1
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Sun Y, Tang Y, Zhou J, Guo B, Yuan F, Yao B, Yu Y, Li C. Computational design of myoglobin-based carbene transferases for monoterpene derivatization. Biochem Biophys Res Commun 2024; 722:150160. [PMID: 38795453 DOI: 10.1016/j.bbrc.2024.150160] [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: 05/17/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Carbene transfer reactions have emerged as pivotal methodologies for the synthesis of complex molecular architectures. Heme protein-catalyzed carbene transfer reactions have shown promising results on model compounds. However, their limited substrate scope has hindered their application in natural product functionalization. Building upon the foundation of previously published work on a carbene transferase-myoglobin variant, this study employs computer-aided protein engineering to design myoglobin variants, using either docking or the deep learning-based LigandMPNN method. These variants were utilized as catalysts in carbene transfer reactions with a selection of monoterpene substrates featuring C-C double bonds, leading to seven target products. This cost-effective methodology broadens the substrate scope for heme protein-catalyzed reactions, thereby opening novel pathways for research in heme protein functionalities and offering fresh perspectives in the synthesis of bioactive molecules.
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Affiliation(s)
- Yiyang Sun
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China
| | - Yinian Tang
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China
| | - Jing Zhou
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China
| | - Bingchen Guo
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China
| | - Feiyan Yuan
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China.
| | - Bo Yao
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China
| | - Yang Yu
- MIIT Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488 China.
| | - Chun Li
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing, China.
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2
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Seitz C, Ahn SH, Wei H, Kyte M, Cook GM, Krause KL, McCammon JA. Targeting Tuberculosis: Novel Scaffolds for Inhibiting Cytochrome bd Oxidase. J Chem Inf Model 2024. [PMID: 38874541 DOI: 10.1021/acs.jcim.4c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Discovered in the 1920s, cytochrome bd is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first determined in 2016. Only found in prokaryotes, we study it here as a drug target for Mycobacterium tuberculosis (Mtb). Most previous drug discovery efforts toward cytochrome bd have involved analogues of the canonical substrate quinone, known as Aurachin D. Here, we report six new cytochrome bd inhibitor scaffolds determined from a computational screen and confirmed on target activity through in vitro testing. These scaffolds provide new avenues for lead optimization toward Mtb therapeutics.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Surl-Hee Ahn
- Department of Chemical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Haixin Wei
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Matson Kyte
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Kurt L Krause
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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3
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Wujieti B, Feng X, Liu E, Li D, Hao M, Zhou L, Cui W. A theoretical study on the activity and selectivity of IDO/TDO inhibitors. Phys Chem Chem Phys 2024; 26:16747-16764. [PMID: 38818624 DOI: 10.1039/d3cp06036e] [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: 06/01/2024]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO) is a tryptophan (Trp) metabolic enzyme along the kynurenine (NFK) pathway. Under pathological conditions, IDO overexpressed by tumor cells causes depletion of tryptophan and the accumulation of metabolic products, which inhibit the local immune response and form immune escape. Therefore, the suppression of IDO activity is one of the strategies for tumor immunotherapy, and drug design for this target has been the focus of research for more than two decades. Apart from IDO, tryptophan dioxygenase (TDO) of the same family can also catalyze the same biochemical reaction in the human body, but it has different tissue distribution and substrate selectivity from IDO. Based on the principle of drug design with high potency and low cross-reactivity to specific targets, in this subject, the activity and selectivity of IDO and TDO toward small molecular inhibitors were studied from the perspective of thermodynamics and kinetics. The aim was to elucidate the structural requirements for achieving favorable biological activity and selectivity of IDO and TDO inhibitors. Specifically, the interactions of inhibitors from eight families with IDO and TDO were initially investigated through molecular docking and molecular dynamics simulations, and the thermodynamic data for binding of inhibitors were predicted by the molecular mechanics/generalized Born surface area (MM/GBSA) method. Secondly, we explored the free energy landscape of JKloops, the kinetic control element of IDO/TDO, using temperature replica exchange molecular dynamics (T-REMD) simulations and elucidated the connection between the rules of IDO/TDO conformational changes and the inhibitor selectivity mechanism. Furthermore, the binding and dissociation processes of the C1 inhibitor (NLG919) were simulated by the adaptive steering molecular dynamics (ASMD) method, which not only addressed the possible stable, metastable, and transition states for C1 inhibitor-IDO/TDO interactions, but also accurately predicted kinetic data for C1 inhibitor binding and dissociation. In conclusion, we have constructed a complete process from enzyme (IDO/TDO) conformational activation to inhibitor binding/dissociation and used the thermodynamic and kinetic data of each link as clues to verify the control mechanism of IDO/TDO on inhibitor selectivity. This is of great significance for us to understand the design principles of tumor immunotherapy drugs and to avoid drug resistance of immunotherapy drugs.
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Affiliation(s)
- Baerlike Wujieti
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Xinping Feng
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Erxia Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Deqing Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Mingtian Hao
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Luqi Zhou
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
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4
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Lv N, Cao Z. Subpocket-Based Analysis Approach for the Protein Pocket Dynamics. J Chem Theory Comput 2024; 20:4909-4920. [PMID: 38772734 DOI: 10.1021/acs.jctc.4c00476] [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: 05/23/2024]
Abstract
Structural and dynamic characteristics of protein pockets remarkably influence their biological functions and are also important for enzyme engineering and new drug research and development. To date, several softwares have been developed to analyze the dynamic properties of protein pockets. However, due to the complexity and diversity of the pocket information during the kinetic relaxation, further improvement and capacity expansion of current tools are required. Here, we developed a platform software AlphaTraj in which a computational strategy that divides the whole protein pocket into subpockets and examines various properties of the subpockets such as survival time, stability, and correlation was proposed and implemented. We also proposed a scoring function for the subpockets as well as the whole pocket to visualize the quality of the pocket. Furthermore, we implemented automated conformational search functions for ligand docking and ligand optimization. These functions may help us to gain a deep understanding of the dynamic properties of protein pockets and accelerate the protein engineering and the design of inhibitors and small-molecule drugs. The software is freely available at https://github.com/dooo12332/AlphaTraj.git under the GNU GPL license.
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Affiliation(s)
- Nan Lv
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, People's Republic of China
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5
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Bosio S, Bernetti M, Rocchia W, Masetti M. Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin. J Chem Inf Model 2024; 64:4570-4586. [PMID: 38800845 DOI: 10.1021/acs.jcim.4c00420] [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: 05/29/2024]
Abstract
It is nowadays clear that RNA molecules can play active roles in several biological processes. As a result, an increasing number of RNAs are gradually being identified as potentially druggable targets. In particular, noncoding RNAs can adopt highly organized conformations that are suitable for drug binding. However, RNAs are still considered challenging targets due to their complex structural dynamics and high charge density. Thus, elucidating relevant features of drug-RNA binding is fundamental for advancing drug discovery. Here, by using Molecular Dynamics simulations, we compare key features of ligand binding to proteins with those observed in RNA. Specifically, we explore similarities and differences in terms of (i) conformational flexibility of the target, (ii) electrostatic contribution to binding free energy, and (iii) water and ligand dynamics. As a test case, we examine binding of the same ligand, namely riboflavin, to protein and RNA targets, specifically the riboflavin (RF) kinase and flavin mononucleotide (FMN) riboswitch. The FMN riboswitch exhibited enhanced fluctuations and explored a wider conformational space, compared to the protein target, underscoring the importance of RNA flexibility in ligand binding. Conversely, a similar electrostatic contribution to the binding free energy of riboflavin was found. Finally, greater stability of water molecules was observed in the FMN riboswitch compared to the RF kinase, possibly due to the different shape and polarity of the pockets.
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Affiliation(s)
- Stefano Bosio
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Mattia Bernetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
| | - Walter Rocchia
- Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab, Istituto Italiano di Tecnologia, Via Melen - 83, B Block, 16152 Genova, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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6
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Evans D, Sheraz S, Lau A. SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595309. [PMID: 38826232 PMCID: PMC11142162 DOI: 10.1101/2024.05.22.595309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state-of-the-art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedrals angles in transmitting allosteric signals.
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Affiliation(s)
- Daniel Evans
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Samreen Sheraz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Albert Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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7
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Zheng Y, Chen N, Ji Z, Ye Q, Huang P, Chen X, Cui G, Duan L, Zhang F. Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site. J Chem Inf Model 2024; 64:3933-3941. [PMID: 38666964 DOI: 10.1021/acs.jcim.4c00297] [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: 05/14/2024]
Abstract
β-Amyrin synthase (bAS) is a representative plant oxidosqualene cyclase (OSC), and previous studies have identified many functional residues and mutants that can alter its catalytic activity. However, the regulatory mechanism of the active site architecture for adjusting the catalytic activity remains unclear. In this study, we investigate the function of key residues and their regulatory effects on the catalytic activity of Glycyrrhiza glabra β-amyrin synthase (GgbAS) through molecular dynamics simulations and site-directed mutagenesis experiments. We identified the plasticity residues located in two active site regions and explored the interactions between these residues and tetracyclic/pentacyclic intermediates. Based on computational and experimental results, we further categorize these plasticity residues into three types: effector, adjuster, and supporter residues, according to their functions in the catalytic process. This study provides valuable insights into the catalytic mechanism and active site plasticity of GgbAS, offering important references for the rational enzyme engineering of other OSC enzyme.
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Affiliation(s)
- Ying Zheng
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, P. R. China
| | - Nianhang Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Zhongju Ji
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Qiongyu Ye
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Pingping Huang
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Xiaodie Chen
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Guanghong Cui
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing 100700, P. R. China
| | - Lixin Duan
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
| | - Fan Zhang
- Guangzhou University of Chinese Medicine, Guangzhou 510006, P.R. China
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
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8
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Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024; 64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.
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Affiliation(s)
- Hong Ha Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jim Tufts
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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9
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Molina GA, Mendes LFS, Fuzo CA, Costa-Filho AJ, Ward RJ. Mapping secondary substrate-binding sites on the GH11 xylanase from Bacillus subtilis. FEBS Lett 2024; 598:363-376. [PMID: 38253842 DOI: 10.1002/1873-3468.14799] [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: 09/18/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
Xylanases are of significant interest for biomass conversion technologies. Here, we investigated the allosteric regulation of xylan hydrolysis by the Bacillus subtilis GH11 endoxylanase. Molecular dynamics simulations (MDS) in the presence of xylobiose identified binding to the active site and two potential secondary binding sites (SBS) around surface residues Asn54 and Asn151. Arabinoxylan titration experiments with single cysteine mutants N54C and N151C labeled with the thiol-reactive fluorophore acrylodan or the ESR spin-label MTSSL validated the MDS results. Ligand binding at the SBS around Asn54 confirms previous reports, and analysis of the second SBS around N151C discovered in the present study includes residues Val98/Ala192/Ser155/His156. Understanding the regulation of xylanases contributes to efforts for industrial decarbonization and to establishing a sustainable energy matrix.
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Affiliation(s)
- Gustavo Avelar Molina
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Luis Felipe Santos Mendes
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Carlos Alessandro Fuzo
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonio José Costa-Filho
- Department of Physics, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard John Ward
- Department of Chemistry, Faculty of Philosophy, Sciences and Literature at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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10
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Fernandes PMP, Guedes RA, Victor BL, Salvador JAR, Guedes RC. Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome. Front Chem 2024; 11:1322628. [PMID: 38260042 PMCID: PMC10801056 DOI: 10.3389/fchem.2023.1322628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Acquired resistance to drugs that modulate specific protein functions, such as the human proteasome, presents a significant challenge in targeted therapies. This underscores the importance of devising new methodologies to predict drug binding and potential resistance due to specific protein mutations. In this work, we conducted an extensive computational analysis to ascertain the effects of selected mutations (Ala49Thr, Ala50Val, and Cys52Phe) within the active site of the human proteasome. Specifically, we sought to understand how these mutations might disrupt protein function either by altering protein stability or by impeding interactions with a clinical administered drug. Leveraging molecular dynamics simulations and molecular docking calculations, we assessed the effect of these mutations on protein stability and ligand affinity. Notably, our results indicate that the Cys52Phe mutation critically impacts protein-ligand binding, providing valuable insights into potential proteasome inhibitor resistance.
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Affiliation(s)
- Pedro M. P. Fernandes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Bruno L. Victor
- BioISI─Biosystems & Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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11
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Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci 2023; 14:13159-13175. [PMID: 38023523 PMCID: PMC10664576 DOI: 10.1039/d3sc04195f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
Understanding the interaction of ligands with biomolecules is an integral component of drug discovery and development. Challenges for computing thermodynamic and kinetic quantities for pharmaceutically relevant receptor-ligand complexes include the size and flexibility of the ligands, large-scale conformational rearrangements of the receptor, accurate force field parameters, simulation efficiency, and sufficient sampling associated with rare events. Our recently developed multiscale milestoning simulation approach, SEEKR2 (Simulation Enabled Estimation of Kinetic Rates v.2), has demonstrated success in predicting unbinding (koff) kinetics by employing molecular dynamics (MD) simulations in regions closer to the binding site. The MD region is further subdivided into smaller Voronoi tessellations to improve the simulation efficiency and parallelization. To date, all MD simulations are run using general molecular mechanics (MM) force fields. The accuracy of calculations can be further improved by incorporating quantum mechanical (QM) methods into generating system-specific force fields through reparameterizing ligand partial charges in the bound state. The force field reparameterization process modifies the potential energy landscape of the bimolecular complex, enabling a more accurate representation of the intermolecular interactions and polarization effects at the bound state. We present QMrebind (Quantum Mechanical force field reparameterization at the receptor-ligand binding site), an ORCA-based software that facilitates reparameterizing the potential energy function within the phase space representing the bound state in a receptor-ligand complex. With SEEKR2 koff estimates and experimentally determined kinetic rates, we compare and interpret the receptor-ligand unbinding kinetics obtained using the newly reparameterized force fields for model host-guest systems and HSP90-inhibitor complexes. This method provides an opportunity to achieve higher accuracy in predicting receptor-ligand koff rate constants.
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Affiliation(s)
- Anupam Anand Ojha
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Lane William Votapka
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla California 92093 USA
| | - Rommie Elizabeth Amaro
- Department of Molecular Biology, University of California San Diego La Jolla California 92093 USA
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12
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Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry 2023; 62:2982-2996. [PMID: 37788430 PMCID: PMC10774088 DOI: 10.1021/acs.biochem.3c00449] [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: 10/05/2023]
Abstract
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.
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Affiliation(s)
- Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Westley Pawloski
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sonal Agarwal
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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13
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Van Wieren A, Durrant JD, Majumdar S. Computational and experimental analyses of alanine racemase suggest new avenues for developing allosteric small-molecule antibiotics. Drug Dev Res 2023; 84:999-1007. [PMID: 37129190 PMCID: PMC10524904 DOI: 10.1002/ddr.22068] [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: 12/13/2022] [Revised: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
Given the ever-present threat of antibacterial resistance, there is an urgent need to identify new antibacterial drugs and targets. One such target is alanine racemase (Alr), an enzyme required for bacterial cell-wall biosynthesis. Alr is an attractive drug target because it is essential for bacterial survival but is absent in humans. Existing drugs targeting Alr lack specificity and have severe side effects. We here investigate alternative mechanisms of Alr inhibition. Alr functions exclusively as an obligate homodimer, so we probed seven conserved interactions on the dimer interface, distant from the enzymatic active site, to identify possible allosteric influences on activity. Using the Alr from Mycobacterium tuberculosis (MT) as a model, we found that the Lys261/Asp135 salt bridge is critical for catalytic activity. The Lys261Ala mutation completely inactivated the enzyme, and the Asp135Ala mutation reduced catalytic activity eight-fold. Further investigation suggested a potential drug-binding site near the Lys261/Asp135 salt bridge that may be useful for allosteric drug discovery.
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Affiliation(s)
- Arie Van Wieren
- Madia Department of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, PA 15705
- Current address: The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Sudipta Majumdar
- Madia Department of Chemistry, Biochemistry, Physics and Engineering, Indiana University of Pennsylvania, Indiana, PA 15705
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14
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Al-Najjar BO, Saqallah FG. Unlocking the Conformational Changes of P2Y 12: Exploring an Acridinone Compound's Effect on Receptor Activity and Conformation. Molecules 2023; 28:molecules28093878. [PMID: 37175288 PMCID: PMC10180088 DOI: 10.3390/molecules28093878] [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: 04/08/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The P2Y12 receptor is an important member of the purinergic receptor family, known for its critical role in platelet activation and thrombosis. In our previously published study, the acridinone analogue NSC618159 was identified as a potent antagonist of P2Y12. In this work, we investigate the conformational changes in P2Y12 when bound to NSC618159 using molecular dynamics simulations on the receptor's active and inactive forms (4PXZ and 4NTJ, respectively). It was observed that it took the systems about 7 ns and 12 ns to stabilise when NSC618159 was in complex with the active and inactive forms of P2Y12, respectively. Additionally, the binding pocket of the crystal structure 4PXZ expanded from 172.34 Å3 to an average of 661.55 Å3 when bound to NSC618159, with a maximum pocket volume of 820.49 Å3. This expansion was attributed to the pulled away transmembrane (TM) helices and the adoption of a more open conformation by extracellular loop 2 (EL2). In contrast, 4NTJ's pocket volume was mostly consistent and had an average of 1203.82 Å3. Moreover, the RMSF profile of the NSC618159-4PXZ complex showed that residues of TM-I and TM-VII had similar fluctuations to the 4NTJ crystal structure, representing the inactive form of P2Y12. Finally, the energy components and binding affinities of NSC618159 towards the active and inactive forms of P2Y12 were predicted using the MM-PBSA approach. According to the results, the binding affinity of NSC618159 towards both active (4PXZ) and inactive (4NTJ) forms of P2Y12 was found to be almost identical, with values of -43.52 and -41.68 kcal/mol, respectively. In conclusion, our findings provide new insights into the conformational changes of P2Y12 upon binding to NSC618159 and may have implications for the development of new P2Y12 antagonists with enhanced potency and specificity.
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Affiliation(s)
- Belal O Al-Najjar
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 19328, Jordan
- Diagnostic Research Centre, Al-Ahliyya Amman University, Amman 19328, Jordan
| | - Fadi G Saqallah
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 19328, Jordan
- Diagnostic Research Centre, Al-Ahliyya Amman University, Amman 19328, Jordan
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15
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Guerra JVS, Alves LFG, Bourissou D, Lopes-de-Oliveira PS, Szalóki G. Cavity Characterization in Supramolecular Cages. J Chem Inf Model 2023. [PMID: 37129917 DOI: 10.1021/acs.jcim.3c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.
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Affiliation(s)
- João V S Guerra
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - Luiz F G Alves
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - Didier Bourissou
- Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA, UMR 5069), CNRS, Université Toulouse III─Paul Sabatier, 118 Route de Narbonne, Toulouse 31062, Cedex 09, France
| | - Paulo S Lopes-de-Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - György Szalóki
- Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA, UMR 5069), CNRS, Université Toulouse III─Paul Sabatier, 118 Route de Narbonne, Toulouse 31062, Cedex 09, France
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16
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Agrahari AK, Srivastava M, Singh M, Asthana S. SARS-CoV-2 envelope protein attain K ac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface. J Biomol Struct Dyn 2023; 41:15305-15319. [PMID: 36907648 DOI: 10.1080/07391102.2023.2188430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023]
Abstract
Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (Kac63) to mimic the N-terminally placed acetylated lysine Kac5GGKac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position Kac and increase the volume of the pocket. Secondary, after positioning of Kac, a common durable interaction network N140:Kac5; Kac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between Kac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine Kac8 position and its interaction as polar contact with Kac5 were also mimicked by E peptide through interaction network P82:W5; W5:Kac63; W5:W6; W6:Kac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position Kac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana, India
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17
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Rasouli A, Yu Q, Dehghani-Ghahnaviyeh S, Wen PC, Kowal J, Locher KP, Tajkhorshid E. Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Proc Natl Acad Sci U S A 2023; 120:e2213437120. [PMID: 36580587 PMCID: PMC9910490 DOI: 10.1073/pnas.2213437120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/20/2022] [Indexed: 12/31/2022] Open
Abstract
ABCG2 is an ATP-binding cassette (ABC) transporter that extrudes a wide range of xenobiotics and drugs from the cell and contributes to multidrug resistance in cancer cells. Following our recent structural characterization of topotecan-bound ABCG2, here, we present cryo-EM structures of ABCG2 under turnover conditions in complex with a special modulator and slow substrate, tariquidar, in nanodiscs. The structures reveal that similar to topotecan, tariquidar induces two distinct ABCG2 conformations under turnover conditions (turnover-1 and turnover-2). μs-scale molecular dynamics simulations of drug-bound and apo ABCG2 in native-like lipid bilayers, in both topotecan- and tariquidar-bound states, characterize the ligand size as a major determinant of its binding stability. The simulations highlight direct lipid-drug interactions for the smaller topotecan, which exhibits a highly dynamic binding mode. In contrast, the larger tariquidar occupies most of the available volume in the binding pocket, thus leaving little space for lipids to enter the cavity and interact with it. Similarly, when simulating ABCG2 in the apo inward-open state, we also observe spontaneous penetration of phospholipids into the binding cavity. The captured phospholipid diffusion pathway into ABCG2 offers a putative general path to recruit any hydrophobic/amphiphilic substrates directly from the membrane. Our simulations also reveal that ABCG2 rejects cholesterol as a substrate, which is omnipresent in plasma membranes that contain ABCG2. At the same time, cholesterol is found to prohibit the penetration of phospholipids into ABCG2. These molecular findings have direct functional ramifications on ABCG2's function as a transporter.
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Affiliation(s)
- Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Qin Yu
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
| | - Julia Kowal
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Kaspar P. Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, University of Illinois, Urbana, IL61801
- Center for Biophysics and Quantitative Biology University of Illinois, Urbana, IL61801
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18
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Singh AP, Kumar R, Gupta D. Structural insights into the mechanism of human methyltransferase hPRMT4. J Biomol Struct Dyn 2022; 40:10821-10834. [PMID: 34308797 DOI: 10.1080/07391102.2021.1950567] [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: 10/20/2022]
Abstract
Human PRMT4, also known as CARM1, is a type I arginine methyltransferase protein that catalyse the formation of asymmetrical dimethyl arginine product. Structural studies done to date on PRMT4 have shown that the N-terminal region, Rossmann fold and dimerization arm play an important role in PRMT4 activity. Elucidating the functions of these regions in catalysis remains to be explored. Studies have shown the existence of communication pathways in PRMT4, which need further elucidation. The molecular dynamics (MD) simulations performed in this study show differences in different monomeric and dimeric forms of hPRMT4, revealing the role of the N-terminal region, Rossmann fold and dimerization arm. The study shows the conformational changes that occur during dimerization and SAM binding. Our cross-correlation analysis showed a correlation between these regions. Further, we performed PSN and network analysis to establish the existence of communication networks and an allosteric pathway. This study shows the use of MD simulations and network analysis to explore the aspects of PRMT4 dimerization, SAM binding and demonstrates the existence of an allosteric network. These findings shed novel insights into the conformational changes associated with hPRMT4, the mechanism of its dimerization, SAM binding and clues for better inhibitor designs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Pratap Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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19
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Cognate RNA-Binding Modes by the Alternative-Splicing Regulator MBNL1 Inferred from Molecular Dynamics. Int J Mol Sci 2022; 23:ijms232416147. [PMID: 36555788 PMCID: PMC9780971 DOI: 10.3390/ijms232416147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The muscleblind-like protein family (MBNL) plays a prominent role in the regulation of alternative splicing. Consequently, the loss of MBNL function resulting from sequestration by RNA hairpins triggers the development of a neuromuscular disease called myotonic dystrophy (DM). Despite the sequence and structural similarities between the four zinc-finger domains that form MBNL1, recent studies have revealed that the four binding domains have differentiated splicing activity. The dynamic behaviors of MBNL1 ZnFs were simulated using conventional molecular dynamics (cMD) and steered molecular dynamics (sMD) simulations of a structural model of MBNL1 protein to provide insights into the binding selectivity of the four zinc-finger (ZnF) domains toward the GpC steps in YGCY RNA sequence. In accordance with previous studies, our results suggest that both global and local residue fluctuations on each domain have great impacts on triggering alternative splicing, indicating that local motions in RNA-binding domains could modulate their affinity and specificity. In addition, all four ZnF domains provide a distinct RNA-binding environment in terms of structural sampling and mobility that may be involved in the differentiated MBNL1 splicing events reported in the literature.
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20
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Brain permeable curcumin-based pyrazoline analogs: MAO inhibitory and antioxidant activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Hinge Region Mediates Signal Transmission of Luteinizing Hormone and Chorionic Gonadotropin Receptor. Comput Struct Biotechnol J 2022; 20:6503-6511. [DOI: 10.1016/j.csbj.2022.11.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
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22
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Droege DG, Parker AL, Milligan GM, Jenkins R, Johnstone TC. Synthesis and Functionalization of Challenging meso-Substituted Aryl Bis-pocket Porphyrins Accessed via Suzuki-Miyaura Cross-Coupling. J Org Chem 2022; 87:11783-11795. [PMID: 35976791 PMCID: PMC9447288 DOI: 10.1021/acs.joc.2c01538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Herein we report an investigation into the synthesis,
metalation,
and functionalization of bis-pocket porphyrins using the Suzuki–Miyaura
cross-coupling reaction. Steric limitations to accessing bis-pocket
porphyrins were overcome by using this Pd-catalyzed C–C-bond-forming
strategy to introduce steric bulk after macrocyclization:
2,6-dibromo-4-trimethylsilybenzaldehyde was condensed with pyrrole,
and a variety of boronic acids were coupled to the resulting porphyrin
in up to 95% yield. Furthermore, we show that these porphyrins can
be metalated with a variety of metals and sulfonated to create water-soluble
bis-pocket porphyrins.
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Affiliation(s)
- Daniel G Droege
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - A Leila Parker
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Griffin M Milligan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Robert Jenkins
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Timothy C Johnstone
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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23
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Waltenspühl Y, Ehrenmann J, Vacca S, Thom C, Medalia O, Plückthun A. Structural basis for the activation and ligand recognition of the human oxytocin receptor. Nat Commun 2022; 13:4153. [PMID: 35851571 PMCID: PMC9293896 DOI: 10.1038/s41467-022-31325-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/10/2022] [Indexed: 01/19/2023] Open
Abstract
The small cyclic neuropeptide hormone oxytocin (OT) and its cognate receptor play a central role in the regulation of social behaviour and sexual reproduction. Here we report the single-particle cryo-electron microscopy structure of the active oxytocin receptor (OTR) in complex with its cognate ligand oxytocin. Our structure provides high-resolution insights into the OT binding mode, the OTR activation mechanism as well as the subtype specificity within the oxytocin/vasopressin receptor family. Here, Waltenspühl et al. report the cryo-EM structure of active human oxytocin receptor in complex with oxytocin and with a heterotrimeric G protein, providing insights into this hormone system critically involved in the regulation of social behaviour and reproduction.
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Affiliation(s)
- Yann Waltenspühl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,Novo Nordisk A/S, Novo Nordisk Park 1, DK-2760, Måløv, Denmark
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,leadXpro AG, PARK innovAARE, CH-5234, Villigen, Switzerland
| | - Santiago Vacca
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristian Thom
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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24
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Wang L, Wang L, Yan F. Understanding the molecular mechanism of endothelin ETA receptor selecting isopeptides endothelin-1 and -3. Biophys J 2022; 121:2490-2502. [DOI: 10.1016/j.bpj.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/02/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
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25
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Wang J, Wu M, Chen Z, Wu L, Wang T, Cao D, Wang H, Liu S, Xu Y, Li F, Liu J, Chen N, Zhao S, Cheng J, Wang S, Hua T. The unconventional activation of the muscarinic acetylcholine receptor M4R by diverse ligands. Nat Commun 2022; 13:2855. [PMID: 35606397 PMCID: PMC9126879 DOI: 10.1038/s41467-022-30595-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/04/2022] [Indexed: 01/22/2023] Open
Abstract
Muscarinic acetylcholine receptors (mAChRs) respond to the neurotransmitter acetylcholine and play important roles in human nervous system. Muscarinic receptor 4 (M4R) is a promising drug target for treating neurological and mental disorders, such as Alzheimer's disease and schizophrenia. However, the lack of understanding on M4R's activation by subtype selective agonists hinders its therapeutic applications. Here, we report the structural characterization of M4R selective allosteric agonist, compound-110, as well as agonist iperoxo and positive allosteric modulator LY2119620. Our cryo-electron microscopy structures of compound-110, iperoxo or iperoxo-LY2119620 bound M4R-Gi complex reveal their different interaction modes and activation mechanisms of M4R, and the M4R-ip-LY-Gi structure validates the cooperativity between iperoxo and LY2119620 on M4R. Through the comparative structural and pharmacological analysis, compound-110 mostly occupies the allosteric binding pocket with vertical binding pose. Such a binding and activation mode facilitates its allostersic selectivity and agonist profile. In addition, in our schizophrenia-mimic mouse model study, compound-110 shows antipsychotic activity with low extrapyramidal side effects. Thus, this study provides structural insights to develop next-generation antipsychotic drugs selectively targeting on mAChRs subtypes.
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Affiliation(s)
- Jingjing Wang
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Meng Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Zhangcheng Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Tian Wang
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Dongmei Cao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Huan Wang
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Shenhui Liu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Yueming Xu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Fei Li
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Junlin Liu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Na Chen
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.
| | - Sheng Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
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26
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Duan J, Shen DD, Zhao T, Guo S, He X, Yin W, Xu P, Ji Y, Chen LN, Liu J, Zhang H, Liu Q, Shi Y, Cheng X, Jiang H, Eric Xu H, Zhang Y, Xie X, Jiang Y. Molecular basis for allosteric agonism and G protein subtype selectivity of galanin receptors. Nat Commun 2022; 13:1364. [PMID: 35292680 PMCID: PMC8924211 DOI: 10.1038/s41467-022-29072-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide hormones and neuropeptides are complex signaling molecules that predominately function through G protein-coupled receptors (GPCRs). Two unanswered questions remaining in the field of peptide-GPCR signaling systems pertain to the basis for the diverse binding modes of peptide ligands and the specificity of G protein coupling. Here, we report the structures of a neuropeptide, galanin, bound to its receptors, GAL1R and GAL2R, in complex with their primary G protein subtypes Gi and Gq, respectively. The structures reveal a unique binding pose of galanin, which almost ‘lays flat’ on the top of the receptor transmembrane domain pocket in an α-helical conformation, and acts as an ‘allosteric-like’ agonist via a distinct signal transduction cascade. The structures also uncover the important features of intracellular loop 2 (ICL2) that mediate specific interactions with Gq, thus determining the selective coupling of Gq to GAL2R. ICL2 replacement in Gi-coupled GAL1R, μOR, 5-HT1AR, and Gs-coupled β2AR and D1R with that of GAL2R promotes Gq coupling of these receptors, highlighting the dominant roles of ICL2 in Gq selectivity. Together our results provide insights into peptide ligand recognition and allosteric activation of galanin receptors and uncover a general structural element for Gq coupling selectivity. The basis for the diverse peptide-binding modes and the G protein selectivity of peptide GPCRs remains elusive. Here, the authors offer a structural basis for allosteric-like agonism and G protein selectivity of a neuropeptide GPCR, galanin receptor.
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Affiliation(s)
- Jia Duan
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tingting Zhao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shimeng Guo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xinheng He
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wanchao Yin
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Peiyu Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yujie Ji
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Nan Chen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jinyu Liu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Huibing Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qiufeng Liu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Shi
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xi Cheng
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - H Eric Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Yan Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China. .,MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Key Laboratory of Immunity and Inflammatory Diseases of Zhejiang Province, Hangzhou, Zhejiang, China.
| | - Xin Xie
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210046, China. .,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Yi Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Lingang Laboratory, Shanghai, 200031, China.
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27
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Hellemann E, Walker JL, Lesko MA, Chandrashekarappa DG, Schmidt MC, O’Donnell AF, Durrant JD. Novel mutation in hexokinase 2 confers resistance to 2-deoxyglucose by altering protein dynamics. PLoS Comput Biol 2022; 18:e1009929. [PMID: 35235554 PMCID: PMC8920189 DOI: 10.1371/journal.pcbi.1009929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 02/16/2022] [Indexed: 01/16/2023] Open
Abstract
Glucose is central to many biological processes, serving as an energy source and a building block for biosynthesis. After glucose enters the cell, hexokinases convert it to glucose-6-phosphate (Glc-6P) for use in anaerobic fermentation, aerobic oxidative phosphorylation, and the pentose-phosphate pathway. We here describe a genetic screen in Saccharomyces cerevisiae that generated a novel spontaneous mutation in hexokinase-2, hxk2G238V, that confers resistance to the toxic glucose analog 2-deoxyglucose (2DG). Wild-type hexokinases convert 2DG to 2-deoxyglucose-6-phosphate (2DG-6P), but 2DG-6P cannot support downstream glycolysis, resulting in a cellular starvation-like response. Curiously, though the hxk2G238V mutation encodes a loss-of-function allele, the affected amino acid does not interact directly with bound glucose, 2DG, or ATP. Molecular dynamics simulations suggest that Hxk2G238V impedes sugar binding by altering the protein dynamics of the glucose-binding cleft, as well as the large-scale domain-closure motions required for catalysis. These findings shed new light on Hxk2 dynamics and highlight how allosteric changes can influence catalysis, providing new structural insights into this critical regulator of carbohydrate metabolism. Given that hexokinases are upregulated in some cancers and that 2DG and its derivatives have been studied in anti-cancer trials, the present work also provides insights that may apply to cancer biology and drug resistance. Glucose fuels many of the energy-production processes required for normal cell growth. Before glucose can participate in these processes, it must first be chemically modified by proteins called hexokinases. To better understand how hexokinases modify glucose—and how mutations in hexokinase genes might confer drug resistance—we evolved resistance in yeast to a toxic hexokinase-binding molecule called 2DG. We discovered a mutation in the hexokinase gene that confers 2DG resistance and reduces the protein’s ability to modify glucose. Biochemical analyses and computer simulations of the hexokinase protein suggest that the mutation diminishes glucose binding by altering enzyme flexibility. This work shows how cells can evolve resistance to toxins via only modest changes to protein structures. Furthermore, because cancer-cell hexokinases are particularly active, 2DG has been studied as cancer chemotherapy. Thus, the insights this work provides might also apply to cancer biology.
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Affiliation(s)
- Erich Hellemann
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer L. Walker
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (AFO); (JDD)
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28
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Abstract
The parasitic trypanosomatids cause lethal and debilitating diseases, the leishmaniases, Chagas disease, and the African trypanosomiases, with major impacts on human and animal health. Sustained research has borne fruit by assisting efforts to reduce the burden of disease and by improving our understanding of fundamental molecular and cell biology. But where has the research primarily been conducted, and which research areas have received the most attention? These questions are addressed below using publication and citation data from the past few decades.
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Affiliation(s)
- David Horn
- The Wellcome Trust Centre for Anti-Infectives Research, Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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29
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Nie Z, Liu P, Wang Y, Guo X, Tan Z, Shen J, Tang Z, Lin J, Sun J, Zheng P, Zhu L. Directed Evolution and Rational Design of Mechanosensitive Channel MscCG2 for Improved Glutamate Excretion Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15660-15669. [PMID: 34928605 DOI: 10.1021/acs.jafc.1c07086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mechanosensitive amino acid exporters have drawn increasing attention due to their important roles in extracellular accumulation of the target amino acids. Protein engineering is a powerful approach to tailor the properties of amino acid exporters and illustrate structure-function relationships. Here we report the first protein engineering effort on the mechanosensitive glutamate exporter MscCG2 from Corynebacterium glutamicum for improved excretion efficiency of glutamate and understanding of the structure-function relationship. MscCG2 was engineered through directed evolution and computer-assisted design with a coupled assay in microtiter plate format. Improved MscCG2 variants were identified with up to 2.5-fold increase in the level of glutamate excretion in the early stage of fermentation and 1.5-fold in the late stage of fermentation under experimental conditions. Furthermore, the identified variants exhibited enhanced efflux of 4-fluoroglutamate (4-FG), an analog of glutamate. Structure analysis employing homology modeling and molecular dynamics (MD) simulation reveal that identified amino acid substitutions enlarge the size of the seven portals on the equator of MscCG2 and expand the narrowest rim of its inner channel, respectively. This study demonstrates the great potential of protein engineering in improving the secretion efficiency of exporters for enhanced bioproduction.
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Affiliation(s)
- Zhihua Nie
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yu Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xuan Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zijian Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jie Shen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Zijing Tang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jianping Lin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Leilei Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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30
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Mo QH, Yan MQ, Zhou XL, Luo Q, Huang XS, Liang CQ. Phloroglucinol derivatives rhotomensones A-G from Rhodomyrtus tomentosa. PHYTOCHEMISTRY 2021; 190:112890. [PMID: 34388480 DOI: 10.1016/j.phytochem.2021.112890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/18/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Undescribed phloroglucinol derivatives, rhotomensones A-G, and a known derivative rhodomyrtosone B, were isolated from the leaves of Rhodomyrtus tomentosa. Rhotomensones A-D and G have unreported structural characteristics, in which rhotomensone A substitutes a benzene ring, rhotomensones B-D are bonded with a 2-methylbutanoyl group, and rhotomensone G has two fewer carbons. The structures of these compounds were determined by NMR spectroscopy, circular dichroism (CD) spectroscopy and X-ray crystallography. The inhibitory activities against α-glucosidase of rhotomensones E and F were evaluated in vitro, with IC50 values of 0.50 ± 0.14 mg/mL and 0.07 ± 0.02 mg/mL. Moreover, rhodomyrtosone B showed significant antibacterial activity against some bacteria, with MIC values ranging from 0.50 to 16.00 μg/mL.
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Affiliation(s)
- Qing-Hu Mo
- College of Pharmacy, Guilin Medical University, Guilin, 541199, PR China
| | - Meng-Qi Yan
- College of Pharmacy, Guilin Medical University, Guilin, 541199, PR China
| | - Xian-Li Zhou
- College of Biotechnology, Guilin Medical University, Guilin, 541199, PR China.
| | - Qin Luo
- Science Experiment Center, Guilin Medical University, Guilin, 541199, PR China
| | - Xi-Shan Huang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences of Guangxi Normal University, Guilin, 541004, PR China.
| | - Cheng-Qin Liang
- College of Pharmacy, Guilin Medical University, Guilin, 541199, PR China.
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31
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Wu X, Chen Y, Wang X, Wei W, Liang Y. Origin of Site Selectivity in Toluene Hydroxylation by Cytochrome P450 Enzymes. J Org Chem 2021; 86:13768-13773. [PMID: 34533309 DOI: 10.1021/acs.joc.1c01295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computational studies are utilized to reveal factors that determine the site selectivity in toluene hydroxylation by cytochrome P450 enzymes (CYPs). The DFT-computed inherent barriers suggest that the priority of product formation is in the order of benzyl alcohol > ortho- ≈ para- > meta-cresol. However, the specific size and shape of the cavities at the active sites of different CYPs dramatically affect the binding orientation of toluene, and thus, the site selectivity can be reordered.
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Affiliation(s)
- Xuan Wu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yu Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Xin Wang
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wanqing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023,China
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32
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Xiong W, Liu B, Shen Y, Jing K, Savage TR. Protein engineering design from directed evolution to de novo synthesis. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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33
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Zoh MG, Bonneville JM, Tutagata J, Laporte F, Fodjo BK, Mouhamadou CS, Sadia CG, McBeath J, Schmitt F, Horstmann S, Reynaud S, David JP. Experimental evolution supports the potential of neonicotinoid-pyrethroid combination for managing insecticide resistance in malaria vectors. Sci Rep 2021; 11:19501. [PMID: 34593941 PMCID: PMC8484614 DOI: 10.1038/s41598-021-99061-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022] Open
Abstract
The introduction of neonicotinoids for managing insecticide resistance in mosquitoes is of high interest as they interact with a biochemical target not previously used in public health. In this concern, Bayer developed a combination of the neonicotinoid clothianidin and the pyrethroid deltamethrin (brand name Fludora Fusion) as a new vector control tool. Although this combination proved to be efficient against pyrethroid-resistant mosquitoes, its ability to prevent the selection of pyrethroid and neonicotinoid resistance alleles was not investigated. In this context, the objective of this work was to study the dynamics and the molecular mechanisms of resistance of An. gambiae to the separated or combined components of this combination. A field-derived An. gambiae line carrying resistance alleles to multiple insecticides at low frequencies was used as a starting for 33 successive generations of controlled selection. Resistance levels to each insecticide and target site mutation frequencies were monitored throughout the selection process. Cross resistance to other public health insecticides were also investigated. RNA-seq was used to compare gene transcription variations and polymorphisms across all lines. This study confirmed the potential of this insecticide combination to impair the selection of resistance as compared to its two separated components. Deltamethrin selection led to the rapid enrichment of the kdr L1014F target-site mutation. Clothianidin selection led to the over-transcription of multiple cytochrome P450s including some showing high homology with those conferring neonicotinoid resistance in other insects. A strong selection signature associated with clothianidin selection was also observed on a P450 gene cluster previously associated with resistance. Within this cluster, the gene CYP6M1 showed the highest selection signature together with a transcription profile supporting a role in clothianidin resistance. Modelling the impact of point mutations selected by clothianidin on CYP6M1 protein structure showed that selection retained a protein variant with a modified active site potentially enhancing clothianidin metabolism. In the context of the recent deployment of neonicotinoids for mosquito control and their frequent usage in agriculture, the present study highlights the benefit of combining them with other insecticides for preventing the selection of resistance and sustaining vector control activities.
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Affiliation(s)
- Marius Gonse Zoh
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jean-Marc Bonneville
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jordan Tutagata
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Frederic Laporte
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Behi K Fodjo
- Centre Suisse de La Recherche Scientifique (CSRS), Abidjan, Côte d'Ivoire
| | | | - Christabelle Gba Sadia
- Centre Suisse de La Recherche Scientifique (CSRS), Abidjan, Côte d'Ivoire.,University of Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Justin McBeath
- Bayer CropScience Ltd, Cambridge Science Park, Cambridge, UK
| | | | | | - Stephane Reynaud
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France
| | - Jean-Philippe David
- Laboratoire d'Ecologie Alpine (LECA) UMR 5553 CNRS Grenoble-Alpes University, Grenoble, France.
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34
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Cai T, Sun H, Qiao J, Zhu L, Zhang F, Zhang J, Tang Z, Wei X, Yang J, Yuan Q, Wang W, Yang X, Chu H, Wang Q, You C, Ma H, Sun Y, Li Y, Li C, Jiang H, Wang Q, Ma Y. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 2021; 373:1523-1527. [PMID: 34554807 DOI: 10.1126/science.abh4049] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Tao Cai
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Hongbing Sun
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jing Qiao
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Leilei Zhu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Fan Zhang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jie Zhang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zijing Tang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xinlei Wei
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiangang Yang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qianqian Yuan
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wangyin Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xue Yang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huanyu Chu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qian Wang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chun You
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongwu Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanxia Sun
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yin Li
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Huifeng Jiang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qinhong Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.,National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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35
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Huang YMM. Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors. Biophys J 2021; 120:3881-3892. [PMID: 34453922 PMCID: PMC8511166 DOI: 10.1016/j.bpj.2021.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 01/09/2023] Open
Abstract
Protein kinases are one of the most important drug targets in the past 10 years. Understanding the inhibitor association processes will profoundly impact new binder designs with preferred binding kinetics. However, after more than a decade of effort, a complete atomistic-level study of kinase inhibitor binding pathways is still lacking. As all kinases share a similar scaffold, we used p38 kinase as a model system to investigate the conformational dynamics and free energy transition of inhibitor binding toward kinases. Two major kinase conformations, Asp-Phe-Gly (DFG)-in and DFG-out, and three types of inhibitors, type I, II, and III, were thoroughly investigated in this work. We performed Brownian dynamics simulations and up to 340 μs Gaussian-accelerated molecular dynamics simulations to capture the inhibitor binding paths and a series of conformational transitions of the p38 kinase from its apo to inhibitor-bound form. Eighteen successful binding trajectories, including all types of inhibitors, are reported herein. Our simulations suggest a mechanism of inhibitor recruitment, a faster ligand association step to a pre-existing DFG-in/DFG-out p38 protein, followed by a slower molecular rearrangement step to adjust the protein-ligand conformation followed by a shift in the energy landscape to reach the final bound state. The ligand association processes also reflect the energetic favor of type I and type II/III inhibitor binding through ATP and allosteric channels, respectively. These different binding routes are directly responsible for the fast (type I binders) and slow (type II/III binders) kinetics of different types of p38 inhibitors. Our findings also echo the recent study of p38 inhibitor dissociation, implying that ligand unbinding could undergo a reverse path of binding, and both processes share similar metastates. This study deepens the understanding of molecular and energetic features of kinase inhibitor-binding processes and will inspire future drug development from a kinetic point of view.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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36
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Huang J, Xu Q, Liu Z, Jain N, Tyagi M, Wei DQ, Hong L. Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. Molecules 2021; 26:5693. [PMID: 34577164 PMCID: PMC8470667 DOI: 10.3390/molecules26185693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA;
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Shenzhen 518055, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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37
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Kumari A, Mittal L, Srivastava M, Pathak DP, Asthana S. Conformational Characterization of the Co-Activator Binding Site Revealed the Mechanism to Achieve the Bioactive State of FXR. Front Mol Biosci 2021; 8:658312. [PMID: 34532338 PMCID: PMC8439381 DOI: 10.3389/fmolb.2021.658312] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
FXR bioactive states are responsible for the regulation of metabolic pathways, which are modulated by agonists and co-activators. The synergy between agonist binding and ‘co-activator’ recruitment is highly conformationally driven. The characterization of conformational dynamics is essential for mechanistic and therapeutic understanding. To shed light on the conformational ensembles, dynamics, and structural determinants that govern the activation process of FXR, molecular dynamic (MD) simulation is employed. Atomic insights into the ligand binding domain (LBD) of FXR revealed significant differences in inter/intra molecular bonding patterns, leading to structural anomalies in different systems of FXR. The sole presence of an agonist or ‘co-activator’ fails to achieve the essential bioactive conformation of FXR. However, the presence of both establishes the bioactive conformation of FXR as they modulate the internal wiring of key residues that coordinate allosteric structural transitions and their activity. We provide a precise description of critical residue positioning during conformational changes that elucidate the synergy between its binding partners to achieve an FXR activation state. Our study offers insights into the associated modulation occurring in FXR at bound and unbound forms. Thereafter, we also identified hot-spots that are critical to arrest the activation mechanism of FXR that would be helpful for the rational design of its agonists.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, India.,Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
| | - Dharam Pal Pathak
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India.,Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), New Delhi, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, India
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Goto Y, Omagari S, Sato R, Yamakado T, Achiwa R, Dey N, Suga K, Vacha M, Saito S. Dynamic Polymer Free Volume Monitored by Single-Molecule Spectroscopy of a Dual Fluorescent Flapping Dopant. J Am Chem Soc 2021; 143:14306-14313. [PMID: 34448563 DOI: 10.1021/jacs.1c06428] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-molecule spectroscopy (SMS) of a dual fluorescent flapping molecular probe (N-FLAP) enabled real-time nanoscale monitoring of local free volume dynamics in polystyrenes. The SMS study was realized by structural improvement of a previously reported flapping molecule by nitrogen substitution, leading to increased brightness (22 times) of the probe. In a polystyrene thin film at the temperature of 5 K above the glass transition, the spectra of a single N-FLAP molecule undergo frequent jumps between short- and long-wavelength forms, the latter one indicating planarization of the molecule in the excited state. The observed spectral jumps were statistically analyzed to reveal the dynamics of the molecular environment. The analysis together with MD and QM/MM calculations show that the excited-state planarization of the flapping probe occurs only when sufficiently large polymer free volume of more than, at least, 280 Å3 is available close to the molecule, and that such free volume lasts for an average of 1.2 s.
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Affiliation(s)
- Yuma Goto
- Department of Materials Science and Engineering, School of Materials and Chemical Engineering, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo 152-8552, Japan
| | - Shun Omagari
- Department of Materials Science and Engineering, School of Materials and Chemical Engineering, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo 152-8552, Japan
| | - Ryuma Sato
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Takuya Yamakado
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryo Achiwa
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nilanjan Dey
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kensuke Suga
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Martin Vacha
- Department of Materials Science and Engineering, School of Materials and Chemical Engineering, Tokyo Institute of Technology, Ookayama 2-12-1-S8-44, Meguro-ku, Tokyo 152-8552, Japan
| | - Shohei Saito
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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Chen J, White A, Nelson DC, Shukla D. Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed. J Biol Chem 2021; 297:101092. [PMID: 34437903 PMCID: PMC8487064 DOI: 10.1016/j.jbc.2021.101092] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/26/2021] [Accepted: 08/16/2021] [Indexed: 01/14/2023] Open
Abstract
Witchweed, or Striga hermonthica, is a parasitic weed that destroys billions of dollars' worth of crops globally every year. Its germination is stimulated by strigolactones exuded by its host plants. Despite high sequence, structure, and ligand-binding site conservation across different plant species, one strigolactone receptor in witchweed, ShHTL7, uniquely exhibits a picomolar EC50 for downstream signaling. Previous biochemical and structural analyses have hypothesized that this unique ligand sensitivity can be attributed to a large binding pocket volume in ShHTL7 resulting in enhanced ability to bind substrates, but additional structural details of the substrate-binding process would help explain its role in modulating the ligand selectivity. Using long-timescale molecular dynamics simulations, we demonstrate that mutations at the entrance of the binding pocket facilitate a more direct ligand-binding pathway to ShHTL7, whereas hydrophobicity at the binding pocket entrance results in a stable “anchored” state. We also demonstrate that several residues on the D-loop of AtD14 stabilize catalytically inactive conformations. Finally, we show that strigolactone selectivity is not modulated by binding pocket volume. Our results indicate that while ligand binding is not the sole modulator of strigolactone receptor selectivity, it is a significant contributing factor. These results can be used to inform the design of selective antagonists for strigolactone receptors in witchweed.
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Affiliation(s)
- Jiming Chen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alexandra White
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - David C Nelson
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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40
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Conformational dynamics of androgen receptors bound to agonists and antagonists. Sci Rep 2021; 11:15887. [PMID: 34354111 PMCID: PMC8342701 DOI: 10.1038/s41598-021-94707-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022] Open
Abstract
The androgen receptor (AR) is critical in the progression of prostate cancer (PCa). Small molecule antagonists that bind to the ligand binding domain (LBD) of the AR have been successful in treating PCa. However, the structural basis by which the AR antagonists manifest their therapeutic efficacy remains unclear, due to the lack of detailed structural information of the AR bound to the antagonists. We have performed accelerated molecular dynamics (aMD) simulations of LBDs bound to a set of ligands including a natural substrate (dihydrotestosterone), an agonist (RU59063) and three antagonists (bicalutamide, enzalutamide and apalutamide) as well as in the absence of ligand (apo). We show that the binding of AR antagonists at the substrate binding pocket alter the dynamic fluctuations of H12, thereby disrupting the structural integrity of the agonistic conformation of AR. Two antagonists, enzalutamide and apalutamide, induce considerable structural changes to the agonist conformation of LBD, when bound close to H12 of AR LBD. When the antagonists bind to the pocket with different orientations having close contact with H11, no significant conformational changes were observed, suggesting the AR remains in the functionally activated (agonistic) state. The simulations on a drug resistance mutant F876L bound to enzalutamide demonstrated that the mutation stabilizes the agonistic conformation of AR LBD, which compromises the efficacy of the antagonists. Principal component analysis (PCA) of the structural fluctuations shows that the binding of enzalutamide and apalutamide induce conformational fluctuations in the AR, which are markedly different from those caused by the agonist as well as another antagonist, bicalutamide. These fluctuations could only be observed with the use of aMD.
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41
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Soler J, Paiva P, Ramos MJ, Fernandes PA, Brut M. Unraveling the cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations. Phys Chem Chem Phys 2021; 23:9524-9531. [PMID: 33885101 DOI: 10.1039/d1cp00378j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic GMP-AMP Synthase (cGAS) is activated upon DNA binding and catalyzes the synthesis of 2',3'-cGAMP from GTP and ATP. This cyclic dinucleotide is a messenger that triggers the autoimmune system of eukaryotic cells. In this study, we propose a Molecular Dynamics (MD) investigation of cGAS activation. We notably provide insights into the motion of the activation loop, both from a mechanical point of view and considering its role in the catalysis of cGAMP production. We finally shed light on the reaction resulting in cGAMP synthesis. Two possible catalytic routes (referred to as GTP-ATP and ATP-GTP) are proposed based on the active site occupancy, paving the way toward further exploration of the reaction mechanism.
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Affiliation(s)
- Jordi Soler
- Institute of Computational Chemistry and Catalysis, and Department of Chemistry, University of Girona, Girona, Spain
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42
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Sztain T, Amaro R, McCammon JA. Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J Chem Inf Model 2021; 61:3495-3501. [PMID: 33939913 PMCID: PMC8117783 DOI: 10.1021/acs.jcim.1c00140] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Indexed: 01/09/2023]
Abstract
The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site. These simulations sampled comparable dynamics and pocket volumes to conventional brute force simulations carried out on two orders of magnitude greater timescales.
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Affiliation(s)
| | - Rommie Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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43
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Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst) 2021; 103:103125. [PMID: 33940558 PMCID: PMC8206044 DOI: 10.1016/j.dnarep.2021.103125] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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44
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Evans DJ, Yovanno RA, Rahman S, Cao DW, Beckett MQ, Patel MH, Bandak AF, Lau AY. Finding Druggable Sites in Proteins Using TACTICS. J Chem Inf Model 2021; 61:2897-2910. [PMID: 34096704 DOI: 10.1021/acs.jcim.1c00204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structure-based drug discovery efforts require knowledge of where drug-binding sites are located on target proteins. To address the challenge of finding druggable sites, we developed a machine-learning algorithm called TACTICS (trajectory-based analysis of conformations to identify cryptic sites), which uses an ensemble of molecular structures (such as molecular dynamics simulation data) as input. First, TACTICS uses k-means clustering to select a small number of conformations that represent the overall conformational heterogeneity of the data. Then, TACTICS uses a random forest model to identify potentially bindable residues in each selected conformation, based on protein motion and geometry. Lastly, residues in possible binding pockets are scored using fragment docking. As proof-of-principle, TACTICS was applied to the analysis of simulations of the SARS-CoV-2 main protease and methyltransferase and the Yersinia pestis aryl carrier protein. Our approach recapitulates known small-molecule binding sites and predicts the locations of sites not previously observed in experimentally determined structures. The TACTICS code is available at https://github.com/Albert-Lau-Lab/tactics_protein_analysis.
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Affiliation(s)
- Daniel J Evans
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - David W Cao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Morgan Q Beckett
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Milan H Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Afif F Bandak
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
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45
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Kumari A, Mittal L, Srivastava M, Asthana S. Binding mode characterization of 13b in the monomeric and dimeric states of SARS-CoV-2 main protease using molecular dynamics simulations. J Biomol Struct Dyn 2021; 40:9287-9305. [PMID: 34029506 DOI: 10.1080/07391102.2021.1927844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The main protease, Mpro/3CLpro, plays an essential role in processing polyproteins translated from viral RNA to produce functional viral proteins and therefore serve as an attractive target for discovering COVID-19 therapeutics. The availability of both monomer and dimer crystal bound with a common ligand, '13b' (α-ketoamide inhibitor), opened up opportunities to understand the Mpro mechanism of action. A comparative analysis of both forms of Mpro was carried out to elucidate the binding site architectural differences in the presence and absence of '13b'. Molecular dynamics simulations suggest that the presence of '13b' enhances the stability of Mpro than the unbound APO form. The N- and C- terminals of both the protomers stabilize each other, and making it's interface essential for the active form of Mpro. In comparison to monomer, the relatively high affinity of '13b' is gained in dimer pocket due to the high stability of the pocket by the interaction of S1 residue of chain B with residues F140, E166 and H172 of chain A, which is absent in monomer. The comprehensive essential dynamics, protein structure network analysis and thermodynamic profiling highlight the hot-spots, pivotal in molecular recognition process at protein-ligand and protein-protein interaction levels, cross-validated through computational alanine scanning study. A comparative description of '13b' binding mechanism in both forms illustrates valuable insights into the inhibition mechanism and the selection of critical residues suitable for the structure-based approaches for the identification of more potent Mpro inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
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46
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Sanner MF, Zoghebi K, Hanna S, Mozaffari S, Rahighi S, Tiwari RK, Parang K. Cyclic Peptides as Protein Kinase Inhibitors: Structure-Activity Relationship and Molecular Modeling. J Chem Inf Model 2021; 61:3015-3026. [PMID: 34000187 DOI: 10.1021/acs.jcim.1c00320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Under-expression or overexpression of protein kinases has been shown to be associated with unregulated cell signal transduction in cancer cells. Therefore, there is major interest in designing protein kinase inhibitors as anticancer agents. We have previously reported [WR]5, a peptide containing alternative arginine (R) and tryptophan (W) residues as a non-competitive c-Src tyrosine kinase inhibitor. A number of larger cyclic peptides containing alternative hydrophobic and positively charged residues [WR]x (x = 6-9) and hybrid cyclic-linear peptides, [R6K]W6 and [R5K]W7, containing R and W residues were evaluated for their protein kinase inhibitory potency. Among all the peptides, cyclic peptide [WR]9 was found to be the most potent tyrosine kinase inhibitor. [WR]9 showed higher inhibitory activity (IC50 = 0.21 μM) than [WR]5, [WR]6, [WR]7, and [WR]8 with IC50 values of 0.81, 0.57, 0.35, and 0.33 μM, respectively, against c-Src kinase as determined by a radioactive assay using [γ-33P]ATP. Consistent with the result above, [WR]9 inhibited other protein kinases such as Abl kinase activity with an IC50 value of 0.35 μM, showing 2.2-fold higher inhibition than [WR]5 (IC50 = 0.79 μM). [WR]9 also inhibited PKCa kinase activity with an IC50 value of 2.86 μM, approximately threefold higher inhibition than [WR]5 (IC50 = 8.52 μM). A similar pattern was observed against Braf, c-Src, Cdk2/cyclin A1, and Lck. [WR]9 exhibited IC50 values of <0.25 μM against Akt1, Alk, and Btk. These data suggest that [WR]9 is consistently more potent than other cyclic peptides with a smaller ring size and hybrid cyclic-linear peptides [R6K]W6 and [R5K]W7 against selected protein kinases. Thus, the presence of R and W residues in the ring, ring size, and the number of amino acids in the structure of the cyclic peptide were found to be critical in protein kinase inhibitory potency. We identified three putative binding pockets through automated blind docking of cyclic peptides [WR](5-9). The most populated pocket is located between the SH2, SH3, and N-lobe domains on the opposite side of the ATP binding site. The second putative pocket is formed by the same domains and located on the ATP binding site side of the protein. Finally, a third pocket was identified between the SH2 and SH3 domains. These results are consistent with the non-competitive nature of the inhibition displayed by these molecules. Molecular dynamics simulations of the protein-peptide complexes indicate that the presence of either [WR]5 or [WR]9 affects the plasticity of the protein and in particular the volume of the ATP binding site pocket in different ways. These results suggest that the second pocket is most likely the site where these peptides bind and offer a plausible rationale for the increased affinity of [WR]9.
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Affiliation(s)
- Michel F Sanner
- The Scripps Research Institute, La Jolla, California 92037, United States
| | - Khalid Zoghebi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States.,Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Samara Hanna
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Saghar Mozaffari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Simin Rahighi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Rakesh K Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, California 92618, United States
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47
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Luo S, Huang K, Zhao X, Cong Y, Zhang JZH, Duan L. Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 M pro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations. NANOSCALE 2021; 13:8313-8332. [PMID: 33900318 DOI: 10.1039/d0nr07833f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading around the world. However, a universally effective treatment regimen has not been developed to date. The main protease (Mpro), a key enzyme of SARS-CoV-2, plays a crucial role in the replication and transcription of this virus in cells and has become the ideal target for rational antiviral drug design. In this study, we performed molecular dynamics simulations three times for these complexes of Mpro (monomeric and dimeric) and nine potential drugs that have a certain effect on the treatment of COVID-19 to explore their binding mechanism. In addition, a total of 12 methods for calculating binding free energy were employed to determine the optimal drug. Ritonavir, Arbidol, and Chloroquine consistently showed an outstanding binding ability to monomeric Mpro under various methods. Ritonavir, Arbidol, and Saquinavir presented the best performance when binding to a dimer, which was independent of the protonated state of Hie41 (protonated at Nε) and Hid41 (protonated at Nδ), and these findings suggest that Chloroquine may not effectively inhibit the activity of dimeric Mproin vivo. Furthermore, three common hot-spot residues of Met165, Hie41, and Gln189 of monomeric Mpro systems dominated the binding of Ritonavir, Arbidol, and Chloroquine. In dimeric Mpro, Gln189, Met165, and Met49 contributed significantly to binding with Ritonavir, Arbidol, and Saquinavir; therefore, Gln189 and Met165 might serve as the focus in the discovery and development of anti-COVID-19 drugs. In addition, the van der Waals interaction played a significant role in the binding process, and the benzene ring of the drugs showed an apparent inhibitory effect on the normal function of Mpro. The binding cavity had great flexibility to accommodate these different drugs. The results would be notably helpful for enabling a detailed understanding of the binding mechanisms for these important drug-Mpro interactions and provide valuable guidance for the design of potent inhibitors.
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Affiliation(s)
- Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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48
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Codony S, Calvó-Tusell C, Valverde E, Osuna S, Morisseau C, Loza MI, Brea J, Pérez C, Rodríguez-Franco MI, Pizarro-Delgado J, Corpas R, Griñán-Ferré C, Pallàs M, Sanfeliu C, Vázquez-Carrera M, Hammock BD, Feixas F, Vázquez S. From the Design to the In Vivo Evaluation of Benzohomoadamantane-Derived Soluble Epoxide Hydrolase Inhibitors for the Treatment of Acute Pancreatitis. J Med Chem 2021; 64:5429-5446. [PMID: 33945278 PMCID: PMC8634379 DOI: 10.1021/acs.jmedchem.0c01601] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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The
pharmacological inhibition of soluble epoxide hydrolase (sEH)
is efficient for the treatment of inflammatory and pain-related diseases.
Numerous potent sEH inhibitors (sEHIs) present adamantyl or phenyl
moieties, such as the clinical candidates AR9281 or EC5026. Herein,
in a new series of sEHIs, these hydrophobic moieties have been merged
in a benzohomoadamantane scaffold. Most of the new sEHIs have excellent
inhibitory activities against sEH. Molecular dynamics simulations
suggested that the addition of an aromatic ring into the adamantane
scaffold produced conformational rearrangements in the enzyme to stabilize
the aromatic ring of the benzohomoadamantane core. A screening cascade
permitted us to select a candidate for an in vivo efficacy study in a murine model of cerulein-induced acute pancreatitis.
The administration of 22 improved the health status of
the animals and reduced pancreatic damage, demonstrating that the
benzohomoadamantane unit is a promising scaffold for the design of
novel sEHIs.
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Affiliation(s)
- Sandra Codony
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Carla Calvó-Tusell
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Elena Valverde
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Sílvia Osuna
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Christophe Morisseau
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis 95616, California, United States
| | - M Isabel Loza
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - José Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica, University of Santiago de Compostela (USC), Santiago de Compostela 15782, Spain
| | - Concepción Pérez
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - María Isabel Rodríguez-Franco
- Institute of Medicinal Chemistry, Spanish National Research Council (CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - Javier Pizarro-Delgado
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, Madrid 28029, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, Esplugues de Llobregat 08950, Spain
| | - Rubén Corpas
- Institute of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain.,CIBER Epidemiology and Public Health (CIBERESP)-Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Christian Griñán-Ferré
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institut de Neurociències, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Mercè Pallàs
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institut de Neurociències, University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
| | - Coral Sanfeliu
- Institute of Biomedical Research of Barcelona (IIBB), CSIC and IDIBAPS, Barcelona 08036, Spain.,CIBER Epidemiology and Public Health (CIBERESP)-Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Manuel Vázquez-Carrera
- Pharmacology Section. Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Diseases (CIBERDEM)-Instituto de Salud Carlos III, Madrid 28029, Spain.,Pediatric Research Institute-Hospital Sant Joan de Déu, Esplugues de Llobregat 08950, Spain
| | - Bruce D Hammock
- Department of Entomology and Nematology and Comprehensive Cancer Center, University of California Davis, One Shields Avenue, Davis 95616, California, United States
| | - Ferran Feixas
- CompBioLab Group, Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, C/ Maria Aurèlia Capmany 69, Girona 17003, Spain
| | - Santiago Vázquez
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Departament de Farmacologia, Toxicologia i Química Terapèutica, Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona 08028, Spain
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49
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Musa MM, Vieille C, Phillips RS. Secondary Alcohol Dehydrogenases from Thermoanaerobacter pseudoethanolicus and Thermoanaerobacter brockii as Robust Catalysts. Chembiochem 2021; 22:1884-1893. [PMID: 33594812 DOI: 10.1002/cbic.202100043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/15/2021] [Indexed: 11/06/2022]
Abstract
Alcohol dehydrogenases (ADHs) are an important type of enzyme that have significant applications as biocatalysts. Secondary ADHs from Thermoanaerobacter pseudoethanolicus (TeSADH) and Thermoanaerobacter brockii (TbSADH) are well-known as robust catalysts. However, like most other ADHs, these enzymes suffer from their high substrate specificities (i. e., limited substrate scope), which to some extent restricts their use as biocatalysts. This minireview discusses recent efforts to expand the substrate scope and tune the enantioselectivity of TeSADH and TbSADH by using site-directed mutagenesis and directed evolution. Various examples of asymmetric synthesis of optically active alcohols using both enzymes are highlighted. Moreover, the unique thermal stability and organic solvent tolerance of these enzymes is illustrated by their concurrent inclusion with other interesting reactions to synthesize optically active alcohols and amines. For instance, TeSADH has been used in quantitative non-stereoselective oxidation of alcohols to deracemize alcohols via cyclic deracemization and in the racemization of enantiopure alcohols to accomplish a bienzymatic dynamic kinetic resolution.
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Affiliation(s)
- Musa M Musa
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Saudi Arabia
| | - Claire Vieille
- Department of Microbiology and Molecular Genetics and, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert S Phillips
- Department of Chemistry and, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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50
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Kim SS, Alves MJ, Gygli P, Otero J, Lindert S. Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex. Curr Comput Aided Drug Des 2021; 17:57-68. [PMID: 31889491 DOI: 10.2174/1573409916666191231113055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Given the diverse roles of cyclin A2 both in cell cycle regulation and in DNA damage response, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. OBJECTIVE Based on cyclin A2's recently discovered role in DNA repair, we hypothesized that small molecule inhibitors that were predicted to bind to both cyclin A2 and CDK2 will be useful as a radiosensitizer of cancer cells. In this study, we used structure-based drug discovery to find inhibitors that target both cyclin A2 and CDK2. METHODS Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme. We then used structure-based virtual screening to find potential dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2-CDK2 function was used for experimental verification. RESULTS Four lead inhibitors of cyclin A2-CDK2 complex have been identified using a relaxed complex scheme virtual screen have been verified in a biochemical luminescence assay of cyclin A2- CDK2 function. Two of the four lead inhibitors had inhibitory concentrations in the nanomolar range. CONCLUSION The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that were specifically designed not to target the cyclin A2-CDK2 protein-protein interface. Overall, our results highlight the potential of combined advanced computational tools and biochemical verification to discover novel binding scaffolds.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
| | - Michele J Alves
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Patrick Gygli
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Jose Otero
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
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