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Hurley MFD, Raddi RM, Pattis JG, Voelz VA. Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge. Phys Chem Chem Phys 2023; 25:32393-32406. [PMID: 38009066 PMCID: PMC10760931 DOI: 10.1039/d3cp02197a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
As part of the SAMPL9 community-wide blind host-guest challenge, we implemented an expanded ensemble workflow to predict absolute binding free energies for 13 small molecules against pillar[6]arene. Notable features of our protocol include consideration of a variety of protonation and enantiomeric states for both host and guests, optimization of alchemical intermediates, and analysis of free energy estimates and their uncertainty using large numbers of simulation replicates performed using distributed computing. Our predictions of absolute binding free energies resulted in a mean absolute error of 2.29 kcal mol-1 and an R2 of 0.54. Overall, results show that expanded ensemble calculations using all-atom molecular dynamics simulations are a valuable and efficient computational tool in predicting absolute binding free energies.
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Affiliation(s)
| | - Robert M Raddi
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
| | - Jason G Pattis
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA.
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Samrat SK, Xu J, Xie X, Gianti E, Chen H, Zou J, Pattis JG, Elokely K, Lee H, Li Z, Klein ML, Shi PY, Zhou J, Li H. Allosteric inhibitors of the main protease of SARS-CoV-2. Antiviral Res 2022; 205:105381. [PMID: 35835291 PMCID: PMC9272661 DOI: 10.1016/j.antiviral.2022.105381] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 12/19/2022]
Abstract
SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC50 values similar to that of known covalent inhibitor boceprevir. In a cell-based antiviral assay, these inhibitors can inhibit the virus growth with EC50 in the range of 2-3 μM. The mechanism of action of JMX0286, JMX0301, and JMX0941 were characterized by enzyme kinetics, affinity binding and protein-based substrate digestion. Molecular docking, molecular dynamics (MD) simulations and hydration studies suggested that JMX0286, JMX0301, JMX0941 bind specifically to an allosteric pocket of the SARS-CoV-2 3CL protease. This study provides three potent compounds for further studies.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA.
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Eleonora Gianti
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jason G Pattis
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Khaled Elokely
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences at College of Pharmacy and Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA; BIO5 Institute, The University of Arizona, Tucson, Tucson, AZ, 85721, USA.
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Pattis JG, May ER. Markov State Model of Lassa Virus Nucleoprotein Reveals Large Structural Changes during the Trimer to Monomer Transition. Structure 2020; 28:548-554.e3. [PMID: 32234493 DOI: 10.1016/j.str.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Lassa virus contains a nucleoprotein (NP) that encapsulates the viral genomic RNA forming the ribonucleoprotein (RNP). The NP forms trimers that do not bind RNA, but a structure of only the NP N-terminal domain was co-crystallized with RNA bound. These structures suggested a model in which the NP forms a trimer to keep the RNA gate closed, but then is triggered to undergo a change to a form competent for RNA binding. Here, we investigate the scenario in which the trimer is disrupted to observe whether monomeric NP undergoes significant conformational changes. From multi-microsecond molecular dynamics simulations and an adaptive sampling scheme to sample the conformational space, a Markov state model (MSM) is constructed. The MSM reveals an energetically favorable conformational change, with the most significant changes occurring at the domain interface. These results support a model in which significant structural reorganization of the NP is required for RNP formation.
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Affiliation(s)
- Jason G Pattis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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Pattis JG, Kamal S, Li B, May ER. Catalytic Domains of Phosphodiesterase 5, 6, and 5/6 Chimera Display Differential Dynamics and Ligand Dissociation Energy Barriers. J Phys Chem B 2019; 123:825-835. [PMID: 30616346 PMCID: PMC6502234 DOI: 10.1021/acs.jpcb.8b11370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The enzyme phosphodiesterase 6 (PDE6) is a critical component of the visual signaling pathway and functions to convert cGMP to GMP. The ability of PDE6 to affect cellular cGMP levels leads to deactivation of cGMP-gated ion channels in both rod and cone cells. PDE6 has been difficult to structurally characterize experimentally, though the structures of the closely related PDE5 and a PDE5/6 chimera have been determined by X-ray crystallography. In this work, we employ a computational approach to study the dynamics of the catalytic domains of PDE6, PDE5, and the PDE5/6 chimera. Through equilibrium molecular dynamics (MD) simulations, we identify a region of PDE6 (α12) to be correlated to distal regions of the enzyme (H- and M-loops), which surround the catalytic center. These correlations are not observed for PDE5, and we speculate that these unique motions in PDE6 may relate to the high catalytic efficiency of PDE6 and the requirement for an endogenous inhibitory subunit (Pγ). We further investigate the ligand binding pathways and energetics by enhanced sampling simulations (metadynamics) using the inhibitor sildenafil and GMP. The energetics and pathways of ligand binding are consistent with the high efficiency of PDE6 and further implicate the α12 region as an important regulatory element for PDE6 functional dynamics.
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Affiliation(s)
| | | | - Boyang Li
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
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Pattis JG, May ER. Influence of RNA Binding on the Structure and Dynamics of the Lassa Virus Nucleoprotein. Biophys J 2016; 110:1246-54. [PMID: 27028635 DOI: 10.1016/j.bpj.2016.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/03/2016] [Accepted: 02/02/2016] [Indexed: 12/18/2022] Open
Abstract
Lassa virus protects its viral genome through the formation of a ribonucleoprotein complex in which the nucleoprotein (NP) encapsidates the single-stranded RNA genome. Crystal structures provide evidence that a conformational change must occur to allow for RNA binding. In this study, the mechanism by which NP binds to RNA and how the conformational changes in NP are achieved was investigated with molecular-dynamics simulations. NP was structurally characterized in an open configuration when bound to RNA and in a closed form in the absence of RNA. Our results show that when NP is bound to RNA, the protein is highly dynamic and the system undergoes spontaneous deviations away from the open-state configuration. The equilibrium simulations are supported by free-energy calculations that quantify the influence of RNA on the free-energy surface, which governs NP dynamics. We predict that the globally stable states are qualitatively in agreement with the observed crystal structures, but that both open and closed conformations are thermally accessible in the presence of RNA. The free-energy calculations also provide a prediction of the location of the transition state for RNA binding and identify an intermediate metastable state that exhibits correlated motions that could promote RNA binding.
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Affiliation(s)
- Jason G Pattis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
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