1
|
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.
Collapse
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
| |
Collapse
|
2
|
Feng Y, Gong C, Zhu J, Liu G, Tang Y, Li W. Unraveling the Ligand-Binding Sites of CYP3A4 by Molecular Dynamics Simulations with Solvent Probes. J Chem Inf Model 2024; 64:3451-3464. [PMID: 38593186 DOI: 10.1021/acs.jcim.4c00089] [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: 04/11/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is one of the most important drug-metabolizing enzymes in the human body and is well known for its complicated, atypical kinetic characteristics. The existence of multiple ligand-binding sites in CYP3A4 has been widely recognized as being capable of interfering with the active pocket through allosteric effects. The identification of ligand-binding sites other than the canonical active site above the heme is especially important for understanding the atypical kinetic characteristics of CYP3A4 and the intriguing association between the ligand and the receptor. In this study, we first employed mixed-solvent molecular dynamics (MixMD) simulations coupled with the online computational predictive tools to explore potential ligand-binding sites in CYP3A4. The MixMD approach demonstrates better performance in dealing with the receptor flexibility compared with other computational tools. From the sites identified by MixMD, we then picked out multiple sites for further exploration using ensemble docking and conventional molecular dynamics (cMD) simulations. Our results indicate that three extra sites are suitable for ligand binding in CYP3A4, including one experimentally confirmed site and two novel sites.
Collapse
Affiliation(s)
- Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Changda Gong
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jieyu Zhu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| |
Collapse
|
3
|
de Santiago-Silva KM, Camargo PG, Carvalho Constant LE, Costa SDS, Frensel GB, Allonso D, Nakazato G, Lima CHDS, Bispo MDLF. Molecular modelling studies and in vitro enzymatic assays identified A 4-(nitrobenzyl)guanidine derivative as inhibitor of SARS-CoV-2 Mpro. Sci Rep 2024; 14:8620. [PMID: 38616188 PMCID: PMC11016540 DOI: 10.1038/s41598-024-59292-0] [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: 12/28/2023] [Accepted: 04/09/2024] [Indexed: 04/16/2024] Open
Abstract
Scientists and researchers have been searching for drugs targeting the main protease (Mpro) of SARS-CoV-2, which is crucial for virus replication. This study employed a virtual screening based on molecular docking to identify benzoylguanidines from an in-house chemical library that can inhibit Mpro on the active site and three allosteric sites. Molecular docking was performed on the LaSMMed Chemical Library using 88 benzoylguanidine compounds. Based on their RMSD values and conserved pose, three potential inhibitors (BZG1, BZG2, and BZG3) were selected. These results indicate that BZG1 and BZG3 may bind to the active site, while BZG2 may bind to allosteric sites. Molecular dynamics data suggest that BZG2 selectively targets allosteric site 3. In vitro tests were performed to measure the proteolytic activity of rMpro. The tests showed that BZG2 has uncompetitive inhibitory activity, with an IC50 value of 77 µM. These findings suggest that benzoylguanidines possess potential as Mpro inhibitors and pave the way towards combating SARS-Cov-2 effectively.
Collapse
Affiliation(s)
- Kaio Maciel de Santiago-Silva
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Priscila Goes Camargo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Larissa Esteves Carvalho Constant
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Stephany da Silva Costa
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Giovanna Barbosa Frensel
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Diego Allonso
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Gerson Nakazato
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Camilo Henrique da Silva Lima
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelle de Lima Ferreira Bispo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil.
| |
Collapse
|
4
|
Utgés JS, MacGowan SA, Ives CM, Barton GJ. Classification of likely functional class for ligand binding sites identified from fragment screening. Commun Biol 2024; 7:320. [PMID: 38480979 PMCID: PMC10937669 DOI: 10.1038/s42003-024-05970-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Fragment screening is used to identify binding sites and leads in drug discovery, but it is often unclear which binding sites are functionally important. Here, data from 37 experiments, and 1309 protein structures binding to 1601 ligands were analysed. A method to group ligands by binding sites is introduced and sites clustered according to profiles of relative solvent accessibility. This identified 293 unique ligand binding sites, grouped into four clusters (C1-4). C1 includes larger, buried, conserved, and population missense-depleted sites, enriched in known functional sites. C4 comprises smaller, accessible, divergent, missense-enriched sites, depleted in functional sites. A site in C1 is 28 times more likely to be functional than one in C4. Seventeen sites, which to the best of our knowledge are novel, in 13 proteins are identified as likely to be functionally important with examples from human tenascin and 5-aminolevulinate synthase highlighted. A multi-layer perceptron, and K-nearest neighbours model are presented to predict cluster labels for ligand binding sites with an accuracy of 96% and 100%, respectively, so allowing functional classification of sites for proteins not in this set. Our findings will be of interest to those studying protein-ligand interactions and developing new drugs or function modulators.
Collapse
Affiliation(s)
- Javier S Utgés
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Stuart A MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Callum M Ives
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Geoffrey J Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
| |
Collapse
|
5
|
Kubra B, Badshah SL, Faisal S, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids. J Biomol Struct Dyn 2023; 41:9103-9120. [PMID: 36404610 DOI: 10.1080/07391102.2022.2140201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/19/2022] [Indexed: 11/22/2022]
Abstract
Since its emergence in 2019, coronavirus infection (COVID-19) has become a global pandemic and killed several million people worldwide. Even though several types of vaccines are available against the COVID-19 virus, SARS-CoV-2, new strains are emerging that pose a constant danger to vaccine effectiveness. In this computational study, we identified and predicted potent allosteric inhibitors of the SARS-CoV-2 main protease (Mpro). Via molecular docking and simulations, more than 100 distinct flavonoids were docked with the allosteric site of Mpro. Docking experiments revealed four top hit compounds (Hesperidin, Schaftoside, Brickellin, and Marein) that bound strongly to the Mpro predicted allosteric site. Simulation analyses further revealed that these continually interacted with the enzyme's allosteric region throughout the simulation time. ADMET and Lipinski drug likenesses were calculated to indicate the therapeutic value of the top four hits: They were non-toxic and exhibited high human intestinal absorption concentrations. These novel allosteric site inhibitors provide a higher chance of drugging SARS-CoV2 Mpro due to the rapid mutation rate of the viral enzyme's active sites. Our findings provide a new avenue for developing novel allosteric inhibitors of SARS-CoV-2 Mpro.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar, Pakistan
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohnad Abdalla
- Pediatric Research Institute, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
| |
Collapse
|
6
|
SARS-CoV-2 proteases Mpro and PLpro: Design of inhibitors with predicted high potency and low mammalian toxicity using artificial neural networks, ligand-protein docking, molecular dynamics simulations, and ADMET calculations. Comput Biol Med 2023; 153:106449. [PMID: 36586228 PMCID: PMC9788855 DOI: 10.1016/j.compbiomed.2022.106449] [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: 10/23/2022] [Revised: 11/28/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
The main (Mpro) and papain-like (PLpro) proteases are highly conserved viral proteins essential for replication of the COVID-19 virus, SARS-COV-2. Therefore, a logical plan for producing new drugs against this pathogen is to discover inhibitors of these enzymes. Accordingly, the goal of the present work was to devise a computational approach to design, characterize, and select compounds predicted to be potent dual inhibitors - effective against both Mpro and PLpro. The first step employed LigDream, an artificial neural network, to create a virtual ligand library. Ligands with computed ADMET profiles indicating drug-like properties and low mammalian toxicity were selected for further study. Initial docking of these ligands into the active sites of Mpro and PLpro was done with GOLD, and the highest-scoring ligands were redocked with AutoDock Vina to determine binding free energies (ΔG). Compounds 89-00, 89-07, 89-32, and 89-38 exhibited favorable ΔG values for Mpro (-7.6 to -8.7 kcal/mol) and PLpro (-9.1 to -9.7 kcal/mol). Global docking of selected compounds with the Mpro dimer identified prospective allosteric inhibitors 89-00, 89-27, and 89-40 (ΔG -8.2 to -8.9 kcal/mol). Molecular dynamics simulations performed on Mpro and PLpro active site complexes with the four top-scoring ligands from Vina demonstrated that the most stable complexes were formed with compounds 89-32 and 89-38. Overall, the present computational strategy generated new compounds with predicted drug-like characteristics, low mammalian toxicity, and high inhibitory potencies against both target proteases to form stable complexes. Further preclinical studies will be required to validate the in silico findings before the lead compounds could be considered for clinical trials.
Collapse
|
7
|
Cao JF, Gong Y, Wu M, Xiong L, Chen S, Huang H, Zhou X, Peng YC, Shen XF, Qu J, Wang YL, Zhang X. Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival. Front Cell Infect Microbiol 2022; 12:1044770. [PMID: 36506032 PMCID: PMC9729774 DOI: 10.3389/fcimb.2022.1044770] [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: 09/15/2022] [Accepted: 11/08/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose 2019 Coronavirus disease (COVID-19) is endangering health of populations worldwide. Latest research has proved that Lianhua Qingwen granules (LHQW) can reduce tissue damage caused by inflammatory reactions and relieve patients' clinical symptoms. However, the mechanism of LHQW treats COVID-19 is currently lacking. Therefore, we employed computer simulations to investigate the mechanism of LHQW treats COVID-19 by modulating inflammatory response. Methods We employed bioinformatics to screen active ingredients in LHQW and intersection gene targets. PPI, GO and KEGG was used to analyze relationship of intersection gene targets. Molecular dynamics simulations validated the binding stability of active ingredients and target proteins. Binding free energy, radius of gyration and the solvent accessible surface area were analyzed by supercomputer platform. Results COVID-19 had 4628 gene targets, LHQW had 1409 gene targets, intersection gene targets were 415. Bioinformatics analysis showed that intersection targets were closely related to inflammation and immunomodulatory. Molecular docking suggested that active ingredients (including: licopyranocoumarin, Glycyrol and 3-3-Oxopropanoic acid) in LHQW played a role in treating COVID-19 by acting on CSF2, CXCL8, CCR5, NLRP3, IFNG and TNF. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets. Conclusion The mechanism of active ingredients in LHQW treats COVID-19 was investigated by computer simulations. We found that active ingredients in LHQW not only reduce cell damage and tissue destruction by inhibiting the inflammatory response through CSF2, CXCL8, CCR5 and IFNG, but also regulate cell survival and growth through NLRP3 and TNF thereby reducing apoptosis.
Collapse
Affiliation(s)
- Jun-Feng Cao
- Chengdu Medical College, Chengdu, China,Chengdu Medical College of Basic Medical Sciences, Chengdu, China
| | | | - Mei Wu
- Chengdu Medical College, Chengdu, China
| | - Li Xiong
- Chengdu Medical College, Chengdu, China
| | | | | | | | - Ying-chun Peng
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Xue-fang Shen
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Jinyu Qu
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi-li Wang
- Chengdu Medical College, Chengdu, China,The First Affifiliated Hospital of Chengdu Medical College, Chengdu, China,*Correspondence: Yi-li Wang, ; Xiao Zhang,
| | - Xiao Zhang
- Chengdu Medical College, Chengdu, China,Chengdu Medical College of Basic Medical Sciences, Chengdu, China,*Correspondence: Yi-li Wang, ; Xiao Zhang,
| |
Collapse
|
8
|
Strömich L, Wu N, Barahona M, Yaliraki SN. Allosteric Hotspots in the Main Protease of SARS-CoV-2. J Mol Biol 2022; 434:167748. [PMID: 35843284 PMCID: PMC9288249 DOI: 10.1016/j.jmb.2022.167748] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
Inhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph-theoretical methods: Bond-to-bond propensity, which has been previously successful in identifying allosteric sites in extensive benchmark data sets without a priori knowledge, and Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. Using statistical bootstrapping, we score the highest ranking sites against random sites at similar distances, and we identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.
Collapse
Affiliation(s)
- Léonie Strömich
- Department of Chemistry Imperial College London, United Kingdom
| | - Nan Wu
- Department of Chemistry Imperial College London, United Kingdom
| | | | | |
Collapse
|
9
|
Andrzejczyk J, Jovic K, Brown LM, Pascetta VG, Varga K, Vashisth H. Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative. Proteins 2022; 90:1896-1907. [PMID: 35567429 PMCID: PMC9347825 DOI: 10.1002/prot.26385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/17/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022]
Abstract
We report molecular interactions and inhibition of the main protease (MPro) of SARS‐CoV‐2, a key enzyme involved in the viral life cycle. By using a thiadiazolidinone (TDZD) derivative as a chemical probe, we explore the conformational dynamics of MPro via docking protocols and molecular dynamics simulations in all‐atom detail. We reveal the local and global dynamics of MPro in the presence of this inhibitor and confirm the inhibition of the enzyme with an IC50 value of 1.39 ± 0.22 μM, which is comparable to other known inhibitors of this enzyme.
Collapse
Affiliation(s)
- Jacob Andrzejczyk
- Department of Chemical Engineering University of New Hampshire Durham New Hampshire USA
| | - Katarina Jovic
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Logan M. Brown
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Valerie G. Pascetta
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Services University of New Hampshire Durham New Hampshire USA
| | - Harish Vashisth
- Department of Chemical Engineering University of New Hampshire Durham New Hampshire USA
| |
Collapse
|