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Oliveira AA, Róg T, da Silva ABF, Amaro RE, Johnson MS, Postila PA. Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations. Biomolecules 2022; 12:183. [PMID: 35204684 PMCID: PMC8961577 DOI: 10.3390/biom12020183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022] Open
Abstract
The outer mitochondrial membrane (OMM) is involved in multiple cellular functions such as apoptosis, inflammation and signaling via its membrane-associated and -embedded proteins. Despite the central role of the OMM in these vital phenomena, the structure and dynamics of the membrane have regularly been investigated in silico using simple two-component models. Accordingly, the aim was to generate the realistic multi-component model of the OMM and inspect its properties using atomistic molecular dynamics (MD) simulations. All major lipid components, phosphatidylinositol (PI), phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), were included in the probed OMM models. Because increased levels of anionic PS lipids have potential effects on schizophrenia and, more specifically, on monoamine oxidase B enzyme activity, the effect of varying the PS concentration was explored. The MD simulations indicate that the complex membrane lipid composition (MLC) behavior is notably different from the two-component PC-PE model. The MLC changes caused relatively minor effects on the membrane structural properties such as membrane thickness or area per lipid; however, notable effects could be seen with the dynamical parameters at the water-membrane interface. Increase of PS levels appears to slow down lateral diffusion of all lipids and, in general, the presence of anionic lipids reduced hydration and slowed down the PE headgroup rotation. In addition, sodium ions could neutralize the membrane surface, when PI was the main anionic component; however, a similar effect was not seen for high PS levels. Based on these results, it is advisable for future studies on the OMM and its protein or ligand partners, especially when wanting to replicate the correct properties on the water-membrane interface, to use models that are sufficiently complex, containing anionic lipid types, PI in particular.
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Affiliation(s)
- Aline A. Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Tomasz Róg
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland;
| | - Albérico B. F. da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, São Carlos 13560-970, Brazil;
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
| | - Pekka A. Postila
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA 92093-0340, USA; (A.A.O.); (R.E.A.)
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- InFLAMES Research Flagship Center, Åbo Akademi University, 20520 Turku, Finland
- Institute of Biomedicine, Kiinamyllynkatu 10, Integrative Physiology and Pharmacy, University of Turku, FI-20520 Turku, Finland
- Aurlide Ltd., FI-21420 Lieto, Finland
- InFLAMES Research Flagship Center, University of Turku, FI-20520 Turku, Finland
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2
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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3
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Abstract
We have structure, a wealth of kinetic data, thousands of chemical ligands and clinical information for the effects of a range of drugs on monoamine oxidase activity in vivo. We have comparative information from various species and mutations on kinetics and effects of inhibition. Nevertheless, there are what seem like simple questions still to be answered. This article presents a brief summary of existing experimental evidence the background and poses questions that remain intriguing for chemists and biochemists researching the chemical enzymology of and drug design for monoamine oxidases (FAD-containing EC 4.1.3.4).
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4
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Canale V, Grychowska K, Kurczab R, Ryng M, Keeri AR, Satała G, Olejarz-Maciej A, Koczurkiewicz P, Drop M, Blicharz K, Piska K, Pękala E, Janiszewska P, Krawczyk M, Walczak M, Chaumont-Dubel S, Bojarski AJ, Marin P, Popik P, Zajdel P. A dual-acting 5-HT 6 receptor inverse agonist/MAO-B inhibitor displays glioprotective and pro-cognitive properties. Eur J Med Chem 2020; 208:112765. [PMID: 32949963 DOI: 10.1016/j.ejmech.2020.112765] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/15/2020] [Indexed: 01/06/2023]
Abstract
The complex etiology of Alzheimer's disease has initiated a quest for multi-target ligands to address the multifactorial causes of this neurodegenerative disorder. In this context, we designed dual-acting 5-HT6 receptor (5-HT6R) antagonists/MAO-B inhibitors using pharmacophore hybridization strategy. Our approach involved linking priviliged scaffolds of 5-HT6R with aryloxy fragments derived from reversible and irreversible MAO-B inhibitors. The study identified compound 48 that acts as an inverse agonist of 5-HT6R at Gs signaling and an irreversible MAO-B inhibitor. Compound 48 showed moderate metabolic stability in rat microsomal assay, artificial membrane permeability, no hepatotoxicity, and it was well distributed to the brain. Additionally, 48 showed glioprotective properties in a model of cultured astrocytes using 6-OHDA as the cytotoxic agent. Finally, compound 48 (MED = 1 mg/kg, p.o.) fully reversed memory deficits in the NOR task induced by scopolamine in rats. A better understanding of effects exerted by dual-acting 5-HT6R/MAO-B modulators may impact the future development of neurodegenerative-directed treatment strategies.
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Affiliation(s)
- Vittorio Canale
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Katarzyna Grychowska
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 12 Smętna Str., 31-324, Kraków, Poland
| | - Mateusz Ryng
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 12 Smętna Str., 31-324, Kraków, Poland
| | - Abdul Raheem Keeri
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Grzegorz Satała
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 12 Smętna Str., 31-324, Kraków, Poland
| | - Agnieszka Olejarz-Maciej
- Jagiellonian University Medical College, Department of Technology and Biotechnology of Drugs, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Paulina Koczurkiewicz
- Jagiellonian University Medical College, Department of Pharmaceutical Biochemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Marcin Drop
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Klaudia Blicharz
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Kamil Piska
- Jagiellonian University Medical College, Department of Pharmaceutical Biochemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Elżbieta Pękala
- Jagiellonian University Medical College, Department of Pharmaceutical Biochemistry, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Paulina Janiszewska
- Jagiellonian University Medical College, Department of Toxicology, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Martyna Krawczyk
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of New Drug Development, 12 Smętna Str., 31-324, Kraków, Poland
| | - Maria Walczak
- Jagiellonian University Medical College, Department of Toxicology, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Severine Chaumont-Dubel
- Institut de Génomique Fonctionelle, Université de Montpellier, CNRS INSERM, 34094, Montpellier, France
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of Medicinal Chemistry, 12 Smętna Str., 31-324, Kraków, Poland
| | - Philippe Marin
- Institut de Génomique Fonctionelle, Université de Montpellier, CNRS INSERM, 34094, Montpellier, France
| | - Piotr Popik
- Maj Institute of Pharmacology, Polish Academy of Sciences, Department of New Drug Development, 12 Smętna Str., 31-324, Kraków, Poland
| | - Paweł Zajdel
- Jagiellonian University Medical College, Department of Medicinal Chemistry, 9 Medyczna Str., 30-688, Kraków, Poland.
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5
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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6
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Jones HBL, Crean RM, Mullen A, Kendrick EG, Bull SD, Wells SA, Carbery DR, MacMillan F, van der Kamp MW, Pudney CR. Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B. Biochemistry 2019; 58:2362-2372. [PMID: 30964996 DOI: 10.1021/acs.biochem.9b00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an increasing realization that structure-based drug design may show improved success by understanding the ensemble of conformations accessible to an enzyme and how the environment affects this ensemble. Human monoamine oxidase B (MAO-B) catalyzes the oxidation of amines and is inhibited for the treatment of both Parkinson's disease and depression. Despite its clinical importance, its catalytic mechanism remains unclear, and routes to drugging this target would be valuable. Evidence of a radical in either the transition state or the resting state of MAO-B is present throughout the literature and is suggested to be a flavin semiquinone, a tyrosyl radical, or both. Here we see evidence of a resting-state flavin semiquinone, via absorption redox studies and electron paramagnetic resonance, suggesting that the anionic semiquinone is biologically relevant. On the basis of enzyme kinetic studies, enzyme variants, and molecular dynamics simulations, we find evidence for the importance of the membrane environment in mediating the activity of MAO-B and that this mediation is related to the protein dynamics of MAO-B. Further, our MD simulations identify a hitherto undescribed entrance for substrate binding, membrane modulated substrate access, and indications for half-site reactivity: only one active site is accessible to binding at a time. Our study combines both experimental and computational evidence to illustrate the subtle interplay between enzyme activity and protein dynamics and the immediate membrane environment. Understanding key biomedical enzymes to this level of detail will be crucial to inform strategies (and binding sites) for rational drug design for these targets.
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Affiliation(s)
| | | | - Anna Mullen
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | | | | | | | | | - Fraser MacMillan
- School of Chemistry , University of East Anglia , Norwich Research Park , Norwich NR4 7TJ , United Kingdom
| | - Marc W van der Kamp
- School of Biochemistry , University of Bristol , Biomedical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
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7
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Tripathi RKP, Ayyannan SR. Monoamine oxidase-B inhibitors as potential neurotherapeutic agents: An overview and update. Med Res Rev 2019; 39:1603-1706. [PMID: 30604512 DOI: 10.1002/med.21561] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 12/23/2022]
Abstract
Monoamine oxidase (MAO) inhibitors have made significant contributions and remain an indispensable approach of molecular and mechanistic diversity for the discovery of antineurodegenerative drugs. However, their usage has been hampered by nonselective and/or irreversible action which resulted in drawbacks like liver toxicity, cheese effect, and so forth. Hence, the search for selective MAO inhibitors (MAOIs) has become a substantial focus in current drug discovery. This review summarizes our current understanding on MAO-A/MAO-B including their structure, catalytic mechanism, and biological functions with emphases on the role of MAO-B as a potential therapeutic target for the development of medications treating neurodegenerative disorders. It also highlights the recent developments in the discovery of potential MAO-B inhibitors (MAO-BIs) belonging to diverse chemical scaffolds, arising from intensive chemical-mechanistic and computational studies documented during past 3 years (2015-2018), with emphases on their potency and selectivity. Importantly, readers will gain knowledge of various newly established MAO-BI scaffolds and their development potentials. The comprehensive information provided herein will hopefully accelerate ideas for designing novel selective MAO-BIs with superior activity profiles and critical discussions will inflict more caution in the decision-making process in the MAOIs discovery.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India.,Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
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8
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Mondal A, Chatterjee R, Datta S. Umbrella Sampling and X-ray Crystallographic Analysis Unveil an Arg-Asp Gate Facilitating Inhibitor Binding Inside Phosphopantetheine Adenylyltransferase Allosteric Cleft. J Phys Chem B 2018; 122:1551-1559. [PMID: 29345931 DOI: 10.1021/acs.jpcb.7b09543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phosphopantetheine adenylyltransferase (PPAT) is a rate-limiting enzyme essential for biosynthesis of coenzyme A (CoA), which in turn is responsible to regulate the secretion of exotoxins via type III secretion system in Pseudomonas aeruginosa, causing severe health concerns ranging from nosocomial infections to respiratory failure. Acetyl coenzyme A (AcCoA) is a newly reported inhibitor of PPAT, believed to regulate the cellular levels of CoA and thereby the pathogenesis. Very little is known so far regarding the mechanistic details of AcCoA binding inside PPAT-binding cleft. Herein, we have used extensive umbrella sampling simulations to decipher mechanistic insight into the inhibitor accommodation inside the binding cavity. We found that R90 and D94 residues act like a gate near the binding cavity to accommodate and stabilize the incoming ligand. Mutational models concerning these residues also show considerable difference in AcCoA-binding thermodynamics. To substantiate our findings, we have solved the first crystal structure of apo-PPAT from P. aeruginosa, which also found to agree with the simulation results. Collectively, these results describe the mechanistic details of accommodation of inhibitor molecule inside PPAT-binding cavity and also offer valuable insight into regulating cellular levels of CoA/AcCoA and thus controlling the pathogenicity.
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Affiliation(s)
- A Mondal
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , 4 Raja SC Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - R Chatterjee
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , 4 Raja SC Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - S Datta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology , 4 Raja SC Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
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9
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Mangiatordi GF, Alberga D, Pisani L, Gadaleta D, Trisciuzzi D, Farina R, Carotti A, Lattanzi G, Catto M, Nicolotti O. A rational approach to elucidate human monoamine oxidase molecular selectivity. Eur J Pharm Sci 2017; 101:90-99. [DOI: 10.1016/j.ejps.2017.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/27/2017] [Accepted: 02/05/2017] [Indexed: 02/05/2023]
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10
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Mathew B, Adeniyi AA, Dev S, Joy M, Ucar G, Mathew GE, Singh-Pillay A, Soliman MES. Pharmacophore-Based 3D-QSAR Analysis of Thienyl Chalcones as a New Class of Human MAO-B Inhibitors: Investigation of Combined Quantum Chemical and Molecular Dynamics Approach. J Phys Chem B 2017; 121:1186-1203. [DOI: 10.1021/acs.jpcb.6b09451] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bijo Mathew
- Division
of Drug Design and Medicinal Chemistry Research Lab, Department of
Pharmaceutical Chemistry, Ahalia School of Pharmacy, Palakkad 678557, Kerala, India
| | - Adebayo A. Adeniyi
- School
of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Sanal Dev
- Department
of Pharmaceutical Chemistry, Al Shifa College of Pharmacy, Perinthalmanna 679325, Kerala, India
| | - Monu Joy
- School of Pure & Applied Physics, M.G. University, Kottayam 686560, India
| | - Gülberk Ucar
- Department
of Biochemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
| | | | - Ashona Singh-Pillay
- School
of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- School
of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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11
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Ayee MAA, Roth CW, Akpa BS. Structural perturbation of a dipalmitoylphosphatidylcholine (DPPC) bilayer by warfarin and its bolaamphiphilic analogue: A molecular dynamics study. J Colloid Interface Sci 2016; 468:227-237. [PMID: 26852346 PMCID: PMC4762473 DOI: 10.1016/j.jcis.2016.01.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/24/2016] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
Abstract
Compounds with nominally similar biological activity may exhibit differential toxicity due to differences in their interactions with cell membranes. Many pharmaceutical compounds are amphiphilic and can be taken up by phospholipid bilayers, interacting strongly with the lipid-aqueous interface whether or not subsequent permeation through the bilayer is possible. Bolaamphiphilic compounds, which possess two hydrophilic ends and a hydrophobic linker, can likewise undergo spontaneous uptake by bilayers. While membrane-spanning bolaamphiphiles can stabilize membranes, small molecules with this characteristic have the potential to create membrane defects via disruption of bilayer structure and dynamics. When compared to the amphiphilic therapeutic anticoagulant, warfarin, the bolaamphiphilic analogue, brodifacoum, exhibits heightened toxicity that goes beyond superior inhibition of the pharmacological target enzyme. We explore, herein, the consequences of anticoagulant accumulation in a dipalmitoylphosphatidylcholine (DPPC) bilayer. Coarse-grained molecular dynamics simulations reveal that permeation of phospholipid bilayers by brodifacoum causes a disruption of membrane barrier function that is driven by the bolaamphiphilic nature and size of this molecule. We find that brodifacoum partitioning into bilayers causes membrane thinning and permeabilization and promotes lipid flip-flop - phenomena that are suspected to play a role in triggering cell death. These phenomena are either absent or less pronounced in the case of the less toxic, amphiphilic compound, warfarin.
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Affiliation(s)
- Manuela Aseye Ayele Ayee
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA; Department of Medicine, University of Illinois at Chicago, 909 S. Wolcott Ave., Chicago, IL 60612, USA.
| | - Charles William Roth
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA.
| | - Belinda Sena Akpa
- Department of Chemical Engineering, University of Illinois at Chicago, 810 S. Clinton St., Chicago, IL 60607, USA; Department of Molecular Biomedical Sciences, North Carolina State University, 1060 William Moore Dr., Raleigh, NC 27607, USA.
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12
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Veselovsky AV, Ivanov AS, Medvedev AE. [Computer modelling of monoaminoxidases]. BIOMEDITSINSKAIA KHIMIIA 2015; 61:265-271. [PMID: 25978392 DOI: 10.18097/pbmc20156102265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The article summarized results of studies on active site structures of monoamine oxidases (MAO) performed in the Institute of Biomedical Chemistry (Russia) by computer modelling approaches. MAO, catalyzing the reaction of oxidative deamination of major neurotransmitter monoamines, exists in two highly homologous forms, MAO A and MAO B, distinguished by substrate specificity and inhibitor selectivity. The development of approaches for active site modelling of these enzymes (with unknown three-dimensional structures) started from analysis of relationship between the geometrical sizes of rigid indole and isatin derivatives and their inhibitory activity. These studies resulted in molding of the active site structures of MAO A and MAO B. These molds reflect the sizes and shapes of active sites of these enzymes. These mold models have been used for virtual screening of molecular databases for new inhibitors. The models obtained at different stages of MAO investigations have been compared with recently appeared three-dimensional structures of MAO A and MAO B.
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Affiliation(s)
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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Basile L, Pappalardo M, Guccione S, Milardi D, Ramsay RR. Computational Comparison of Imidazoline Association with the I2 Binding Site in Human Monoamine Oxidases. J Chem Inf Model 2014; 54:1200-7. [DOI: 10.1021/ci400346k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livia Basile
- Etnalead
s.r.l., c/o EtnaBuilding, Scuola Superiore di Catania, Università degli Studi di Catania, via S. Nullo 5/i, I-95123 Catania, Italy
| | - Matteo Pappalardo
- Dipartimento
di Scienze Chimiche, Università degli Studi di Catania, Viale
A.Doria 6 Ed.3, Città Universitaria, I- 95125 Catania, Italy
| | - Salvatore Guccione
- Etnalead
s.r.l., c/o EtnaBuilding, Scuola Superiore di Catania, Università degli Studi di Catania, via S. Nullo 5/i, I-95123 Catania, Italy
- Dipartimento
di Scienze del Farmaco, Università degli Studi di Catania, Viale A.Doria 6 Ed. 2, Città Universitaria, I-95125 Catania, Italy
| | - Danilo Milardi
- IBB-CNR,
Istituto di Biostrutture e Bioimmagini, UOS di Catania c/o Dipartimento
di Scienze Chimiche, Università degli Studi di Catania, Viale
A.Doria 6 Ed.3, Città Universitaria, I- 95125 Catania, Italy
| | - Rona R. Ramsay
- Biomedical
Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews KY16 8QP, U.K
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14
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Naserian-Nik AM, Tahani M, Karttunen M. Molecular dynamics study of DNA oligomers under angled pulling. RSC Adv 2014. [DOI: 10.1039/c3ra45604h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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15
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Qin SS, Yu YX, Li QK, Yu ZW. Interaction of Human Synovial Phospholipase A2 with Mixed Lipid Bilayers: A Coarse-Grain and All-Atom Molecular Dynamics Simulation Study. Biochemistry 2013; 52:1477-89. [DOI: 10.1021/bi3012687] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shan-Shan Qin
- Key Laboratory of Bioorganic
Phosphorous Chemistry and Chemical Biology (Ministry of Education),
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yang-Xin Yu
- Laboratory of Chemical Engineering
Thermodynamics, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Qi-Kai Li
- Department of Mechanical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Zhi-Wu Yu
- Key Laboratory of Bioorganic
Phosphorous Chemistry and Chemical Biology (Ministry of Education),
Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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16
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Schlesier T, Diezemann G. Performance of Different Force Fields in Force Probe Simulations. J Phys Chem B 2013; 117:1862-71. [DOI: 10.1021/jp3115644] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Schlesier
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
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17
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Naserian-Nik AM, Tahani M, Karttunen M. Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details. RSC Adv 2013. [DOI: 10.1039/c3ra23213a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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18
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Abstract
This minireview focuses on recent developments in the application of molecular dynamics to drug design. Recent applications of endpoint free-energy computational methods such as molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and generalized Born surface area (MM-GBSA) and linear response methods are described. Recent progress in steered molecular dynamics applied to drug design is reviewed.
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19
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Targeting imidazoline site on monoamine oxidase B through molecular docking simulations. J Mol Model 2012; 18:3877-86. [DOI: 10.1007/s00894-012-1390-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
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