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Hu Z, Martí J. Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an "off-like" state. Comput Struct Biotechnol J 2024; 23:2418-2428. [PMID: 38882681 PMCID: PMC11176632 DOI: 10.1016/j.csbj.2024.05.038] [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: 03/25/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The NRAS-mutant subset of melanoma represent some of the most aggressive and deadliest types associated with poor overall survival. Unfortunately, for more than 40 years, no therapeutic agent directly targeting NRAS mutations has been clinically approved. In this work, based on microsecond scale molecular dynamics simulations, the effect of Q61 mutations on NRAS conformational characteristics is revealed at the atomic level. The GTP-bound NRAS-Q61R and Q61K mutations show a specific targetable pocket between Switch-II and α-helix 3 whereas the NRAS-Q61L non-polar mutation category shows a different targetable pocket. Moreover, a new isomer-sourced structure iteration method has been developed for the in silico design of potential inhibitor prototypes for oncogenes. We show the possibility of a designed prototype HM-387 to target activated NRAS-Q61R and that it can gradually induce the transition from the activated NRAS-Q61R to an "off-like" state.
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Affiliation(s)
- Zheyao Hu
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Polytechnic University of Catalonia-Barcelona Tech, B4-B5 Northern Campus UPC, Barcelona, 08034, Catalonia, Spain
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2
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Xue M, Cao Y, Shen C, Guo W. Computational Advances of Protein/Neurotransmitter-membrane Interactions Involved in Vesicle Fusion and Neurotransmitter Release. J Mol Biol 2023; 435:167818. [PMID: 36089056 DOI: 10.1016/j.jmb.2022.167818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/04/2022] [Indexed: 02/04/2023]
Abstract
Vesicle fusion is of crucial importance to neuronal communication at neuron terminals. The exquisite but complex fusion machinery for neurotransmitter release is tightly controlled and regulated by protein/neurotransmitter-membrane interactions. Computational 'microscopies', in particular molecular dynamics simulations and related techniques, have provided notable insight into the physiological process over the past decades, and have made enormous contributions to fields such as neurology, pharmacology and pathophysiology. Here we review the computational advances of protein/neurotransmitter-membrane interactions related to presynaptic vesicle-membrane fusion and neurotransmitter release, and outline the in silico challenges ahead for understanding this important physiological process.
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Affiliation(s)
- Minmin Xue
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yuwei Cao
- State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Chun Shen
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China; State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China.
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Foreseeing the future of green Technology. Molecular dynamic investigation on passive membrane penetration by the products of the CO2 and 1,3-butadiene reaction. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kumar C, Srivastava S. Structural and Dynamical Studies of a Lipid-Nanoclay Composite Layer at the Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10400-10411. [PMID: 35973133 DOI: 10.1021/acs.langmuir.2c00987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We modulate the adsorption affinities of nanoclay particles for the air-water interface by changing the cationic surface charge composition of the lipid monolayer and thereby tune the attractive electrostatic interaction between the positively charged lipid layer and the zwitterionic nanoclay particles in the water subphase. Our findings emphasize the significance of electrostatic interaction between lipids and the nanoclay, as well as its impact on the structural and viscoelastic features of the composite layer. We use surface pressure (Π)-mean molecular area (A) isotherms, atomic force microscope (AFM), Brewster angle microscopy (BAM), and energy dispersive X-ray spectrsocopy (EDXS) measurements to analyze the structure phases of lipid and lipid-nanoclay composite interfacial layer. The Π-A isotherm curve shows that the lipid-nanoclay composite layer has a larger lift-off area than the neat lipid layer, indicating that nanoparticles adsorb at the lipid layer via electrostatic interaction between lipid and nanoclay molecules. The surface density of the adsorbed nanoclay particles increases with an increase in the composition of the cationic lipid molecules. The stress relaxation response of the composite layer, measured using step compression measurements, exhibits exponential decay and ubiquitous dependence on the cationic dimyristoy-trimethylammonium propane (DMTAP) composition in the lipid layer with crossover to faster relaxation dynamics at DMTAP > 0.75. The power-law study of the frequency-dependent dynamic viscoelastic responses of the interfacial layer, measured using the barrier oscillation method, reveals a transition from glass-like response from neat lipid layer to gel-like dynamic response for the lipid-nanoclay composite layer. A solid-like behavior is evident for all the interface layers with dilation elastic modulus (E') > dilational viscous modulus (E″); however, the dynamic response of the neat layer is largely frequency-independent, whereas lipid-nanoclay composite layers with DMTAP > 0.75 reveal a frequency-dependent dynamic responses. The frequency-dependent power-law exponent of E', E″ increases on increasing the fractional composition of cationic DMTAP from 0.1 to 1.0, which forms a saturated interface of laponite particles and behaves as a viscoelastic gel in 2D.
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Affiliation(s)
- Chandan Kumar
- Soft Matter and Nanomaterials Laboratory, Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sunita Srivastava
- Soft Matter and Nanomaterials Laboratory, Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Hu Z, Marti J. In Silico Drug Design of Benzothiadiazine Derivatives Interacting with Phospholipid Cell Membranes. MEMBRANES 2022; 12:membranes12030331. [PMID: 35323806 PMCID: PMC8949146 DOI: 10.3390/membranes12030331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/09/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022]
Abstract
The use of drugs derived from benzothiadiazine, a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension, low blood sugar or the human immunodeficiency virus, among others. In this work we have investigated the interactions of benzothiadiazine and four of its derivatives designed in silico with model zwitterionic cell membranes formed by dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine and cholesterol at the liquid–crystal phase inside aqueous potassium chloride solution. We have elucidated the local structure of benzothiadiazine by means of microsecond molecular dynamics simulations of systems including a benzothiadiazine molecule or one of its derivatives. Such derivatives were obtained by the substitution of a single hydrogen site of benzothiadiazine by two different classes of chemical groups, one of them electron-donating groups (methyl and ethyl) and another one by electron-accepting groups (fluorine and trifluoromethyl). Our data have revealed that benzothiadiazine derivatives have a strong affinity to stay at the cell membrane interface although their solvation characteristics can vary significantly—they can be fully solvated by water in short periods of time or continuously attached to specific lipid sites during intervals of 10–70 ns. Furthermore, benzothiadiazines are able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of characteristic lengths between 1.6 and 2.1 Å.
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Elisi GM, Scalvini L, Lodola A, Mor M, Rivara S. Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. J Chem Inf Model 2021; 62:210-222. [PMID: 34932329 PMCID: PMC8757440 DOI: 10.1021/acs.jcim.1c01183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The effects of the
neurohormone melatonin are mediated by the activation
of the GPCRs MT1 and MT2 in a variety of tissues.
Crystal structures suggest ligand access to the orthosteric binding
site of MT1 and MT2 receptors through a lateral
channel between transmembrane (TM) helices IV and V. We investigated
the feasibility of this lipophilic entry route for 2-iodomelatonin,
a nonselective agonist with a slower dissociation rate from the MT2 receptor, applying enhanced sampling simulations and free-energy
calculations. 2-Iodomelatonin unbinding was investigated with steered
molecular dynamics simulations which revealed different trajectories
passing through the gap between TM helices IV and V for both receptors.
For one of these unbinding trajectories from the MT1 receptor,
an umbrella-sampling protocol with path-collective variables provided
a calculated energy barrier consistent with the experimental dissociation
rate. The side-chain flexibility of Tyr5.38 was significantly different
in the two receptor subtypes, as assessed by metadynamics simulations,
and during ligand unbinding it frequently assumes an open conformation
in the MT1 but not in the MT2 receptor, favoring
2-iodomelatonin egress. Taken together, our simulations are consistent
with the possibility that the gap between TM IV and V is a way of
connecting the orthosteric binding site and the membrane core for
lipophilic melatonin receptor ligands. Our simulations also suggest
that the open state of Tyr5.38 generates a small pocket on the surface
of MT1 receptor, which could participate in the recognition
of MT1-selective ligands and may be exploited in the design
of new selective compounds.
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Affiliation(s)
- Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy.,Microbiome Research Hub, University of Parma, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
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Energy landscapes and dynamics of ion translocation through membrane transporters: a meeting ground for physics, chemistry, and biology. J Biol Phys 2021; 47:401-433. [PMID: 34792702 DOI: 10.1007/s10867-021-09591-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2021] [Indexed: 10/19/2022] Open
Abstract
The dynamics of ion translocation through membrane transporters is visualized from a comprehensive point of view by a Gibbs energy landscape approach. The ΔG calculations have been performed with the Kirkwood-Tanford-Warshel (KTW) electrostatic theory that properly takes into account the self-energies of the ions. The Gibbs energy landscapes for translocation of a single charge and an ion pair are calculated, compared, and contrasted as a function of the order parameter, and the characteristics of the frustrated system with bistability for the ion pair are described and quantified in considerable detail. These calculations have been compared with experimental data on the ΔG of ion pairs in proteins. It is shown that, under suitable conditions, the adverse Gibbs energy barrier can be almost completely compensated by the sum of the electrostatic energy of the charge-charge interactions and the solvation energy of the ion pair. The maxima in ΔGKTW with interionic distance in the bound H+ - A- charge pair on the enzyme is interpreted in thermodynamic and molecular mechanistic terms, and biological implications for molecular mechanisms of ATP synthesis are discussed. The timescale at which the order parameter moves between two stable states has been estimated by solving the dynamical equations of motion, and a wealth of novel insights into energy transduction during ATP synthesis by the membrane-bound FOF1-ATP synthase transporter is offered. In summary, a unifying analytical framework that integrates physics, chemistry, and biology has been developed for ion translocation by membrane transporters for the first time by means of a Gibbs energy landscape approach.
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Hu Z, Martí J, Lu H. Structure of benzothiadiazine at zwitterionic phospholipid cell membranes. J Chem Phys 2021; 155:154303. [PMID: 34686044 DOI: 10.1063/5.0065163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of drugs derived from benzothiadiazine, which is a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension (treated with diuretics such as bendroflumethiazide or chlorothiazide), low blood sugar (treated with non-diuretic diazoxide), or the human immunodeficiency virus, among others. In this work, we have investigated the interactions of benzothiadiazine with the basic components of cell membranes and solvents, such as phospholipids, cholesterol, ions, and water. The analysis of the mutual microscopic interactions is of central importance to elucidate the local structure of benzothiadiazine as well as the mechanisms responsible for the access of benzothiadiazine to the interior of the cell. We have performed molecular dynamics simulations of benzothiadiazine embedded in three different model zwitterionic bilayer membranes made by dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine, and cholesterol inside aqueous sodium-chloride solution in order to systematically examine microscopic interactions of benzothiadiazine with the cell membrane at liquid-crystalline phase conditions. From data obtained through radial distribution functions, hydrogen-bonding lengths, and potentials of mean force based on reversible work calculations, we have observed that benzothiadiazine has a strong affinity to stay at the cell membrane interface although it can be fully solvated by water in short periods of time. Furthermore, benzothiadiazine is able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of different characteristic lengths.
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Affiliation(s)
- Zheyao Hu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus UPC, 08034 Barcelona, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus UPC, 08034 Barcelona, Catalonia, Spain
| | - Huixia Lu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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Lu H, Martí J. Long-lasting Salt Bridges Provide the Anchoring Mechanism of Oncogenic Kirsten Rat Sarcoma Proteins at Cell Membranes. J Phys Chem Lett 2020; 11:9938-9945. [PMID: 33170712 DOI: 10.1021/acs.jpclett.0c02809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RAS proteins work as GDP-GTP binary switches and regulate cytoplasmic signaling networks that are able to control several cellular processes, playing an essential role in signal transduction pathways involved in cell growth, differentiation, and survival, so that overacting RAS signaling can lead to cancer. One of the hardest challenges to face is the design of mutation-selective therapeutic strategies. In this work, a G12D-mutated farnesylated GTP-bound Kirsten RAt sarcoma (KRAS) protein has been simulated at the interface of a DOPC/DOPS/cholesterol model anionic cell membrane. A specific long-lasting salt bridge connection between farnesyl and the hypervariable region of the protein has been identified as the main mechanism responsible for the binding of oncogenic farnesylated KRAS-4B to the cell membrane. Free-energy landscapes allowed us to characterize local and global minima of KRAS-4B binding to the cell membrane, revealing the main pathways between anchored and released states.
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Affiliation(s)
- Huixia Lu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Barcelona, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Barcelona, Catalonia, Spain
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Chiral Recognition of Flexible Melatonin Receptor Ligands Induced by Conformational Equilibria. Molecules 2020; 25:molecules25184057. [PMID: 32899888 PMCID: PMC7570888 DOI: 10.3390/molecules25184057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
N-anilinoethylamides are a class of melatoninergic agents with the aniline portion mimicking the indole ring of the natural ligand and the ethylamide chain reproducing that of melatonin. The simplest compound in this class, N-{2-[(3-methoxyphenyl)methylamino]ethyl}acetamide (UCM793), has nanomolar binding affinity for MT1 and MT2 membrane receptors. To explore the effect of chain conformation on receptor binding, a methyl group was inserted on the methylene alpha or beta to the amide nitrogen and conformational equilibria were investigated by NMR spectroscopy and molecular dynamics simulations. Receptor affinity was conserved only for the beta-methyl derivative, which also showed significant stereoselectivity, with the (S) enantiomer being the eutomer. Molecular dynamics simulations, validated by NMR spectroscopy, showed that the beta-methyl group affects the conformational preferences of the ethylamide chain. Docking into the receptor crystal structure provides a rationale for the observed chiral recognition, suggesting that the (S)-beta-methyl group favors the conformation that better fits the receptor binding site.
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Teajaroen W, Phimwapi S, Daduang J, Klaynongsruang S, Tipmanee V, Daduang S. A Role of Newly Found Auxiliary Site in Phospholipase A 1 from Thai Banded Tiger Wasp ( Vespa affinis) in Its Enzymatic Enhancement: In Silico Homology Modeling and Molecular Dynamics Insights. Toxins (Basel) 2020; 12:toxins12080510. [PMID: 32784438 PMCID: PMC7472737 DOI: 10.3390/toxins12080510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
Phospholipase A1 from Thai banded tiger wasp (Vespa affinis) venom also known as Ves a 1 plays an essential role in fatal vespid allergy. Ves a 1 becomes an important therapeutic target for toxin remedy. However, established Ves a 1 structure or a mechanism of Ves a 1 function were not well documented. This circumstance has prevented efficient design of a potential phospholipase A1 inhibitor. In our study, we successfully recruited homology modeling and molecular dynamic (MD) simulation to model Ves a 1 three-dimensional structure. The Ves a 1 structure along with dynamic behaviors were visualized and explained. In addition, we performed molecular docking of Ves a 1 with 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid to assess a possible lipid binding site. Interestingly, molecular docking predicted another lipid binding region apart from its corresponding catalytic site, suggesting an auxiliary role of the alternative site at the Ves a 1 surface. The new molecular mechanism related to the surface lipid binding site (auxiliary site) provided better understanding of how phospholipase A1 structure facilitates its enzymatic function. This auxiliary site, conserved among Hymenoptera species as well as some mammalian lipases, could be a guide for interaction-based design of a novel phospholipase A1 inhibitor.
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Affiliation(s)
- Withan Teajaroen
- Biomedical Sciences Program, Graduate School of Khon Kaen University, Khon Kaen 40002, Thailand;
| | | | - Jureerut Daduang
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Sompong Klaynongsruang
- Protein and Proteomics Research Center for Commercial and Industrial Purposes (ProCCI), Khon Kaen 40002, Thailand;
| | - Varomyalin Tipmanee
- EZ-Mol-Design Laboratory and Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence: (V.T.); (S.D.); Tel.: +66-74-45-1180 (V.T.); +66-43-34-2911 (S.D.)
| | - Sakda Daduang
- Division of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
- Correspondence: (V.T.); (S.D.); Tel.: +66-74-45-1180 (V.T.); +66-43-34-2911 (S.D.)
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