1
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Hasse T, Huang YMM. Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems. J Chem Theory Comput 2024. [PMID: 39085770 DOI: 10.1021/acs.jctc.4c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
This study introduces a novel method named multiple parameter replica exchange Gaussian accelerated molecular dynamics (MP-Rex-GaMD), building on the Gaussian accelerated molecular dynamics (GaMD) algorithm. GaMD enhances sampling and retrieves free energy information for biomolecular systems by adding a harmonic boost potential to smooth the potential energy surface without the need for predefined reaction coordinates. Our innovative approach advances the acceleration power and energetic reweighting accuracy of GaMD by incorporating a replica exchange algorithm that enables the exchange of multiple parameters, including the GaMD boost parameters of force constant and energy threshold, as well as temperature. Applying MP-Rex-GaMD to the three model systems of dialanine, chignolin, and HIV protease, we demonstrate its superior capability over conventional molecular dynamics and GaMD simulations in exploring protein conformations and effectively navigating various biomolecular states across energy barriers. MP-Rex-GaMD allows users to accurately map free energy landscapes through energetic reweighting, capturing the ensemble of biomolecular states from low-energy conformations to rare high-energy transitions within practical computational time scales.
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Affiliation(s)
- Timothy Hasse
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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2
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Liu Y, Wang K, Cao F, Gao N, Li W. Interactions between Inhibitors and 5-Lipoxygenase: Insights from Gaussian Accelerated Molecular Dynamics and Markov State Models. Int J Mol Sci 2024; 25:8295. [PMID: 39125865 PMCID: PMC11311652 DOI: 10.3390/ijms25158295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Inflammation is a protective stress response triggered by external stimuli, with 5-lipoxygenase (5LOX) playing a pivotal role as a potent mediator of the leukotriene (Lts) inflammatory pathway. Nordihydroguaiaretic acid (NDGA) functions as a natural orthosteric inhibitor of 5LOX, while 3-acetyl-11-keto-β-boswellic acid (AKBA) acts as a natural allosteric inhibitor targeting 5LOX. However, the precise mechanisms of inhibition have remained unclear. In this study, Gaussian accelerated molecular dynamics (GaMD) simulation was employed to elucidate the inhibitory mechanisms of NDGA and AKBA on 5LOX. It was found that the orthosteric inhibitor NDGA was tightly bound in the protein's active pocket, occupying the active site and inhibiting the catalytic activity of the 5LOX enzyme through competitive inhibition. The binding of the allosteric inhibitor AKBA induced significant changes at the distal active site, leading to a conformational shift of residues 168-173 from a loop to an α-helix and significant negative correlated motions between residues 285-290 and 375-400, reducing the distance between these segments. In the simulation, the volume of the active cavity in the stable conformation of the protein was reduced, hindering the substrate's entry into the active cavity and, thereby, inhibiting protein activity through allosteric effects. Ultimately, Markov state models (MSM) were used to identify and classify the metastable states of proteins, revealing the transition times between different conformational states. In summary, this study provides theoretical insights into the inhibition mechanisms of 5LOX by AKBA and NDGA, offering new perspectives for the development of novel inhibitors specifically targeting 5LOX, with potential implications for anti-inflammatory drug development.
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Affiliation(s)
- Yuyang Liu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (K.W.)
| | - Kaiyu Wang
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (K.W.)
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Nan Gao
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (K.W.)
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3
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Yang W, Wang J, Zhao L, Chen J. Insights into the Interaction Mechanisms of Peptide and Non-Peptide Inhibitors with MDM2 Using Gaussian-Accelerated Molecular Dynamics Simulations and Deep Learning. Molecules 2024; 29:3377. [PMID: 39064955 PMCID: PMC11279683 DOI: 10.3390/molecules29143377] [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: 06/19/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Inhibiting MDM2-p53 interaction is considered an efficient mode of cancer treatment. In our current study, Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and binding free energy calculations were combined together to probe the binding mechanism of non-peptide inhibitors K23 and 0Y7 and peptide ones PDI6W and PDI to MDM2. The GaMD trajectory-based DL approach successfully identified significant functional domains, predominantly located at the helixes α2 and α2', as well as the β-strands and loops between α2 and α2'. The post-processing analysis of the GaMD simulations indicated that inhibitor binding highly influences the structural flexibility and collective motions of MDM2. Calculations of molecular mechanics-generalized Born surface area (MM-GBSA) and solvated interaction energy (SIE) not only suggest that the ranking of the calculated binding free energies is in agreement with that of the experimental results, but also verify that van der Walls interactions are the primary forces responsible for inhibitor-MDM2 binding. Our findings also indicate that peptide inhibitors yield more interaction contacts with MDM2 compared to non-peptide inhibitors. Principal component analysis (PCA) and free energy landscape (FEL) analysis indicated that the piperidinone inhibitor 0Y7 shows the most pronounced impact on the free energy profiles of MDM2, with the piperidinone inhibitor demonstrating higher fluctuation amplitudes along primary eigenvectors. The hot spots of MDM2 revealed by residue-based free energy estimation provide target sites for drug design toward MDM2. This study is expected to provide useful theoretical aid for the development of selective inhibitors of MDM2 family members.
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Affiliation(s)
- Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (L.Z.)
| | | | | | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (L.Z.)
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Pawnikar S, Magenheimer BS, Joshi K, Munoz EN, Haldane A, Maser RL, Miao Y. Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.06.574465. [PMID: 38260358 PMCID: PMC10802338 DOI: 10.1101/2024.01.06.574465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Polycystin-1 (PC1) is the membrane protein product of the PKD1 gene whose mutation is responsible for 85% of the cases of autosomal dominant polycystic kidney disease (ADPKD). ADPKD is primarily characterized by the formation of renal cysts and potential kidney failure. PC1 is an atypical G protein-coupled receptor (GPCR) consisting of 11 transmembrane helices and an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal (NTF) and membrane-embedded C-terminal (CTF) fragments. Recently, signaling activation of the PC1 CTF was shown to be regulated by a stalk tethered agonist (TA), a distinct mechanism observed in the adhesion GPCR family. A novel allosteric activation pathway was elucidated for the PC1 CTF through a combination of Gaussian accelerated molecular dynamics (GaMD), mutagenesis and cellular signaling experiments. Here, we show that synthetic, soluble peptides with 7 to 21 residues derived from the stalk TA, in particular, peptides including the first 9 residues (p9), 17 residues (p17) and 21 residues (p21) exhibited the ability to re-activate signaling by a stalkless PC1 CTF mutant in cellular assays. To reveal molecular mechanisms of stalk peptide-mediated signaling activation, we have applied a novel Peptide GaMD (Pep-GaMD) algorithm to elucidate binding conformations of selected stalk peptide agonists p9, p17 and p21 to the stalkless PC1 CTF. The simulations revealed multiple specific binding regions of the stalk peptide agonists to the PC1 protein including an "intermediate" bound yet inactive state. Our Pep-GaMD simulation findings were consistent with the cellular assay experimental data. Binding of peptide agonists to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of the PC1 CTF signaling activation mechanism. Using sequence covariation analysis of PC1 homologs, we further showed that the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. Therefore, structural dynamic insights into the mechanisms of PC1 activation by stalk-derived peptide agonists have enabled an in-depth understanding of PC1 signaling. They will form a foundation for development of PC1 as a therapeutic target for the treatment of ADPKD.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Brenda S. Magenheimer
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160
| | - Keya Joshi
- Department of Pharmacology and Computational Medicine Program, University of North Carolina – Chapel Hill, Chapel Hill, NC 27599
| | - Ericka Nevarez Munoz
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
| | - Allan Haldane
- Dept of Physics, and Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA 19122
| | - Robin L. Maser
- Departments of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160
| | - Yinglong Miao
- Department of Pharmacology and Computational Medicine Program, University of North Carolina – Chapel Hill, Chapel Hill, NC 27599
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Chen J, Wang J, Yang W, Zhao L, Zhao J, Hu G. Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning. Molecules 2024; 29:2317. [PMID: 38792177 PMCID: PMC11123822 DOI: 10.3390/molecules29102317] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg2+ with the switch domains. It is concluded that the phosphorylation pY32, pY64, and pY137 tune the activity of KRAS through changing conformational dynamics and interactions of the switch domains. We anticipated that this work could provide theoretical aids for deeply understanding the function of KRAS.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Juan Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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6
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Wang J, Yang W, Zhao L, Wei B, Chen J. Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning. Molecules 2024; 29:1857. [PMID: 38675678 PMCID: PMC11054187 DOI: 10.3390/molecules29081857] [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: 04/03/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members.
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Affiliation(s)
- Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
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7
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Rahman MH, Hegazy L. Mechanism of antagonist ligand binding to REV-ERBα. Sci Rep 2024; 14:8401. [PMID: 38600172 PMCID: PMC11006950 DOI: 10.1038/s41598-024-58945-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
REV-ERBα, a therapeutically promising nuclear hormone receptor, plays a crucial role in regulating various physiological processes such as the circadian clock, inflammation, and metabolism. However, the availability of chemical probes to investigate the pharmacology of this receptor is limited, with SR8278 being the only identified synthetic antagonist. Moreover, no X-ray crystal structures are currently available that demonstrate the binding of REV-ERBα to antagonist ligands. This lack of structural information impedes the development of targeted therapeutics. To address this issue, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to investigate the binding pathway of SR8278 to REV-ERBα. For comparison, we also used GaMD to observe the ligand binding process of STL1267, for which an X-ray structure is available. GaMD simulations successfully captured the binding of both ligands to the receptor's orthosteric site and predicted the ligand binding pathway and important amino acid residues involved in the antagonist SR8278 binding. This study highlights the effectiveness of GaMD in investigating protein-ligand interactions, particularly in the context of drug recognition for nuclear hormone receptors.
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Affiliation(s)
- Mohammad Homaidur Rahman
- Center for Clinical Pharmacology, Washington University School of Medicine, University of Health Sciences and Pharmacy, St. Louis, MO, USA
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St. Louis, MO, USA
| | - Lamees Hegazy
- Center for Clinical Pharmacology, Washington University School of Medicine, University of Health Sciences and Pharmacy, St. Louis, MO, USA.
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St. Louis, MO, USA.
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8
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Bao H, Wang W, Sun H, Chen J. The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes. J Biomol Struct Dyn 2024; 42:3363-3381. [PMID: 37216340 DOI: 10.1080/07391102.2023.2213355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Point mutations play a vital role in the conformational transformation of HRAS. In this work, Gaussian accelerated molecular dynamics (GaMD) simulations followed by constructions of free energy landscapes (FELs) were adopted to explore the effect of mutations D33K, A59T and L120A on conformation states of the GDP-bound HRAS. The results from the post-processing analyses on GaMD trajectories suggest that mutations alter the flexibility and motion modes of the switch domains from HRAS. The analyses from FELs show that mutations induce more disordered states of the switch domains and affect interactions of GDP with HRAS, implying that mutations yield a vital effect on the binding of HRAS to effectors. The GDP-residue interaction network revealed by our current work indicates that salt bridges and hydrogen bonding interactions (HBIs) play key roles in the binding of GDP to HRAS. Furthermore, instability in the interactions of magnesium ions and GDP with the switch SI leads to the extreme disorder of the switch domains. This study is expected to provide the energetic basis and molecular mechanism for further understanding the function of HRAS.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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9
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Shen C, Yin J, Wang M, Yu Z, Xu X, Zhou Z, Hu Y, Xia C, Hu G. Mutations influence the conformational dynamics of the GDP/KRAS complex. J Biomol Struct Dyn 2024:1-14. [PMID: 38529923 DOI: 10.1080/07391102.2024.2331627] [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: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Mutations near allosteric sites can have a significant impact on the function of KRAS. Three specific mutations, K104Q, G12D/K104Q, and G12D/G75A, which are located near allosteric positions, were selected to investigate the molecular mechanisms behind mutation-induced influences on the activity of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations followed by the principal component analysis (PCA) were performed to improve the sampling of conformational states. The results revealed that these mutations significantly alter the structural flexibility, correlated motions, and dynamic behavior of the switch regions that are essential for KRAS binding to effectors or regulators. Furthermore, the mutations have a significant impact on the hydrogen bonding interactions between GDP and the switch regions, as well as on the electrostatic interactions of magnesium ions (Mg2+) with these regions. Our results verified that these mutations strongly influence the binding of KRAS to its effectors or regulators and allosterically regulate the activity. We believe that this work can provide valuable theoretical insights into a deeper understanding of KRAS function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Congcong Shen
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Jie Yin
- Qingyun People's Hospital, Dezhou, China
| | - Min Wang
- Qingyun People's Hospital, Dezhou, China
| | - Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Xin Xu
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Zhongshun Zhou
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Yingshi Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Caijuan Xia
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
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10
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Koirala K, Joshi K, Adediwura V, Wang J, Do H, Miao Y. Accelerating Molecular Dynamics Simulations for Drug Discovery. Methods Mol Biol 2024; 2714:187-202. [PMID: 37676600 DOI: 10.1007/978-1-0716-3441-7_11] [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] [Indexed: 09/08/2023]
Abstract
Accurate prediction of ligand binding thermodynamics and kinetics is crucial in drug design. However, it remains challenging for conventional molecular dynamics (MD) simulations due to sampling issues. Gaussian accelerated MD (GaMD) is an enhanced sampling method that adds a harmonic boost to overcome energy barriers, which has demonstrated significant benefits in exploring protein-ligand interactions. Especially, the ligand GaMD (LiGaMD) applies a selective boost potential to the ligand nonbonded potential energy, significantly improving sampling for ligand binding and dissociation. Furthermore, a selective boost potential is applied to the potential of both ligand and protein residues around binding pocket in LiGaMD2 to further increase the sampling of protein-ligand interaction. LiGaMD and LiGaMD2 simulations could capture repetitive ligand binding and unbinding events within microsecond simulations, allowing to simultaneously characterize ligand binding thermodynamics and kinetics, which is expected to greatly facilitate drug design. In this chapter, we provide a brief review of the status of LiGaMD in drug discovery and outline its usage.
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Affiliation(s)
- Kushal Koirala
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Keya Joshi
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Victor Adediwura
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Jinan Wang
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Hung Do
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Yinglong Miao
- Computational Biology Program and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA.
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11
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Chen J, Wang W, Sun H, He W. Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters. Mini Rev Med Chem 2024; 24:1323-1333. [PMID: 38265367 DOI: 10.2174/0113895575252165231122095555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 01/25/2024]
Abstract
Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Weikai He
- School of Science, Shandong Jiaotong University, Jinan-250357, China
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12
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Adediwura VA, Miao Y. Mechanistic Insights into Peptide Binding and Deactivation of an Adhesion G Protein-Coupled Receptor. Molecules 2023; 29:164. [PMID: 38202747 PMCID: PMC10780249 DOI: 10.3390/molecules29010164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Adhesion G protein-coupled receptors (ADGRGs) play critical roles in the reproductive, neurological, cardiovascular, and endocrine systems. In particular, ADGRG2 plays a significant role in Ewing sarcoma cell proliferation, parathyroid cell function, and male fertility. In 2022, a cryo-EM structure was reported for the active ADGRG2 bound by an optimized peptide agonist IP15 and the Gs protein. The IP15 peptide agonist was also modified to antagonists 4PH-E and 4PH-D with mutations of the 4PH residue to Glu and Asp, respectively. However, experimental structures of inactive antagonist-bound ADGRs remain to be resolved, and the activation mechanism of ADGRs such as ADGRG2 is poorly understood. Here, we applied Gaussian accelerated molecular dynamics (GaMD) simulations to probe conformational dynamics of the agonist- and antagonist-bound ADGRG2. By performing GaMD simulations, we were able to identify important low-energy conformations of ADGRG2 in the active, intermediate, and inactive states, as well as explore the binding conformations of each peptide. Moreover, our simulations revealed critical peptide-receptor residue interactions during the deactivation of ADGRG2. In conclusion, through GaMD simulations, we uncovered mechanistic insights into peptide (agonist and antagonist) binding and deactivation of the ADGRG2. These findings will potentially facilitate rational design of new peptide modulators of ADGRG2 and other ADGRs.
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Affiliation(s)
| | - Yinglong Miao
- Department of Pharmacology and Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
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13
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Vögele M, Zhang BW, Kaindl J, Wang L. Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding? J Chem Theory Comput 2023; 19:8414-8422. [PMID: 37943175 DOI: 10.1021/acs.jctc.3c00899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
For an effective drug, strong binding to the target protein is a prerequisite, but it is not enough. To produce a particular functional response, drugs need to either block the proteins' functions or modulate their activities by changing their conformational equilibrium. The binding free energy of a compound to its target is routinely calculated, but the timescales for the protein conformational changes are prohibitively long to be efficiently modeled via physics-based simulations. Thermodynamic principles suggest that the binding free energies of the ligands with different receptor conformations may infer their efficacy. However, this hypothesis has not been thoroughly validated. We present an actionable protocol and a comprehensive study to show that binding thermodynamics provides a strong predictor of the efficacy of a ligand. We apply the absolute binding free energy perturbation method to ligands bound to active and inactive states of eight G protein-coupled receptors and a nuclear receptor and then compare the resulting binding free energies. We find that carefully designed restraints are often necessary to efficiently model the corresponding conformational ensembles for each state. Our method achieves unprecedented performance in classifying ligands as agonists or antagonists across the various investigated receptors, all of which are important drug targets.
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Affiliation(s)
- Martin Vögele
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
| | - Bin W Zhang
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
| | - Jonas Kaindl
- Schrödinger GmbH, Glücksteinallee 25, Mannheim 68163, Germany
| | - Lingle Wang
- Schrödinger, Inc., 1540 Broadway 24th Floor, New York, New York 10036, United States
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14
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Activation/Deactivation Free-Energy Profiles for the β 2-Adrenergic Receptor: Ligand Modes of Action. J Chem Inf Model 2023; 63:6332-6343. [PMID: 37824365 DOI: 10.1021/acs.jcim.3c00805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
We use enhanced-sampling simulations with an effective collective variable to study the activation of the β2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04109 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
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15
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Wu Z, Han Z, Tao L, Sun X, Su J, Hu J, Li C. Dynamic Insights into the Self-Activation Pathway and Allosteric Regulation of the Orphan G-Protein-Coupled Receptor GPR52. J Chem Inf Model 2023; 63:5847-5862. [PMID: 37651308 DOI: 10.1021/acs.jcim.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Within over 800 members of G-protein-coupled receptors, there are numerous orphan receptors whose endogenous ligands are largely unknown, providing many opportunities for novel drug discovery. However, the lack of an in-depth understanding of the intrinsic working mechanism for orphan receptors severely limits the related rational drug design. The G-protein-coupled receptor 52 (GPR52) is a unique orphan receptor that constitutively increases cellular 5'-cyclic adenosine monophosphate (cAMP) levels without binding any exogenous agonists and has been identified as a promising therapeutic target for central nervous system disorders. Although recent structural biology studies have provided snapshots of both active and inactive states of GPR52, the mechanism of the conformational transition between these states remains unclear. Here, an acceptable self-activation pathway for GPR52 was proposed through 6 μs Gaussian accelerated molecular dynamics (GaMD) simulations, in which the receptor spontaneously transitions from the active state to that matching the inactive crystal structure. According to the three intermediate states of the receptor obtained by constructing a reweighted potential of mean force, how the allosteric regulation occurs between the extracellular orthosteric binding pocket and the intracellular G-protein-binding site is revealed. Combined with the independent gradient model, several important microswitch residues and the allosteric communication pathway that directly links the two regions are both identified. Transfer entropy calculations not only reveal the complex allosteric signaling within GPR52 but also confirm the unique role of ECL2 in allosteric regulation, which is mutually validated with the results of GaMD simulations. Overall, this work elucidates the allosteric mechanism of GPR52 at the atomic level, providing the most detailed information to date on the self-activation of the orphan receptor.
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Affiliation(s)
- Zhixiang Wu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Lianci Tao
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xiaohan Sun
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Jingjie Su
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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16
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Liu K, Guo F, Ma Y, Yu X, Fu X, Li W, Han W. Functionalized Fullerene Potentially Inhibits SARS-CoV-2 Infection by Modulating Spike Protein Conformational Changes. Int J Mol Sci 2023; 24:14471. [PMID: 37833919 PMCID: PMC10572755 DOI: 10.3390/ijms241914471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The disease of SARS-CoV-2 has caused considerable morbidity and mortality globally. Spike proteins on the surface of SARS-CoV-2 allow it to bind with human cells, leading to infection. Fullerenes and their derivatives are promising SARS-CoV-2 inhibitors and drug-delivery vehicles. In this study, Gaussian accelerated molecular dynamics simulations and the Markov state model were employed to delve into the inhibitory mechanism of Fullerene-linear-polyglycerol-b-amine sulfate (F-LGPS) on spike proteins. During the study, it was discovered that fullerene derivatives can operate at the interface of the receptor-binding domain (RBD) and the N-terminal domain (NTD), keeping structural domains in a downward conformation. It was also observed that F-LGPS demonstrated superior inhibitory effects on the XBB variant in comparison to the wild-type variant. This study yielded invaluable insights for the potential development of efficient therapeutics targeting the spike protein of SARS-CoV-2.
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Affiliation(s)
- Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
| | - Fangfang Guo
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Yingying Ma
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
| | - Xiangyu Yu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Xueqi Fu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (F.G.); (X.Y.); (X.F.)
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China; (K.L.); (Y.M.)
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17
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Maria-Solano MA, Choi S. Dynamic allosteric networks drive adenosine A 1 receptor activation and G-protein coupling. eLife 2023; 12:RP90773. [PMID: 37656635 PMCID: PMC10473838 DOI: 10.7554/elife.90773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023] Open
Abstract
G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.
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Affiliation(s)
- Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans UniversitySeoulRepublic of Korea
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18
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Lu X, Shi X, Fan J, Li M, Zhang Y, Lu S, Xu G, Chen Z. Mechanistic Elucidation of Activation/Deactivation Signal Transduction within Neurotensin Receptor 1 Triggered by 'Driver Chemical Groups' of Modulators: A Comparative Molecular Dynamics Simulation. Pharmaceutics 2023; 15:2000. [PMID: 37514186 PMCID: PMC10385606 DOI: 10.3390/pharmaceutics15072000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Small-molecule modulators of neurotensin receptor 1 (NTSR1), a class A G-protein-coupled receptor (GPCR), has emerged as promising therapeutic agent for psychiatric disorders and cancer. Interestingly, a chemical group substitution in NTSR1 modulators can launch different types of downstream regulation, highlighting the significance of deciphering the internal fine-tuning mechanism. Here, we conducted a synergistic application of a Gaussian accelerated molecular dynamics simulation, a conventional molecular dynamics simulation, and Markov state models (MSM) to investigate the underlying mechanism of 'driver chemical groups' of modulators triggering inverse signaling. The results indicated that the flexibility of the leucine moiety in NTSR1 agonists contributes to the inward displacement of TM7 through a loosely coupled allosteric pathway, while the rigidity of the adamantane moiety in NTSR1 antagonists leads to unfavorable downward transduction of agonistic signaling. Furthermore, we found that R3226.54, Y3196.51, F3537.42, R1483.32, S3567.45, and S3577.46 may play a key role in inducing the activation of NTSR1. Together, our findings not only highlight the ingenious signal transduction within class A GPCRs but also lay a foundation for the development of targeted drugs harboring different regulatory functions of NTSR1.
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Affiliation(s)
- Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinchao Shi
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuxiang Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guanghuan Xu
- Department of VIP Clinic, Changhai Hospital, Affiliated to Navy Medical University, Shanghai 200433, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai 200433, China
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19
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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife 2023; 12:83477. [PMID: 37248726 DOI: 10.7554/elife.83477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4 muscarinic acetylcholine receptor (M4 mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M4 mAChR. By determining the cryo-electron microscopy structures of the M4 mAChR, bound to a cognate Gi1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.
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Affiliation(s)
- Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Vindhya Nawaratne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Elham Khajehali
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery and Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, United States
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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20
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Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Chem Sci 2023; 14:4681-4696. [PMID: 37181765 PMCID: PMC10171076 DOI: 10.1039/d3sc00166k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Papain-like protease (PLpro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PLpro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PLpro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PLpro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PLpro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PLpro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.
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Affiliation(s)
- Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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21
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. J Chem Inf Model 2023; 63:3105-3117. [PMID: 37161278 DOI: 10.1021/acs.jcim.3c00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present a generally applicable metadynamics protocol for characterizing the activation free-energy profiles of class A G-protein coupled receptors and a proof-of-principle study for the 5HT1A-receptor. The almost universal A100 activation index, which depends on five inter-helix distances, is used as the single collective variable in well-tempered multiple-walker metadynamics simulations. Here, we show free-energy profiles for the serotonin receptor as binary (apo-receptor + G-protein-α-subunit and receptor + ligand) and ternary complexes with two prototypical orthosteric ligands: the full agonist serotonin and the partial agonist aripiprazole. Our results are not only compatible with previously reported experimental and computational data, but they also allow differences between active and inactive conformations to be determined in unprecedented atomic detail, and with respect to the so-called microswitches that have been suggested as determinants of activation, giving insight into their role in the activation mechanism.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Leipzig 04107, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, U.K
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
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22
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Tu G, Xu B, Luo D, Liu J, Liu Z, Chen G, Xue W. Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter. ACS Chem Neurosci 2023; 14:1686-1694. [PMID: 37067527 DOI: 10.1021/acschemneuro.3c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Serotonin transporter (SERT) plays a fundamental role in taking the synaptic cleft serotonin back to the presynaptic neuron. The discovery of allosteric SERT modulators represents the next-generation medication for psychiatric disorders such as depression. Here, based on the cryo-EM structures of ibogaine in complex with SERT in distinct conformations, the multiple functional structures of the transporter bound to serotonin, including outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo and IOholo'), were carefully characterized by induced-fit docking Gaussian-accelerated molecular dynamics (IFD-GaMD) simulation and the free-energy landscape analysis. Further MM/GBSA binding free energy, per-residue contribution, and molecular interaction fingerprint calculations revealed the interaction variations of serotonin with SERT in functional structures, which confirmed the allostery of SERT during serotonin reuptake. Moreover, five unique cryptic allosteric sites, which are druggable and capable of targeting by small molecules, were identified on the characterized multistate structures. These results provide structural and energetic information for the molecular mechanism of serotonin reuptake and will provide opportunities for the development of novel therapeutics based on the identified new allosteric sites on SERT.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Binbin Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jin Liu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Zerong Liu
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Gang Chen
- Central Nervous System Drug Key Laboratory of Sichuan Province, Sichuan Credit Pharmaceutical CO., Ltd., Luzhou 646000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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23
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Li H, Urs NM, Horenstein N. Computational insights into ligand-induced G protein and β-arrestin signaling of the dopamine D1 receptor. J Comput Aided Mol Des 2023; 37:227-244. [PMID: 37060492 DOI: 10.1007/s10822-023-00503-7] [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: 12/03/2022] [Accepted: 03/28/2023] [Indexed: 04/16/2023]
Abstract
The dopamine D1 receptor (D1R), is a class A G protein coupled-receptor (GPCR) which has been a promising drug target for psychiatric and neurological disorders such as Parkinson's disease (PD). Previous studies have suggested that therapeutic effects can be realized by targeting the β-arrestin signaling pathway of dopamine receptors, while overactivation of the G protein-dependent pathways leads to side effects, such as dyskinesias. Therefore, it is highly desirable to develop a D1R ligand that selectively regulates the β-arrestin pathway. Currently, most D1R agonists are signaling-balanced and stimulate both G protein and β-arrestin pathways, with a few reports of G protein biased ligands. However, identification and characterization of β-arrestin biased D1R agonists has been a challenge thus far. In this study, we implemented Gaussian accelerated molecular dynamics (GaMD) simulations to provide valuable computational insights into the possible underlying molecular mechanism of the different signaling properties of two catechol and two non-catechol D1R agonists that are either G protein biased or signaling-balanced. Dynamic network analysis further identified critical residues in the allosteric signaling network of D1R for each ligand at different conformational or binding states. Some of these residues are crucial for G protein or arrestin signals of GPCRs based on previous studies. Finally, we provided a molecular design strategy which can be utilized by medicinal chemists to develop potential β-arrestin biased D1R ligands. The proposed hypotheses are experimentally testable and can guide the development of safer and more effective medications for a variety of CNS disorders.
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Affiliation(s)
- Haoxi Li
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Nikhil M Urs
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Nicole Horenstein
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.
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24
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Hasse T, Zhang Z, Huang YMM. Molecular dynamics study reveals key disruptors of MEIG1-PACRG interaction. Proteins 2023; 91:555-566. [PMID: 36444670 PMCID: PMC10374433 DOI: 10.1002/prot.26449] [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: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/30/2022]
Abstract
Interactions between the meiosis-expressed gene 1 (MEIG1) and Parkin co-regulated gene (PACRG) protein are critical in the formation of mature sperm cells. Targeting either MEIG1 or PACRG protein could be a contraceptive strategy. The W50A and Y68A mutations on MEIG1 are known to interrupt the MEIG1-PACRG interactions resulting in defective sperm cells. However, the details about how the mutants disrupt the protein-protein binding are not clear. In this study, we reveal insights on MEIG1 and PACRG protein dynamics by applying Gaussian-accelerated molecular dynamics (GaMD) simulations and post-GaMD analysis. Our results show that the mutations destabilize the protein-protein interfacial interaction. The effect of the Y68A mutation is more significant than W50A as Y68 forms stronger polar interactions with PACRG. Because both human and mouse models demonstrate similar dynamic properties, the findings from mouse proteins can be applied to the human system. Moreover, we report a potential ligand binding pocket on the MEIG1 and PACRG interaction surface that could be a target for future drug design to inhibit the MEIG1-PACRG interaction. PACRG shows more qualified pockets along the protein-protein interface, implying that it is a better target than MEIG1. Our work provides a fundamental understanding of MEIG1 and PACRG protein dynamics, paving the way for drug discovery in male-based contraception.
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Affiliation(s)
- Timothy Hasse
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, USA
| | - Zhibing Zhang
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
| | - Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan, USA
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25
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Wang J, Do HN, Koirala K, Miao Y. Predicting Biomolecular Binding Kinetics: A Review. J Chem Theory Comput 2023; 19:2135-2148. [PMID: 36989090 DOI: 10.1021/acs.jctc.2c01085] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Biomolecular binding kinetics including the association (kon) and dissociation (koff) rates are critical parameters for therapeutic design of small-molecule drugs, peptides, and antibodies. Notably, the drug molecule residence time or dissociation rate has been shown to correlate with their efficacies better than binding affinities. A wide range of modeling approaches including quantitative structure-kinetic relationship models, Molecular Dynamics simulations, enhanced sampling, and Machine Learning has been developed to explore biomolecular binding and dissociation mechanisms and predict binding kinetic rates. Here, we review recent advances in computational modeling of biomolecular binding kinetics, with an outlook for future improvements.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Hung N Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Kushal Koirala
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
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26
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Han Y, Dawson JRD, DeMarco KR, Rouen KC, Bekker S, Yarov-Yarovoy V, Clancy CE, Xiang YK, Vorobyov I. Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein. Proc Natl Acad Sci U S A 2023; 120:e2215916120. [PMID: 36853938 PMCID: PMC10013855 DOI: 10.1073/pnas.2215916120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/27/2023] [Indexed: 03/01/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest group of membrane receptors for transmembrane signal transduction. Ligand-induced activation of GPCRs triggers G protein activation followed by various signaling cascades. Understanding the structural and energetic determinants of ligand binding to GPCRs and GPCRs to G proteins is crucial to the design of pharmacological treatments targeting specific conformations of these proteins to precisely control their signaling properties. In this study, we focused on interactions of a prototypical GPCR, beta-2 adrenergic receptor (β2AR), with its endogenous agonist, norepinephrine (NE), and the stimulatory G protein (Gs). Using molecular dynamics (MD) simulations, we demonstrated the stabilization of cationic NE, NE(+), binding to β2AR by Gs protein recruitment, in line with experimental observations. We also captured the partial dissociation of the ligand from β2AR and the conformational interconversions of Gs between closed and open conformations in the NE(+)-β2AR-Gs ternary complex while it is still bound to the receptor. The variation of NE(+) binding poses was found to alter Gs α subunit (Gsα) conformational transitions. Our simulations showed that the interdomain movement and the stacking of Gsα α1 and α5 helices are significant for increasing the distance between the Gsα and β2AR, which may indicate a partial dissociation of Gsα The distance increase commences when Gsα is predominantly in an open state and can be triggered by the intracellular loop 3 (ICL3) of β2AR interacting with Gsα, causing conformational changes of the α5 helix. Our results help explain molecular mechanisms of ligand and GPCR-mediated modulation of G protein activation.
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Affiliation(s)
- Yanxiao Han
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - John R. D. Dawson
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
| | - Kyle C. Rouen
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Biophysics Graduate Group, University of California, Davis, CA95616
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Science and Engineering, American River College, Sacramento, CA95841
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA95616
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
| | - Yang K. Xiang
- Department of Pharmacology, University of California, Davis, CA95616
- VA Northern California Health Care System, Mather, CA95655
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA95616
- Department of Pharmacology, University of California, Davis, CA95616
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27
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Chen J, Zeng Q, Wang W, Sun H, Hu G. Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:6118-6132. [PMID: 36440874 DOI: 10.1021/acs.jcim.2c00961] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation of bacterial gene expression at the level of transcription attenuation or translation inhibition. In this study, multiple independent Gaussian-accelerated molecular dynamics simulations were performed to decipher the identification mechanisms of SAM-III (SMK) on ligands SAM, SAH, and EEM. The results reveal that ligand binding highly affects the structural flexibility, internal dynamics, and conformational changes of SAM-III. The dynamic analysis shows that helices P3 and P4 as well as two junctions J23 and J24 of SAM-III are highly susceptible to ligand binding. Analyses of free energy landscapes suggest that ligand binding induces different free energy profiles of SAM-III, which leads to the difference in identification sites of SAM-III on ligands. The information on ligand-nucleotide interactions not only uncovers that the π-π, cation-π, and hydrogen bonding interactions drive identification of SAM-III on the three ligands but also reveals that different electrostatic properties of SAM, SAH, and EEM alter the active sites of SAM-III. Meanwhile, the results also verify that the adenine group of SAM, SAH, and EEM is well recognized by conserved nucleotides G7, A29, U37, A38, and G48. We expect that this study can provide useful information for understanding the applications of SAM-III in chemical, synthetic RNA biology, and biomedical fields.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou253023, China
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28
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Xiaoli A, Yuzhen N, Qiong Y, Yang L, Yao X, Bing Z. Investigating the Dynamic Binding Behavior of PMX53 Cooperating with Allosteric Antagonist NDT9513727 to C5a Anaphylatoxin Chemotactic Receptor 1 through Gaussian Accelerated Molecular Dynamics and Free-Energy Perturbation Simulations. ACS Chem Neurosci 2022; 13:3502-3511. [PMID: 36428153 DOI: 10.1021/acschemneuro.2c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
C5a anaphylatoxin chemotactic receptor 1 (C5aR1) is an important target in anti-inflammatory therapeutics. The cyclic peptide antagonist PMX53 binds to the orthosteric site located in the extracellular vestibule of C5aR1, and the non-peptide antagonist NDT9513727 binds to the allosteric site formed by the middle region of TM3 (trans-membrane helix), TM4, and TM5. We catch a sight of the variational binding mode of PMX53 during the Gaussian accelerated molecular dynamic (GaMD) simulations. In the binary complex of C5aR1 and PMX53, the PMX53 takes a dynamic binding mechanism during the simulation. Namely, the side chain of Arg6 of PMX53 extends to TM6-TM7 (pose 1) or swings to TM5 (pose 2), forming a salt bridge with Glu199. Meanwhile, in the ternary complex of C5aR1 with PMX53 and NDT9513727, the side chain of Arg6 of PMX53 swings to TM5 (pose 2) from extending to TM6-TM7 (pose 1) at the beginning of the GaMD simulation. In subsequent simulation, PMX53 stabilizes in the pose 2 binding mode by forming a stable salt bridge with Glu199. The free-energy perturbation (FEP) calculations demonstrate that pose 1 (ΔGbinding = -10.94 kcal/mol) is more stable in the binary complex and pose 2 (ΔGbinding = -7.91 kcal/mol) is unstable because of highly dynamic TM5. NDT9513727 interacts directly with TM4 and TM5 and stabilizes the hydrophobic stack between the extracellular sides of the two helices. Therefore, pose 2 (ΔGbinding = -16.27 kcal/mol) is notably stable than pose 1 (ΔGbinding = -9.78 kcal/mol) in the ternary complex. The identification of a novel binding mode of PMX53 and the detailed structural information of PMX53 interacting with a receptor obtained by GaMD simulations will be helpful in designing potent antagonists of C5aR1.
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Affiliation(s)
- An Xiaoli
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Niu Yuzhen
- Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing, Yantai 264006, China.,Yantai Zhongke Research Institute of Advanced Materials and Green Chemical Engineering, Yantai 264006, China
| | - Yang Qiong
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Lei Yang
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Zhitong Bing
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
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29
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Chen J, Wang J, Zeng Q, Wang W, Sun H, Wei B. Exploring the deactivation mechanism of human β2 adrenergic receptor by accelerated molecular dynamic simulations. Front Mol Biosci 2022; 9:972463. [PMID: 36111136 PMCID: PMC9468641 DOI: 10.3389/fmolb.2022.972463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The β2 adrenergic receptor (β2AR), one of important members of the G protein coupled receptors (GPCRs), has been suggested as an important target for cardiac and asthma drugs. Two replicas of Gaussian accelerated molecular dynamics (GaMD) simulations are performed to explore the deactivation mechanism of the active β2AR bound by three different substrates, including the agonist (P0G), antagonist (JTZ) and inverse agonist (JRZ). The simulation results indicate that the Gs protein is needed to stabilize the active state of the β2AR. Without the Gs protein, the receptor could transit from the active state toward the inactive state. During the transition process, helix TM6 moves toward TM3 and TM5 in geometric space and TM5 shrinks upwards. The intermediate state is captured during the transition process of the active β2AR toward the inactive one, moreover the changes in hydrophobic interaction networks between helixes TM3, TM5, and TM6 and the formation of a salt bridge between residues Arg3.50 and Glu6.30 drive the transition process. We expect that this finding can provide energetic basis and molecular mechanism for further understanding the function and target roles of the β2AR.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
- *Correspondence: Jianzhong Chen, ; Benzheng Wei,
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao, China
- *Correspondence: Jianzhong Chen, ; Benzheng Wei,
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30
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Copeland M, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B 2022; 126:5810-5820. [PMID: 35895977 PMCID: PMC9773147 DOI: 10.1021/acs.jpcb.2c03765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gaussian accelerated molecular dynamics (GaMD) is a computational technique that provides both unconstrained enhanced sampling and free energy calculations of biomolecules. Here, we present the implementation of GaMD in the OpenMM simulation package and validate it on model systems of alanine dipeptide and RNA folding. For alanine dipeptide, 30 ns GaMD production simulations reproduced free energy profiles of 1000 ns conventional molecular dynamics (cMD) simulations. In addition, GaMD simulations captured the folding pathways of three hyperstable RNA tetraloops (UUCG, GCAA, and CUUG) and binding of the rbt203 ligand to the HIV-1 Tar RNA, both of which involved critical electrostatic interactions such as hydrogen bonding and base stacking. Together with previous implementations, GaMD in OpenMM will allow for wider applications in simulations of proteins, RNA, and other biomolecules.
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Affiliation(s)
- Matthew Copeland
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Hung N. Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Lane Votapka
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
| | - Keya Joshi
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047,To whom correspondence should be addressed:
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31
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Yang Z, Zang Y, Wang H, Kang Y, Zhang J, Li X, Zhang L, Zhang S. Recognition between CD147 and cyclophilin A deciphered by accelerated molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:18905-18914. [PMID: 35913096 DOI: 10.1039/d2cp01975b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
CD147 functions as the receptor of extracellular cyclophilin A (CypA) in various diseases, and CD147-CypA binding ulteriorly underlies the pathological process of various viral infections including HIV-1, SARS, and SARS-CoV-2. Although CyPA has been identified as a key intermediate pro-inflammatory factor, the mechanism by which CD147 cooperates with CypA in the development of the cytokine storm remains largely unknown, and the binding profile of CD147 with CypA remains to be elucidated as well. Here, we prepared three binding models of the CD147-CypA complex, including the active site of CypA severally binding to the groove bound by the Ig1 and Ig2 domains (model-0), P180-G181 (model-1), and P211 (model-2) of CD147, as well as introducing mutations P180A-G181A and P211A individually in each model. All systems were studied using accelerated molecular dynamics simulations and the molecular mechanics generalized Born surface area (MM/GBSA) method. For model-0, CypA bound to the ectodomain of CD147 with the highest binding affinity. Moreover, mutations P180A-G181A of CD147 in model-0 decreased the binding affinity and weakened the dynamic correlation between CD147 and CypA, which resulted in CypA shifting from the initial binding location. Other residue mutations of CD147 did not significantly affect the CD147-CypA binding, as reflected by the energy and structural analyses. Compared with surface plasmon resonance results and nuclear magnetic resonance shift signals, CypA should tend to reciprocally bind to the groove of CD147, and the binding process might be modulated by P180-G181 rather than P211. Besides, residue R201 of CD147 is critical for CD147-CypA binding and needs further experimental verification. These findings further our understanding of the recruitment between CD147 and CypA and its potential role in the development of inflammation and viral infection.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Ying Kang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jianwen Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
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32
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Vora DS, Jaiswal AK, Sundar D. Implementing accelerated dynamics to unravel the effects of high-fidelity Cas9 mutants on target DNA and guide RNA hybrid stability. J Biomol Struct Dyn 2022:1-13. [PMID: 35882048 DOI: 10.1080/07391102.2022.2103032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The clustered regularly interspersed short palindromic repeats (CRISPR) and its associated nuclease (Cas9) offers a unique and easily reprogrammable system for editing eukaryotic genomes. Cas9 is guided to the target by an RNA strand, and precise edits are created by introducing double-stranded breaks. However, nuclease activity of Cas9 is also triggered at other sites other than the target sit, which is a major limitation for various applications. Cas9 variants have been designed to improve the efficacy of the tool by introducing certain mutations. However, the on-target activity of such Cas9 variants is often seen as compromised. Hence, understanding the sub-molecular differences in the variants is essential to elucidate the factors that contribute to efficiency. The study reveals distortions in the PAM-distal regions of the nucleic hybrids as well as changes in the interactions between the Cas9 variants and RNA-DNA hybrid, contributing to the explanation for differences in on-target activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Atul Kumar Jaiswal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, New Delhi, India.,Yardi School of Artificial Intelligence, Indian Institute of Technology (IIT) Delhi, New Delhi, India
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33
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Li M, Wang Y, Fan J, Zhuang H, Liu Y, Ji D, Lu S. Mechanistic Insights into the Long-range Allosteric Regulation of KRAS Via Neurofibromatosis Type 1 (NF1) Scaffold Upon SPRED1 Loading. J Mol Biol 2022; 434:167730. [PMID: 35872068 DOI: 10.1016/j.jmb.2022.167730] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 01/17/2023]
Abstract
Allosteric regulation is the most direct and efficient way of regulating protein function, wherein proteins transmit the perturbations at one site to another distinct functional site. Deciphering the mechanism of allosteric regulation is of vital importance for the comprehension of both physiological and pathological events in vivo as well as the rational allosteric drug design. However, it remains challenging to elucidate dominant allosteric signal transduction pathways, especially for large and multi-component protein machineries where long-range allosteric regulation exits. One of the quintessential examples having long-range allosteric regulation is the ternary complex, SPRED1-RAS-neurofibromin type 1 (NF1, a RAS GTPase-activating protein), in which SPRED1 facilitates RAS-GTP hydrolysis by interacting with NF1 at a distal, allosteric site from the RAS binding site. To address the underlying mechanism, we performed extensive Gaussian accelerated molecular dynamics simulations and Markov state model analysis of KRAS-NF1 complex in the presence and absence of SPRED1. Our findings suggested that SPRED1 loading allosterically enhanced KRAS-NF1 binding, but hindered conformational transformation of the NF1 catalytic center for RAS hydrolysis. Moreover, we unveiled the possible allosteric pathways upon SPRED1 binding through difference contact network analysis. This study not only provided an in-depth mechanistic insight into the allosteric regulation of KRAS by SPRED1, but also shed light on the investigation of long-range allosteric regulation among complex macromolecular systems.
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Affiliation(s)
- Minyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Haiming Zhuang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Dong Ji
- Department of Anesthesiology, Changhai Hospital, Navy Medical University, Shanghai 200433, China.
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.
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34
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In Silico Study of Allosteric Communication Networks in GPCR Signaling Bias. Int J Mol Sci 2022; 23:ijms23147809. [PMID: 35887157 PMCID: PMC9315799 DOI: 10.3390/ijms23147809] [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: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Signaling bias is a promising characteristic of G protein-coupled receptors (GPCRs) as it provides the opportunity to develop more efficacious and safer drugs. This is because biased ligands can avoid the activation of pathways linked to side effects whilst still producing the desired therapeutic effect. In this respect, a deeper understanding of receptor dynamics and implicated allosteric communication networks in signaling bias can accelerate the research on novel biased drug candidates. In this review, we aim to provide an overview of computational methods and techniques for studying allosteric communication and signaling bias in GPCRs. This includes (i) the detection of allosteric communication networks and (ii) the application of network theory for extracting relevant information pipelines and highly communicated sites in GPCRs. We focus on the most recent research and highlight structural insights obtained based on the framework of allosteric communication networks and network theory for GPCR signaling bias.
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35
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Su M, Paknejad N, Zhu L, Wang J, Do HN, Miao Y, Liu W, Hite RK, Huang XY. Structures of β 1-adrenergic receptor in complex with Gs and ligands of different efficacies. Nat Commun 2022; 13:4095. [PMID: 35835792 PMCID: PMC9283524 DOI: 10.1038/s41467-022-31823-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) receive signals from ligands with different efficacies, and transduce to heterotrimeric G-proteins to generate different degrees of physiological responses. Previous studies revealed how ligands with different efficacies activate GPCRs. Here, we investigate how a GPCR activates G-proteins upon binding ligands with different efficacies. We report the cryo-EM structures of β1-adrenergic receptor (β1-AR) in complex with Gs (GαsGβ1Gγ2) and a partial agonist or a very weak partial agonist, and compare them to the β1-AR-Gs structure in complex with a full agonist. Analyses reveal similar overall complex architecture, with local conformational differences. Cellular functional studies with mutations of β1-AR residues show effects on the cellular signaling from β1-AR to the cAMP response initiated by the three different ligands, with residue-specific functional differences. Biochemical investigations uncover that the intermediate state complex comprising β1-AR and nucleotide-free Gs is more stable when binding a full agonist than a partial agonist. Molecular dynamics simulations support the local conformational flexibilities and different stabilities among the three complexes. These data provide insights into the ligand efficacy in the activation of GPCRs and G-proteins.
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Affiliation(s)
- Minfei Su
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lan Zhu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Hung Nguyen Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Xin-Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA.
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Girame H, Garcia-Borràs M, Feixas F. Changes in Protonation States of In-Pathway Residues can Alter Ligand Binding Pathways Obtained From Spontaneous Binding Molecular Dynamics Simulations. Front Mol Biosci 2022; 9:922361. [PMID: 35860361 PMCID: PMC9289141 DOI: 10.3389/fmolb.2022.922361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022] Open
Abstract
Protein-ligand binding processes often involve changes in protonation states that can be key to recognize and orient the ligand in the binding site. The pathways through which (bio)molecules interplay to attain productively bound complexes are intricate and involve a series of interconnected intermediate and transition states. Molecular dynamics (MD) simulations and enhanced sampling techniques are commonly used to characterize the spontaneous binding of a ligand to its receptor. However, the effect of protonation state changes of in-pathway residues in spontaneous binding MD simulations remained mostly unexplored. Here, we used molecular dynamics simulations to reconstruct the trypsin-benzamidine binding pathway considering different protonation states of His57. This residue is part of the trypsin catalytic triad and is located more than 10 Å away from Asp189, which is responsible for benzamidine binding in the trypsin S1 pocket. Our MD simulations showed that the binding pathways that benzamidine follow to target the S1 binding site are critically dependent on the His57 protonation state. Binding of benzamidine frequently occurs when His57 is protonated in the delta nitrogen while the binding process is significantly less frequent when His57 is positively charged. Constant-pH MD simulations retrieved the equilibrium populations of His57 protonation states at trypsin active pH offering a clearer picture of benzamidine recognition and binding. These results indicate that properly accounting for protonation states of distal residues can be important in spontaneous binding MD simulations.
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Abstract
Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.
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38
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Calvó-Tusell C, Maria-Solano MA, Osuna S, Feixas F. Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase. J Am Chem Soc 2022; 144:7146-7159. [PMID: 35412310 PMCID: PMC9052757 DOI: 10.1021/jacs.1c12629] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Deciphering the molecular
mechanisms of enzymatic allosteric regulation
requires the structural characterization of functional states and
also their time evolution toward the formation of the allosterically
activated ternary complex. The transient nature and usually slow millisecond
time scale interconversion between these functional states hamper
their experimental and computational characterization. Here, we combine
extensive molecular dynamics simulations, enhanced sampling techniques,
and dynamical networks to describe the allosteric activation of imidazole
glycerol phosphate synthase (IGPS) from the substrate-free form to
the active ternary complex. IGPS is a heterodimeric bienzyme complex
whose HisH subunit is responsible for hydrolyzing glutamine and delivering
ammonia for the cyclase activity in HisF. Despite significant advances
in understanding the underlying allosteric mechanism, essential molecular
details of the long-range millisecond allosteric activation of IGPS
remain hidden. Without using a priori information
of the active state, our simulations uncover how IGPS, with the allosteric
effector bound in HisF, spontaneously captures glutamine in a catalytically
inactive HisH conformation, subsequently attains a closed HisF:HisH
interface, and finally forms the oxyanion hole in HisH for efficient
glutamine hydrolysis. We show that the combined effector and substrate
binding dramatically decreases the conformational barrier associated
with oxyanion hole formation, in line with the experimentally observed
4500-fold activity increase in glutamine hydrolysis. The allosteric
activation is controlled by correlated time-evolving dynamic networks
connecting the effector and substrate binding sites. This computational
strategy tailored to describe millisecond events can be used to rationalize
the effect of mutations on the allosteric regulation and guide IGPS
engineering efforts.
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Affiliation(s)
- Carla Calvó-Tusell
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Miguel A Maria-Solano
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, 03760 Seoul, Republic of Korea
| | - Sílvia Osuna
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Ferran Feixas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
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Pawnikar S, Miao Y. Mechanism of Peptide Agonist Binding in CXCR4 Chemokine Receptor. Front Mol Biosci 2022; 9:821055. [PMID: 35359589 PMCID: PMC8963245 DOI: 10.3389/fmolb.2022.821055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/14/2022] [Indexed: 01/07/2023] Open
Abstract
Chemokine receptors are key G-protein-coupled receptors (GPCRs) that control cell migration in immune system responses, development of cardiovascular and central nervous systems, and numerous diseases. In particular, the CXCR4 chemokine receptor promotes metastasis, tumor growth and angiogenesis in cancers. CXCR4 is also used as one of the two co-receptors for T-tropic HIV-1 entry into host cells. Therefore, CXCR4 serves as an important therapeutic target for treating cancers and HIV infection. Apart from the CXCL12 endogenous peptide agonist, previous studies suggested that the first 17 amino acids of CXCL12 are sufficient to activate CXCR4. Two 17-residue peptides with positions 1-4 mutated to RSVM and ASLW functioned as super and partial agonists of CXCR4, respectively. However, the mechanism of peptide agonist binding in CXCR4 remains unclear. Here, we have investigated this mechanism through all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method. The Pep-GaMD simulations have allowed us to explore representative binding conformations of each peptide and identify critical low-energy states of CXCR4 activated by the super versus partial peptide agonists. Our simulations have provided important mechanistic insights into peptide agonist binding in CXCR4, which are expected to facilitate rational design of new peptide modulators of CXCR4 and other chemokine receptors.
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40
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Do HN, Wang J, Bhattarai A, Miao Y. GLOW: A Workflow Integrating Gaussian-Accelerated Molecular Dynamics and Deep Learning for Free Energy Profiling. J Chem Theory Comput 2022; 18:1423-1436. [PMID: 35200019 PMCID: PMC9773012 DOI: 10.1021/acs.jctc.1c01055] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We introduce a Gaussian-accelerated molecular dynamics (GaMD), deep learning (DL), and free energy profiling workflow (GLOW) to predict molecular determinants and map free energy landscapes of biomolecules. All-atom GaMD-enhanced sampling simulations are first performed on biomolecules of interest. Structural contact maps are then calculated from GaMD simulation frames and transformed into images for building DL models using a convolutional neural network. Important structural contacts are further determined from DL models of attention maps of the structural contact gradients, which allow us to identify the system reaction coordinates. Finally, free energy profiles are calculated for the selected reaction coordinates through energetic reweighting of the GaMD simulations. We have also successfully demonstrated GLOW for the characterization of activation and allosteric modulation of a G protein-coupled receptor, using the adenosine A1 receptor (A1AR) as a model system. GLOW findings are highly consistent with previous experimental and computational studies of the A1AR, while also providing further mechanistic insights into the receptor function. In summary, GLOW provides a systematic approach to mapping free energy landscapes of biomolecules. The GLOW workflow and its user manual can be downloaded at http://miaolab.org/GLOW.
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Affiliation(s)
- Hung N. Do
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Jinan Wang
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Apurba Bhattarai
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Yinglong Miao
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047,Corresponding author:
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41
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In Silico Screening for Pesticide Candidates against the Desert Locust Schistocerca gregaria. Life (Basel) 2022; 12:life12030387. [PMID: 35330138 PMCID: PMC8953258 DOI: 10.3390/life12030387] [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: 02/07/2022] [Revised: 02/28/2022] [Accepted: 03/05/2022] [Indexed: 11/26/2022] Open
Abstract
Adipokinetic hormone (AKH) is one of the most important metabolic neuropeptides in insects, with actions similar to glucagon in vertebrates. AKH regulates carbohydrate and fat metabolism by mobilizing trehalose and diacylglycerol into circulation from glycogen and triacylglycerol stores, respectively, in the fat body. The short peptide (8 to 10 amino acids long) exerts its function by binding to a rhodopsin-like G protein-coupled receptor located in the cell membrane of the fat body. The AKH receptor (AKHR) is, thus, a potential target for the development of novel specific (peptide) mimetics to control pest insects, such as locusts, which are feared for their prolific breeding, swarm-forming behavior and voracious appetite. Previously, we proposed a model of the interaction between the three endogenous AKHs of the desert locust, Schistocerca gregaria, and the cognate AKHR (Jackson et al., Peer J. 7, e7514, 2019). In the current study we have performed in silico screening of two databases (NCI Open 2012 library and Zinc20) to identify compounds which may fit the endogenous Schgr-AKH-II binding site on the AKHR of S. gregaria. In all, 354 compounds were found to fit the binding site with glide scores < −8. Using the glide scores and binding energies, 7 docked compounds were selected for molecular dynamic simulation in a phosphatidylcholine membrane. Of these 7 compounds, 4 had binding energies which would allow them to compete with Schgr-AKH-II for the receptor binding site and so are proposed as agonistic ligand candidates. One of the ligands, ZINC000257251537, was tested in a homospecific in vivo biological assay and found to have significant antagonistic activity.
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42
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Madhu MK, Debroy A, Murarka RK. Molecular Insights into Phosphorylation-Induced Allosteric Conformational Changes in a β 2-Adrenergic Receptor. J Phys Chem B 2022; 126:1917-1932. [PMID: 35196859 DOI: 10.1021/acs.jpcb.1c08610] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The large conformational flexibility of G protein-coupled receptors (GPCRs) has been a puzzle in structural and pharmacological studies for the past few decades. Apart from structural rearrangements induced by ligands, enzymatic phosphorylations by GPCR kinases (GRKs) at the carboxy-terminal tail (C-tail) of a GPCR also make conformational alterations to the transmembrane helices and facilitates the binding of one of its transducer proteins named β-arrestin. The phosphorylation-induced conformational transition of the receptor that causes specific binding to β-arrestin but prevents the association of other transducers such as G proteins lacks atomistic understanding and is elusive to experimental studies. Using microseconds of all-atom conventional and Gaussian accelerated molecular dynamics (GaMD) simulations, we investigate the allosteric mechanism of phosphorylation induced-conformational changes in β2-adrenergic receptor, a well-characterized GPCR model system. Free energy profiles reveal that the phosphorylated receptor samples a new conformational state in addition to the canonical active state corroborating with recent nuclear magnetic resonance experimental findings. The new state has a smaller intracellular cavity that is likely to accommodate β-arrestin better than G protein. Using contact map and inter-residue interaction energy calculations, we found the phosphorylated C-tail adheres to the cytosolic surface of the transmembrane domain of the receptor. Transfer entropy calculations show that the C-tail residues drive the correlated motions of TM residues, and the allosteric signal is relayed via several residues at the cytosolic surface. Our results also illustrate how the redistribution of inter-residue nonbonding interaction couples with the allosteric communication from the phosphorylated C-tail to the transmembrane. Atomistic insight into phosphorylation-induced β-arrestin specific conformation is therapeutically important to design drugs with higher efficacy and fewer side effects. Our results, therefore, open novel opportunities to fine-tune β-arrestin bias in GPCR signaling.
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Affiliation(s)
- Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India
| | - Annesha Debroy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India
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43
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Do HN, Haldane A, Levy RM, Miao Y. Unique features of different classes of G-protein-coupled receptors revealed from sequence coevolutionary and structural analysis. Proteins 2022; 90:601-614. [PMID: 34599827 PMCID: PMC8738117 DOI: 10.1002/prot.26256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/03/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and represent the primary targets of about one third of currently marketed drugs. Despite the critical importance, experimental structures have been determined for only a limited portion of GPCRs and functional mechanisms of GPCRs remain poorly understood. Here, we have constructed novel sequence coevolutionary models of the A and B classes of GPCRs and compared them with residue contact frequency maps generated with available experimental structures. Significant portions of structural residue contacts were successfully detected in the sequence-based covariational models. "Exception" residue contacts predicted from sequence coevolutionary models but not available structures added missing links that were important for GPCR activation and allosteric modulation. Moreover, we identified distinct residue contacts involving different sets of functional motifs for GPCR activation, such as the Na+ pocket, CWxP, DRY, PIF, and NPxxY motifs in the class A and the HETx and PxxG motifs in the class B. Finally, we systematically uncovered critical residue contacts tuned by allosteric modulation in the two classes of GPCRs, including those from the activation motifs and particularly the extracellular and intracellular loops in class A GPCRs. These findings provide a promising framework for rational design of ligands to regulate GPCR activation and allosteric modulation.
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Affiliation(s)
- Hung N Do
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047
| | - Allan Haldane
- Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122,Corresponding authors: and
| | - Ronald M Levy
- Department of Chemistry, Center for Biophysics and Computational Biology, Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122
| | - Yinglong Miao
- The Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047,Corresponding authors: and
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44
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Li C, Liu K, Chen S, Han L, Han W. Gaussian Accelerated Molecular Dynamics Simulations Investigation on the Mechanism of Angiotensin-Converting Enzyme (ACE) C-Domain Inhibition by Dipeptides. Foods 2022; 11:foods11030327. [PMID: 35159478 PMCID: PMC8834632 DOI: 10.3390/foods11030327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 02/06/2023] Open
Abstract
Angiotensin-converting enzyme (ACE)-inhibitory peptides extracted from food proteins can lower blood pressure by inhibiting ACE activity. A recent study showed that the inhibitory activity of IY (Ile-Tyr, a dipeptide derived from soybean protein) against ACE was much higher than that of LL (Leu-Leu), although they had similar hydrophobic and predicted activity values. It was difficult to reveal the deep molecular mechanism underlying this phenomenon by traditional experimental methods. The Apo and two complex systems (i.e., ACE–LL and ACE–IY) were therefore subjected to 1 μs long Gaussian accelerated molecular dynamics (GaMD) simulations. The results showed that the binding of IY can cause obvious contraction of the active site of ACE, mainly manifested by a significant lateral shift of α13, α14, and α15. In addition, hinge 2 and hinge 3 were more stable in the ACE–IY system, while these phenomena were not present in the ACE–LL system. Moreover, the α10 of the IY-bound ACE kept an inward state during the simulation progress, which facilitated the ACE to remain closed. However, for the LL-bound ACE, the α10 switched between two outward states. To sum up, our study provides detailed insights into inhibitor-induced conformational changes in ACE that may help in the design of specific inhibitors targeting ACE for the treatment of hypertension.
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45
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Pawnikar S, Bhattarai A, Wang J, Miao Y. Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives. Adv Appl Bioinform Chem 2022; 15:1-19. [PMID: 35023931 PMCID: PMC8747661 DOI: 10.2147/aabc.s247950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/20/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular recognition such as binding of small molecules, nucleic acids, peptides and proteins to their target receptors plays key roles in cellular function and has been targeted for therapeutic drug design. Molecular dynamics (MD) is a computational approach to analyze these binding processes at an atomistic level, which provides valuable understandings of the mechanisms of biomolecular recognition. However, the rather slow biomolecular binding events often present challenges for conventional MD (cMD), due to limited simulation timescales (typically over hundreds of nanoseconds to tens of microseconds). In this regard, enhanced sampling methods, particularly accelerated MD (aMD), have proven useful to bridge the gap and enable all-atom simulations of biomolecular binding events. Here, we will review the recent method developments of Gaussian aMD (GaMD), ligand GaMD (LiGaMD) and peptide GaMD (Pep-GaMD), which have greatly expanded our capabilities to simulate biomolecular binding processes. Spontaneous binding of various biomolecules to their receptors has been successfully simulated by GaMD. Microsecond LiGaMD and Pep-GaMD simulations have captured repetitive binding and dissociation of small-molecule ligands and highly flexible peptides, and thus enabled ligand/peptide binding thermodynamics and kinetics calculations. We will also present relevant application studies in simulations of important drug targets and future perspectives for rational computer-aided drug design.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
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Chen J, Zeng Q, Wang W, Hu Q, Bao H. Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes. RSC Adv 2022; 12:1742-1757. [PMID: 35425180 PMCID: PMC8978876 DOI: 10.1039/d1ra07936k] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode the effect of Q61A, Q61H and Q61L on the activity of KRAS. Dynamics analyses based on MR-GaMD trajectory reveal that motion modes and dynamics behavior of the switch domain in KRAS are heavily affected by the three Q61 mutants. Information of free energy landscapes (FELs) shows that Q61A, Q61H and Q61L induce structural disorder of the switch domain and disturb the activity of KRAS. Analysis of the interaction network uncovers that the decrease in the stability of hydrogen bonding interactions (HBIs) of GTP with residues V29 and D30 induced by Q61A, Q61H and Q61L is responsible for the structural disorder of the switch-I and that in the occupancy of the hydrogen bond between GTP and residue G60 leads to the structural disorder of the switch-II. Thus, the high disorder of the switch domain caused by three current Q61 mutants produces a significant effect on binding of KRAS to its effectors. This work is expected to provide useful information for further understanding function and target roles of KRAS in anti-cancer drug development.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Wei Wang
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingquan Hu
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine Jinan 250355 China
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47
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Challenges and frontiers of computational modelling of biomolecular recognition. QRB DISCOVERY 2022. [DOI: 10.1017/qrd.2022.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Biomolecular recognition including binding of small molecules, peptides and proteins to their target receptors plays a key role in cellular function and has been targeted for therapeutic drug design. However, the high flexibility of biomolecules and slow binding and dissociation processes have presented challenges for computational modelling. Here, we review the challenges and computational approaches developed to characterise biomolecular binding, including molecular docking, molecular dynamics simulations (especially enhanced sampling) and machine learning. Further improvements are still needed in order to accurately and efficiently characterise binding structures, mechanisms, thermodynamics and kinetics of biomolecules in the future.
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48
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Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:325-359. [PMID: 35034722 DOI: 10.1016/bs.apcsb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptors (GPCRs) make up the largest superfamily of integral membrane proteins and play critical signal transduction roles in many physiological processes. Developments in molecular biology, biophysical, biochemical, pharmacological, and computational techniques aimed at these important therapeutic targets are beginning to provide unprecedented details on the structural as well as functional basis of their pleiotropic signaling mediated by G proteins, β arrestins, and other transducers. This pleiotropy presents a pharmacological challenge as the same ligand-receptor interaction can cause a therapeutic effect as well as an undesirable on-target side-effect through different downstream pathways. GPCRs don't function as simple binary on-off switches but as finely tuned shape-shifting machines described by conformational ensembles, where unique subsets of conformations may be responsible for specific signaling cascades. X-ray crystallography and more recently cryo-electron microscopy are providing snapshots of some of these functionally-important receptor conformations bound to ligands and/or transducers, which are being utilized by computational methods to describe the dynamic conformational energy landscape of GPCRs. In this chapter, we review the progress in computational conformational sampling methods based on molecular dynamics and discrete sampling approaches that have been successful in complementing biophysical and biochemical studies on these receptors in terms of their activation mechanisms, allosteric effects, actions of biased ligands, and effects of pathological mutations. Some of the sampled simulation time scales are beginning to approach receptor activation time scales. The list of conformational sampling methods and example uses discussed is not exhaustive but includes representative examples that have pushed the limits of classical molecular dynamics and discrete sampling methods to describe the activation energy landscape of GPCRs.
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Affiliation(s)
- Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States.
| | - Erik Serrano
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
| | - Luis Jaimes Santiago
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
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49
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Wang J, Lan L, Wu X, Xu L, Miao Y. Mechanism of RNA recognition by a Musashi RNA-binding protein. Curr Res Struct Biol 2021; 4:10-20. [PMID: 34988468 PMCID: PMC8695263 DOI: 10.1016/j.crstbi.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/31/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
The Musashi RNA-binding proteins (RBPs) regulate translation of target mRNAs and maintenance of cell stemness and tumorigenesis. Musashi-1 (MSI1), long considered as an intestinal and neural stem cell marker, has been more recently found to be over expressed in many cancers. It has served as an important drug target for treating acute myeloid leukemia and solid tumors such as ovarian, colorectal and bladder cancer. One of the reported binding targets of MSI1 is Numb, a negative regulator of the Notch signaling. However, the dynamic mechanism of Numb RNA binding to MSI1 remains unknown, largely hindering effective drug design targeting this critical interaction. Here, we have performed extensive all-atom microsecond-timescale simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which successfully captured multiple times of spontaneous and highly accurate binding of the Numb RNA from bulk solvent to the MSI1 protein target site. GaMD simulations revealed that Numb RNA binding to MSI1 involved largely induced fit in both the RNA and protein. The simulations also identified important low-energy intermediate conformational states during RNA binding, in which Numb interacted mainly with the β2-β3 loop and C terminus of MSI1. The mechanistic understanding of RNA binding obtained from our GaMD simulations is expected to facilitate rational structure-based drug design targeting MSI1 and other RBPs.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology, University of Kansas, Lawrence, KS, 66047, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Xiaoqing Wu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
- Department of Radiation Oncology, The University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Yinglong Miao
- Center for Computational Biology, University of Kansas, Lawrence, KS, 66047, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
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Chen J, Liu J, Yuan Y, Chen X, Zhang F, Pu X. Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor. J Chem Inf Model 2021; 62:5175-5192. [PMID: 34802238 DOI: 10.1021/acs.jcim.1c01016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
β2AR is an important drug target protein involving many diseases. Biased drugs induce specific signaling and provide additional clinical utility to optimize β2AR-based therapies. However, the biased signaling mechanism has not been elucidated. Motivated by the issue, we chose four agonists with divergent bias (balanced agonist, G-protein-biased agonist, and β-arrestin-biased agonists) and utilized Gaussian accelerated molecular dynamics simulation coupled with a dynamic network to probe the molecular mechanisms of distinct biased activation induced by the structural differences between the four agonists. Our simulations reveal that the G-protein-biased agonist induces an open conformation with the outward shifts of TM6 and TM7 for the intracellular domain, which will be beneficial to couple G protein. In contrast, the β-arrestin-biased agonists regulate an occluded conformation with a slightly outward movement of TM6 and an inward shift of TM7, which should favor β-arrestin signaling. The balanced agonist does not induce an observable outward shift for TM6 but, along with a slight tilt for TM7, leads to an inactive-like conformation. In addition, our results reveal the first time that ICL3 presents specific conformations with different agonists. The G-protein-biased agonist drives ICL3 to open so that the G protein-binding pocket can be available, while the β-arrestin-biased agonists induce ICL3 to form a closed conformation with a stable local α-helix. MM/PBSA analysis further reveals that the hydroxyl groups in the resorcinol of the G-protein-biased agonist form strong interactions with Y5.38 and S5.42, thus preventing tilting of the TM5 extracellular end. The catechol of the balanced agonist and the β-arrestin-biased ones induces the rearrangement of two hydrophobic residues F6.52 and W6.48. However, different from the balanced agonist, the ethyl substituent of β-arrestin-biased agonists forms additional hydrophobic interactions with W6.48 and F6.51 after the rearrangement, which should contribute to the β-arrestin bias. The shortest pathway analysis further reveals that the three residues Y7.43, N7.45, and N7.49 are crucial for allosterically regulating G-protein-biased signaling, while the two residues W6.48 and F6.44 make an important contribution to regulate β-arrestin-biased signaling. For the balanced agonist NE, the allosteric regulation pathway simultaneously involves the residue associated with G-protein-biased signaling like S5.46 and the residues related to β-arrestin-biased signaling like W6.48 and F6.44, thus producing unbiased signaling. The observations could advance our understanding of the biased activation mechanism on class A GPCRs and provide a useful guideline for the design of biased drugs.
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Affiliation(s)
- Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jiangting Liu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, China
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
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