2011; 49:9658-66. [PMID: 20923173 DOI: 10.1021/bi1008358] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies aimed at elucidating the unknown Mg2+ binding site in protein farnesyltransferase (FTase) are reported. FTase catalyzes the transfer of a farnesyl group to a conserved cysteine residue (Cys1p) on a target protein, an important step for proteins in the signal transduction pathways (e.g., Ras). Mg2+ ions accelerate the protein farnesylation reaction by up to 700-fold. The exact function of Mg2+ in catalysis and the structural characteristics of its binding remain unresolved to date. Molecular dynamics (MD) simulations addressing the role of magnesium ions in FTase are presented, and relevant octahedral binding motifs for Mg2+ in wild-type (WT) FTase and the Dβ352A mutant are explored. Our simulations suggest that the addition of Mg2+ ions causes a conformational change to occur in the FTase active site, breaking interactions known to keep FPP in its inactive conformation. Two relevant Mg2+ ion binding motifs were determined in WT FTase. In the first binding motif, WT1, the Mg2+ ion is coordinated to D352β, zinc-bound D297β, two water molecules, and one oxygen atom from the α- and β-phosphates of farnesyl diphosphate (FPP). The second binding motif, WT2, is identical with the exception of the zinc-bound D297β being replaced by a water molecule in the Mg2+ coordination complex. In the Dβ352A mutant Mg2+ binding motif, D297β, three water molecules, and one oxygen atom from the α- and β-phosphates of FPP complete the octahedral coordination sphere of Mg2+. Simulations of WT FTase, in which Mg2+ was replaced by water in the active site, recreated the salt bridges and hydrogen-bonding patterns around FPP, validating these simulations. In all Mg2+ binding motifs, a key hydrogen bond was identified between a magnesium-bound water and Cys1p, bridging the two metallic binding sites and, thereby, reducing the equilibrium distance between the reacting atoms of FPP Cys1p. The free energy profiles calculated for these systems provide a qualitative understanding of experimental results. They demonstrate that the two reactive atoms approach each other more readily in the presence of Mg2+ in WT FTase and mutant. The flexible WT2 model was found to possess the lowest barrier toward the conformational change, suggesting it is the preferred Mg2+ binding motif in WT FTase. In the mutant, the absence of D352β makes the transition toward a conformational change harder. Our calculations find support for the proposal that D352β performs a critical role in Mg2+ binding and Mg2+ plays an important role in the conformational transition step.
Collapse
Affiliation(s)
- Yue Yang
- Department of Chemistry and the Quantum Theory Project, University of Florida, Gainesville, FL 32611-8435, USA
| | | | | |
Collapse
|
22
|
Hari Narayana Moorthy NS, Sousa SF, Ramos MJ, Fernandes PA. Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors. J Enzyme Inhib Med Chem 2011; 26:777-91. [DOI: 10.3109/14756366.2011.552885] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- N. S. Hari Narayana Moorthy
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Sergio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| |
Collapse
|
23
|
Khan AH, Prakash A, Kumar D, Rawat AK, Srivastava R, Srivastava S. Virtual screening and pharmacophore studies for ftase inhibitors using Indian plant anticancer compounds database. Bioinformation 2010; 5:62-6. [PMID: 21346865 PMCID: PMC3039991 DOI: 10.6026/97320630005062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/29/2010] [Accepted: 06/08/2010] [Indexed: 11/23/2022] Open
Abstract
Farnesyl transferase (FTase) is an enzyme responsible for post-translational modification in proteins having a carboxy-terminal CaaX motif in
human. It catalyzes the attachment of a lipid group in proteins of RAS superfamily, which is essential in signal transduction. FTase has been recognized
as an important target for anti cancer therapeutics. In this work, we performed virtual screening against FTase with entire 125 compounds from Indian
Plant Anticancer Database using AutoDock 3.0.5 software. All compounds were docked within binding pocket containing Lys164, Tyr300, His248 and
Tyr361 residues in crystal structure of FTase. These complexes were ranked according to their docking score, using methodology that was shown
to achieve maximum accuracy. Finally we got three potent compounds with the best Autodock docking Score (Vinorelbine: -21.28 Kcal/mol,
Vincristine: -21.74 Kcal/mol and Vinblastine: -22.14 Kcal/mol) and their energy scores were better than the FTase bound co-crystallized ligand (L-
739: ―7.9 kcal/mol). These three compounds belong to Vinca alkaloids were analyzed through Python Molecular Viewer for their interaction studies. It
predicted similar orientation and binding modes for these compounds with L-739 in FTase.Thus from the complex scoring and binding ability it is
concluded that these Vinca alkaloids could be promising inhibitors for FTase. A 2-D pharmacophore was generated for these alkaloids using LigandScout
to confirm it. A shared feature pharmacophore was also constructed that shows four common features (one hydogen bond Donar, Two hydrogen bond
Acceptor and one ionizable area) help compounds to interact with this enzyme.
Collapse
Affiliation(s)
- Abdul Hafeez Khan
- Biotechnology and Bioinformatics Division, BIOBRAINZ, 566/29 J, Jai Prakash Nagar, Alambagh, Lucknow 226005, U.P., India
| | | | | | | | | | | |
Collapse
|
24
|
Kuzmanic A, Zagrovic B. Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophys J 2010; 98:861-71. [PMID: 20197040 DOI: 10.1016/j.bpj.2009.11.011] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 10/30/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022] Open
Abstract
Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, <RMSD(2)>(1/2), is directly related to average B-factors (<B>) and <RMSF(2)>(1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability.
Collapse
|
25
|
Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study. J Phys Chem B 2010; 114:4884-95. [DOI: 10.1021/jp907629k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Nicole Audiffren
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jerome de Ruyck
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Marie Ledecq
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Johan Wouters
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| |
Collapse
|
26
|
Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-3034-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|