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Kitaoka H, Yokoyama Y, Sakka T, Nishi N. Salting-out and Competitive Adsorption of Ethanol into Lipid Bilayer Membranes: Conflicting Effects of Salts on Ethanol-Membrane Interactions Studied by Molecular Dynamics Simulations. J Phys Chem B 2024. [PMID: 39046846 DOI: 10.1021/acs.jpcb.4c03399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Small amphiphilic molecules, such as ethanol, disturb the structure of lipid bilayer membranes to increase the membrane permeability, which is important for applications such as drug delivery, disinfection, and fermentation. To investigate how and the extent to which coexisting salts affect membrane disturbance, we performed molecular dynamics (MD) simulations on lipid bilayer membranes composed of zwitterionic lipids in aqueous ethanol solutions containing 0-631 mM NaCl, KCl, and KI salts. The addition of salts at low concentrations induced cationic adsorption on the lipid membrane, which competes with ethanol adsorption, thereby reducing the hydrogen bonds between ethanol and lipid molecules. This competitive adsorption mitigated the membrane disturbance and decreased the permeation of ethanol molecules into the membrane. In contrast, higher salt concentrations enhanced the membrane disturbance and permeability, which was caused by the salting-out of ethanol from the aqueous phase to the lipid bilayer. These conflicting effects appearing at different concentrations were stronger with the chloride salts than with the iodide salt. Among the two chloride salts, NaCl and KCl, the latter showed a greater enhancement in ethanol permeation at high concentrations. This seeming anti-Hofmeister salting-out behavior resulted from greater Na+ adsorption, preventing the ethanol-lipid interactions.
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Affiliation(s)
- Haru Kitaoka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Yuko Yokoyama
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tetsuo Sakka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoya Nishi
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- iCaNS, Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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Rai R, Kumar D, Dhule AA, Rudani BA, Tiwari S. Alkanols Regulate the Fluidity of Phospholipid Bilayer in Accordance to Their Concentration and Polarity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:14057-14065. [PMID: 38935825 DOI: 10.1021/acs.langmuir.4c01499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
In spite of the widespread use of alkanols as penetration enhancers, their effect on vesicular formulations remains largely unexplored. These can affect the stability and integrity of the phospholipid bilayers. In this study, we have investigated the interaction of linear (ethanol, butanol, hexanol, octanol) and branched alkanols (t-amylol and t-butanol) with three phospholipids (soya lecithin, SL; soy L-α-phosphatidylcholine, SPC; and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC). Thermodynamic and structural aspects of these interactions were studied as a function of the alkanol concentration and chain length. Our interpretations are based on isothermal titration calorimetry (ITC) and dynamic light scattering (DLS) experiments. We observed one-site interactions wherein hydroxyl and acyl groups interacted with the polar and nonpolar regions of the phospholipid, respectively. The stability and structural integrity of bilayers appeared to be dependent upon (a) the hydrocarbon chain length and concentration of alcohols, and (b) the degree of unsaturation in the phospholipid molecule. We found that these interactions triggered a reduction in the enthalpy which was compensated by increased entropy, keeping free energy negative. Drop in enthalpy indicates reversible disordering of the bilayer which enables the diffusion of alcohol without triggering destabilization. Ethanol engaged predominantly with the interface, and it resulted in higher enthalpic changes. Interactions became increasingly unfavorable with longer alcohols - a cutoff point was recorded with hexanol. The overall sequence of membrane disordering capability was recorded as follows: ethanol < butanol < octanol < hexanol. Octanol's larger size restricted its penetration in the bilayer, and hence it caused less enthalpic changes relative to hexanol. This could also be verified from the trends in the area ratio of these vesicles obtained from the DLS data. Branched alkanols displayed a lower binding affinity with the phospholipids relative to their linear counterparts. These data are useful while contemplating the inclusion of short-chain alcohols as penetration enhancers in phospholipid vesicles.
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Affiliation(s)
- Ragini Rai
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow 226002, Uttar Pradesh, India
| | - Deepak Kumar
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow 226002, Uttar Pradesh, India
| | - Anjali A Dhule
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow 226002, Uttar Pradesh, India
| | - Binny A Rudani
- IBI-4: Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Sanjay Tiwari
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow 226002, Uttar Pradesh, India
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Shahab M, Danial M, Khan T, Liang C, Duan X, Wang D, Gao H, Zheng G. In Silico Identification of Lead Compounds for Pseudomonas Aeruginosa PqsA Enzyme: Computational Study to Block Biofilm Formation. Biomedicines 2023; 11:biomedicines11030961. [PMID: 36979940 PMCID: PMC10046026 DOI: 10.3390/biomedicines11030961] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium implicated in acute and chronic nosocomial infections and a leading cause of patient mortality. Pseudomonas aeruginosa infections are frequently associated with the development of biofilms, which give the bacteria additional drug resistance and increase their virulence. The goal of this study was to find strong compounds that block the Anthranilate-CoA ligase enzyme made by the pqsA gene. This would stop the P. aeruginosa quorum signaling system. This enzyme plays a crucial role in the pathogenicity of P. aeruginosa by producing autoinducers for cell-to-cell communication that lead to the production of biofilms. Pharmacophore-based virtual screening was carried out utilizing a library of commercially accessible enzyme inhibitors. The most promising hits obtained during virtual screening were put through molecular docking with the help of MOE. The virtual screening yielded 7/160 and 10/249 hits (ZINC and Chembridge). Finally, 2/7 ZINC hits and 2/10 ChemBridge hits were selected as potent lead compounds employing diverse scaffolds due to their high pqsA enzyme binding affinity. The results of the pharmacophore-based virtual screening were subsequently verified using a molecular dynamic simulation-based study (MDS). Using MDS and post-MDS, the stability of the complexes was evaluated. The most promising lead compounds exhibited a high binding affinity towards protein-binding pocket and interacted with the catalytic dyad. At least one of the scaffolds selected will possibly prove useful for future research. However, further scientific confirmation in the form of preclinical and clinical research is required before implementation.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Muhammad Danial
- Shenzhen Institute of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen 518055, China
| | - Taimur Khan
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chaoqun Liang
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiuyuan Duan
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Daixi Wang
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanzi Gao
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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Ghufran M, Ullah M, Khan HA, Ghufran S, Ayaz M, Siddiq M, Abbas SQ, Hassan SSU, Bungau S. In-Silico Lead Druggable Compounds Identification against SARS COVID-19 Main Protease Target from In-House, Chembridge and Zinc Databases by Structure-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations. BIOENGINEERING (BASEL, SWITZERLAND) 2023; 10:bioengineering10010100. [PMID: 36671672 PMCID: PMC9854631 DOI: 10.3390/bioengineering10010100] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/04/2023] [Accepted: 01/08/2023] [Indexed: 01/14/2023]
Abstract
Pharmacological strategies to lower the viral load among patients suffering from severe diseases were researched in great detail during the SARS-CoV-2 outbreak. The viral protease Mpro (3CLpro) is necessary for viral replication and is among the main therapeutic targets proposed, thus far. To stop the pandemic from spreading, researchers are working to find more effective Mpro inhibitors against SARS-CoV-2. The 33.8 kDa Mpro protease of SARS-CoV-2, being a nonhuman homologue, has the possibility of being utilized as a therapeutic target against coronaviruses. To develop drug-like compounds capable of preventing the replication of SARS-main CoV-2's protease (Mpro), a computer-aided drug design (CADD) approach is extremely viable. Using MOE, structure-based virtual screening (SBVS) of in-house and commercial databases was carried out using SARS-CoV-2 proteins. The most promising hits obtained during virtual screening (VS) were put through molecular docking with the help of MOE. The virtual screening yielded 3/5 hits (in-house database) and 56/66 hits (commercial databases). Finally, 3/5 hits (in-house database), 3/5 hits (ZINC database), and 2/7 hits (ChemBridge database) were chosen as potent lead compounds using various scaffolds due to their considerable binding affinity with Mpro protein. The outcomes of SBVS were then validated using an analysis based on molecular dynamics simulation (MDS). The complexes' stability was tested using MDS and post-MDS. The most promising candidates were found to exhibit a high capacity for fitting into the protein-binding pocket and interacting with the catalytic dyad. At least one of the scaffolds selected will possibly prove useful for future research. However, further scientific confirmation in the form of preclinical and clinical research is required before implementation.
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Affiliation(s)
- Mehreen Ghufran
- Department of Pathology, Medical Teaching Institution Bacha Khan Medical College (BKMC) Mardan, Mardan 23200, Pakistan
| | - Mehran Ullah
- District Medical Officer, Sehat Sahulat Program (SSP), KPK, Mardan 23200, Pakistan
- Mardan Medical Complex (MMC) Mardan, Medical Teaching Institution Bacha Khan Medical College (BKMC), Mardan 23200, Pakistan
| | - Haider Ali Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
- Correspondence: (H.A.K.); (S.S.u.H.)
| | - Sabreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Chakdara 18000, Pakistan
| | - Muhammad Siddiq
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Syed Qamar Abbas
- Department of Pharmacy, Sarhad University of Science and technology, Peshawar 25000, Pakistan
| | - Syed Shams ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (H.A.K.); (S.S.u.H.)
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania
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Supramolecular Self-Assembly of Dipalmitoylphosphatidylcholine and Carbon Nanotubes: A Dissipative Particle Dynamics Simulation Study. NANOMATERIALS 2022; 12:nano12152653. [PMID: 35957084 PMCID: PMC9370663 DOI: 10.3390/nano12152653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022]
Abstract
Dissipative particle dynamics simulations were performed to investigate the self-assembly of dipalmitoylphosphatidylcholine (DPPC) as a model lipid membrane on the surface of carbon nanotubes (CNTs). The influence of surface curvature of CNTs on self-assembly was investigated by performing simulations on solutions of DPPC in water in contact with CNTs of different diameters: CNT (10, 10), CNT (14, 14), CNT (20, 20), and CNT (34, 34). DPPC solutions with a wide range of concentrations were chosen to allow for formation of lipid structures of various surface densities, ranging from a submonolayer to a well-organized monolayer and a CNT covered with a lipid monolayer immersed in a planar lipid bilayer. Our results are indicative of a sequence of phase-ordering processes for DPPC on the surface of CNTs. At low surface coverages, the majority of hydrocarbon tail groups of DPPC are in contact with the CNT surface. Increasing the surface coverage leads to the formation of hemimicellar aggregates, and at high surface coverages close to the saturation limit, an organized lipid monolayer self-assembles. An examination of the mechanism of self-assembly reveals a two-step mechanism. The first step involves densification of DPPC on the CNT surface. Here, the lipid molecules do not adopt the order of the target phase (lipid monolayer on the CNT surface). In the second step, when the lipid density on the CNT surface is above a threshold value (close to saturation), the lipid molecules reorient themselves to form an organized monolayer around the tube. Here, the DPPC molecules adopt stretched conformations normal to the surface, the end hydrocarbon groups adsorb on the surface, and the head groups occupy the outermost part of the monolayer. The saturation density and the degree of lipid ordering on the CNT surface depend on the surface curvature. The saturation density increases with increased surface curvature, and better-ordered structures are formed on less curved surfaces.
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Liu J, Song W, Ma G, Li K. Faraday Instability in Viscous Fluids Covered with Elastic Polymer Films. Polymers (Basel) 2022; 14:polym14122334. [PMID: 35745910 PMCID: PMC9231276 DOI: 10.3390/polym14122334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
Faraday instability has great application value in the fields of controlling polymer processing, micromolding colloidal lattices on structured suspensions, organizing particle layers, and conducting cell culture. To regulate Faraday instability, in this article, we attempt to introduce an elastic polymer film covering the surface of a viscous fluid layer and theoretically study the behaviors of the Faraday instability phenomenon and the effect of the elastic polymer film. Based on hydrodynamic theory, the Floquet theory is utilized to formulate its stability criterion, and the critical acceleration amplitude and critical wave number are calculated numerically. The results show that the critical acceleration amplitude for Faraday instability increases with three increasing bending stiffness of the elastic polymer film, and the critical wave number decreases with increasing bending stiffness. In addition, surface tension and viscosity also have important effects on the critical acceleration amplitude and critical wave number. The strategy of controlling Faraday instability by covering an elastic polymer film proposed in this paper has great application potential in new photonic devices, metamaterials, alternative energy, biology, and other fields.
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Affiliation(s)
- Junxiu Liu
- Anhui Province Key Laboratory of Building Structure and Underground Engineering, Anhui Jianzhu University, Hefei 230601, China;
- College of Civil Engineering, Anhui Jianzhu University, Hefei 230601, China; (W.S.); (G.M.)
| | - Wenqiang Song
- College of Civil Engineering, Anhui Jianzhu University, Hefei 230601, China; (W.S.); (G.M.)
| | - Gan Ma
- College of Civil Engineering, Anhui Jianzhu University, Hefei 230601, China; (W.S.); (G.M.)
| | - Kai Li
- Anhui Province Key Laboratory of Building Structure and Underground Engineering, Anhui Jianzhu University, Hefei 230601, China;
- College of Civil Engineering, Anhui Jianzhu University, Hefei 230601, China; (W.S.); (G.M.)
- Correspondence:
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