1
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Chen J, Gou Q, Chen X, Song Y, Zhang F, Pu X. Exploring biased activation characteristics by molecular dynamics simulation and machine learning for the μ-opioid receptor. Phys Chem Chem Phys 2024; 26:10698-10710. [PMID: 38512140 DOI: 10.1039/d3cp05050e] [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: 03/22/2024]
Abstract
Biased ligands selectively activating specific downstream signaling pathways (termed as biased activation) exhibit significant therapeutic potential. However, the conformational characteristics revealed are very limited for the biased activation, which is not conducive to biased drug development. Motivated by the issue, we combine extensive accelerated molecular dynamics simulations and an interpretable deep learning model to probe the biased activation features for two complex systems constructed by the inactive μOR and two different biased agonists (G-protein-biased agonist TRV130 and β-arrestin-biased agonist endomorphin2). The results indicate that TRV130 binds deeper into the receptor core compared to endomorphin2, located between W2936.48 and D1142.50, and forms hydrogen bonding with D1142.50, while endomorphin2 binds above W2936.48. The G protein-biased agonist induces greater outward movements of the TM6 intracellular end, forming a typical active conformation, while the β-arrestin-biased agonist leads to a smaller extent of outward movements of TM6. Compared with TRV130, endomorphin2 causes more pronounced inward movements of the TM7 intracellular end and more complex conformational changes of H8 and ICL1. In addition, important residues determining the two different biased activation states were further identified by using an interpretable deep learning classification model, including some common biased activation residues across Class A GPCRs like some key residues on the TM2 extracellular end, ECL2, TM5 intracellular end, TM6 intracellular end, and TM7 intracellular end, and some specific important residues of ICL3 for μOR. The observations will provide valuable information for understanding the biased activation mechanism for GPCRs.
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Affiliation(s)
- Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Qiaoling Gou
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Yuanpeng Song
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Fuhui Zhang
- Graduate School, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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2
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Arbon R, Zhu Y, Mey ASJS. Markov State Models: To Optimize or Not to Optimize. J Chem Theory Comput 2024; 20:977-988. [PMID: 38163961 PMCID: PMC10809420 DOI: 10.1021/acs.jctc.3c01134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins including protein folding. With all statistical and machine learning (ML) models, choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or hyperparameters, are often evaluated by expert judgment or, in the case of MSMs, by maximizing variational scores such as the VAMP-2 score. Modern ML and statistical pipelines often use automatic hyperparameter selection techniques ranging from the simple, choosing the best score from a random selection of hyperparameters, to the complex, optimization via, e.g., Bayesian optimization. In this work, we ask whether it is possible to automatically select MSM models this way by estimating and analyzing over 16,000,000 observations from over 280,000 estimated MSMs. We find that differences in hyperparameters can change the physical interpretation of the optimization objective, making automatic selection difficult. In addition, we find that enforcing conditions of equilibrium in the VAMP scores can result in inconsistent model selection. However, other parameters that specify the VAMP-2 score (lag time and number of relaxation processes scored) have only a negligible influence on model selection. We suggest that model observables and variational scores should be only a guide to model selection and that a full investigation of the MSM properties should be undertaken when selecting hyperparameters.
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Affiliation(s)
- Robert
E. Arbon
- EaStCHEM
School of Chemistry, David Brewster Road, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, United Kingdom
- Redesign
Science, 180 Varick St., New York, New York 10014, United States
| | - Yanchen Zhu
- EaStCHEM
School of Chemistry, David Brewster Road, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, United Kingdom
| | - Antonia S. J. S. Mey
- EaStCHEM
School of Chemistry, David Brewster Road, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3FJ, United Kingdom
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3
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Hognon C, Bignon E, Monari A, Marazzi M, Garcia-Iriepa C. Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants. Int J Mol Sci 2023; 24:ijms24032517. [PMID: 36768842 PMCID: PMC9916449 DOI: 10.3390/ijms24032517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
After a sudden and first spread of the pandemic caused by the novel SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) wild-type strain, mutants have emerged which have been associated with increased infectivity, inducing surges in the contagions. The first of the so-called variants of concerns, was firstly isolated in the United Kingdom and later renamed Alpha variant. Afterwards, in the middle of 2021, a new variant appeared called Delta. The latter is characterized by the presence of point mutations in the Spike protein of SARS-CoV-2, especially in the Receptor Binding Domain (RBD). When in its active conformation, the RBD can interact with the human receptor Angiotensin-Converting Enzyme 2 (ACE2) to allow the entry of the virions into cells. In this contribution, by using extended all-atom molecular dynamic simulations, complemented with machine learning post-processing, we analyze the changes in the molecular interaction network induced by these different strains in comparison with the wild-type. On one hand, although relevant variations are evidenced, only limited changes in the global stability indicators and in the flexibility profiles have been observed. On the other hand, key differences were obtained by tracking hydrophilic and hydrophobic molecular interactions, concerning both positioning at the ACE2/RBD interface and formation/disruption dynamic behavior.
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Affiliation(s)
- Cécilia Hognon
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
| | - Emmanuelle Bignon
- UMR 7019 LPCT, Université de Lorraine and CNRS, F-5400 Nancy, France
| | - Antonio Monari
- ITODYS, Université Paris Cité and CNRS, F-75006 Paris, France
| | - Marco Marazzi
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
| | - Cristina Garcia-Iriepa
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
- Correspondence: (M.M.); (C.G.-I.)
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4
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Philip AM, Ahmed WS, Biswas KH. Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2. Comput Struct Biotechnol J 2023; 21:1966-1977. [PMID: 36936816 PMCID: PMC10006685 DOI: 10.1016/j.csbj.2023.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/28/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The SARS-CoV-2 Omicron variant containing 15 mutations, including the unique Q493R, in the spike protein receptor binding domain (S1-RBD) is highly infectious. While comparison with previously reported mutations provide some insights, the mechanism underlying the increased infections and the impact of the reversal of the unique Q493R mutation seen in BA.4, BA.5, BA.2.75, BQ.1 and XBB lineages is not yet completely understood. Here, using structural modelling and molecular dynamics (MD) simulations, we show that the Omicron mutations increases the affinity of S1-RBD for ACE2, and a reversal of the unique Q493R mutation further increases the ACE2-S1-RBD affinity. Specifically, we performed all atom, explicit solvent MD simulations using a modelled structure of the Omicron S1-RBD-ACE2 and compared the trajectories with the WT complex revealing a substantial reduction in the Cα-atom fluctuation in the Omicron S1-RBD and increased hydrogen bond and other interactions. Residue level analysis revealed an alteration in the interaction between several residues including a switch in the interaction of ACE2 D38 from S1-RBD Y449 in the WT complex to the mutated R residue (Q493R) in Omicron complex. Importantly, simulations with Revertant (Omicron without the Q493R mutation) complex revealed further enhancement of the interaction between S1-RBD and ACE2. Thus, results presented here not only provide insights into the increased infectious potential of the Omicron variant but also a mechanistic basis for the reversal of the Q493R mutation seen in some Omicron lineages and will aid in understanding the impact of mutations in SARS-CoV-2 evolution.
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Affiliation(s)
- Angelin M. Philip
- Division of Genomics and Translational Biomedicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
- Corresponding author.
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5
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In Silico Study of the Acquired Resistance Caused by the Secondary Mutations of KRAS G12C Protein Using Long Time Molecular Dynamics Simulation and Markov State Model Analysis. Int J Mol Sci 2022; 23:ijms232213845. [PMID: 36430323 PMCID: PMC9694466 DOI: 10.3390/ijms232213845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 11/12/2022] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) is a small GTPase protein which plays an important role in the treatment of KRAS mutant cancers. The FDA-approved AMG510 and MRTX849 (phase III clinical trials) are two potent KRASG12C-selective inhibitors that target KRAS G12C. However, the drug resistance caused by the second-site mutation in KRAS has emerged, and the mechanisms of drug resistance at atom level are still unclear. To clarify the mechanisms of drug resistance, we conducted long time molecular dynamics simulations (75 μs in total) to study the structural and energetic features of KRAS G12C and its four drug resistant variants to inhibitors. The combined binding free energy calculation and protein-ligand interaction fingerprint revealed that these second-site mutations indeed caused KRAS to produce different degrees of resistance to AMG510 and MRTX849. Furthermore, Markov State Models and 2D-free energy landscapes analysis revealed the difference in conformational changes of mutated KRAS bound with and without inhibitors. Furthermore, the comparative analysis of these systems showed that there were differences in their allosteric signal pathways. These findings provide the molecular mechanism of drug resistance, which helps to guide novel KRAS G12C inhibitor design to overcome drug resistance.
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6
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Zhou S, Yang B, Xu Y, Gu A, Peng J, Fu J. Understanding gilteritinib resistance to FLT3-F691L mutation through an integrated computational strategy. J Mol Model 2022; 28:247. [PMID: 35932378 DOI: 10.1007/s00894-022-05254-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/31/2022] [Indexed: 11/25/2022]
Abstract
FMS-like tyrosine kinase 3 (FLT3) serves as an important drug target for acute myeloid leukemia (AML), and gene mutations of FLT3 have been closely associated with AML patients with an incidence rate of ~ 30%. However, the mechanism of the clinically relevant F691L gatekeeper mutation conferred resistance to the drug gilteritinib remained poorly understood. In this study, multiple microsecond molecular dynamics (MD) simulations, end-point free energy calculations, and dynamic correlated and network analyses were performed to investigate the molecular basis of gilteritinib resistance to the FLT3-F691L mutation. The simulations revealed that the resistant mutation largely induced the conformational changes of the activation loop (A-loop), the phosphate-binding loop, and the helix αC of the FLT3 protein. The binding abilities of the gilteritinib to the wild-type and the F691L mutant were different through the binding free energy prediction. The simulation results further indicated that the driving force to determine the binding affinity of gilteritinib was derived from the differences in the energy terms of electrostatic and van der Waals interactions. Moreover, the per-residue free energy decomposition suggested that the four residues (Phe803, Gly831, Leu832, and Ala833) located at the A-loop of FLT3 had a significant impact on the binding affinity of gilteritinib to the F691L mutant. This study may provide useful information for the design of novel FLT3 inhibitors specially targeting the F691L gatekeeper mutant.
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Affiliation(s)
- Shibo Zhou
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Bo Yang
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Yufeng Xu
- Department of Radiotherapy, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Aihua Gu
- Department of Medicine, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Juan Peng
- Department of Ultrasonography, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Jinfeng Fu
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China.
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7
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Liu C, Li Z, Liu Z, Yang S, Wang Q, Chai Z. Understanding the P-Loop Conformation in the Determination of Inhibitor Selectivity Toward the Hepatocellular Carcinoma-Associated Dark Kinase STK17B. Front Mol Biosci 2022; 9:901603. [PMID: 35620482 PMCID: PMC9127184 DOI: 10.3389/fmolb.2022.901603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 12/26/2022] Open
Abstract
As a member of the death-associated protein kinase family of serine/threonine kinases, the STK17B has been associated with diverse diseases such as hepatocellular carcinoma. However, the conformational dynamics of the phosphate-binding loop (P-loop) in the determination of inhibitor selectivity profile to the STK17B are less understood. Here, a multi-microsecond length molecular dynamics (MD) simulation of STK17B in the three different states (ligand-free, ADP-bound, and ligand-bound states) was carried out to uncover the conformational plasticity of the P-loop. Together with the analyses of principal component analysis, cross-correlation and generalized correlation motions, secondary structural analysis, and community network analysis, the conformational dynamics of the P-loop in the different states were revealed, in which the P-loop flipped into the ADP-binding site upon the inhibitor binding and interacted with the inhibitor and the C-lobe, strengthened the communication between the N- and C-lobes. These resulting interactions contributed to inhibitor selectivity profile to the STK17B. Our results may advance our understanding of kinase inhibitor selectivity and offer possible implications for the design of highly selective inhibitors for other protein kinases.
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Affiliation(s)
- Chang Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Zhizhen Li
- Department of Biliary Surgery I, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Zonghan Liu
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Shiye Yang
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
| | - Qing Wang
- Oncology Department, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University (Navy Medical University), Shanghai, China
- Department of Hepatic Surgery, Shanghai Geriatric Center, Shanghai, China
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8
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He X, Du K, Wang Y, Fan J, Li M, Ni D, Lu S, Bian X, Liu Y. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Front Mol Biosci 2022; 9:860962. [PMID: 35463958 PMCID: PMC9023742 DOI: 10.3389/fmolb.2022.860962] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
The Ras-specific guanine nucleotide exchange factors Son of Sevenless (SOS) regulates Ras activation by converting inactive GDP-bound to active GTP-bound states. The catalytic activity of Ras is further allosterically regulated by GTP-Ras bound to a distal site through a positive feedback loop. To address the mechanism underlying the long-range allosteric activation of the catalytic K-Ras4B by an additional allosteric GTP-Ras through SOS, we employed molecular dynamics simulation of the K-Ras4BG13D•SOScat complex with and without an allosteric GTP-bound K-Ras4BG13D. We found that the binding of an allosteric GTP-K-Ras4BG13D enhanced the affinity between the catalytic K-Ras4BG13D and SOScat, forming a more stable conformational state. The peeling away of the switch I from the nucleotide binding site facilitated the dissociation of GDP, thereby contributing to the increased nucleotide exchange rate. The community networks further showed stronger edge connection upon allosteric GTP-K-Ras4BG13D binding, which represented an increased interaction between catalytic K-Ras4BG13D and SOScat. Moreover, GTP-K-Ras4BG13D binding transmitted allosteric signaling pathways though the Cdc25 domain of SOS that enhanced the allosteric regulatory from the K-Ras4BG13D allosteric site to the catalytic site. This study may provide an in-depth mechanism for abnormal activation and allosteric regulation of K-Ras4BG13D.
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Affiliation(s)
- Xuan He
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Yuanhao Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jigang Fan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingyu Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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9
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Ramos RS, Borges RS, de Souza JSN, Araujo IF, Chaves MH, Santos CBR. Identification of Potential Antiviral Inhibitors from Hydroxychloroquine and 1,2,4,5-Tetraoxanes Analogues and Investigation of the Mechanism of Action in SARS-CoV-2. Int J Mol Sci 2022; 23:1781. [PMID: 35163703 PMCID: PMC8836247 DOI: 10.3390/ijms23031781] [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: 12/24/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
This study aimed to identify potential inhibitors and investigate the mechanism of action on SARS-CoV-2 ACE2 receptors using a molecular modeling study and theoretical determination of biological activity. Hydroxychloroquine was used as a pivot structure and antimalarial analogues of 1,2,4,5 tetraoxanes were used for the construction and evaluation of pharmacophoric models. The pharmacophore-based virtual screening was performed on the Molport® database (~7.9 million compounds) and obtained 313 structures. Additionally, a pharmacokinetic study was developed, obtaining 174 structures with 99% confidence for human intestinal absorption and penetration into the blood-brain barrier (BBB); posteriorly, a study of toxicological properties was realized. Toxicological predictions showed that the selected molecules do not present a risk of hepatotoxicity, carcinogenicity, mutagenicity, and skin irritation. Only 54 structures were selected for molecular docking studies, and five structures showed binding affinity (ΔG) values satisfactory for ACE2 receptors (PDB 6M0J), in which the molecule MolPort-007-913-111 had the best ΔG value of -8.540 Kcal/mol, followed by MolPort-002-693-933 with ΔG = -8.440 Kcal/mol. Theoretical determination of biological activity was realized for 54 structures, and five molecules showed potential protease inhibitors. Additionally, we investigated the Mpro receptor (6M0K) for the five structures via molecular docking, and we confirmed the possible interaction with the target. In parallel, we selected the TopsHits 9 with antiviral potential that evaluated synthetic accessibility for future synthesis studies and in vivo and in vitro tests.
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Affiliation(s)
- Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
| | - Rosivaldo S. Borges
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Graduate Program on Medicinal Chemistry and Molecular Modeling, Institute of Health Science, Federal University of Pará, Belém 66075-110, PA, Brazil
| | - João S. N. de Souza
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Inana F. Araujo
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Binational Campus, Federal University of Amapá, Oiapoque 68980-000, AP, Brazil
| | - Mariana H. Chaves
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, AP, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil; (R.S.B.); (I.F.A.)
- Chemistry Department, Federal University of Piauí, Teresina 64049-550, PI, Brazil; (J.S.N.d.S.); (M.H.C.)
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10
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Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J. Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. J Med Chem 2021; 64:17728-17743. [PMID: 34878270 DOI: 10.1021/acs.jmedchem.1c01695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a fundamental and extensive mechanism of intramolecular signal transmission. Allosteric drugs possess several unique pharmacological advantages over traditional orthosteric drugs, including greater selectivity, better physicochemical properties, and lower off-target toxicity. However, owing to the complexity of allosteric regulation, experimental approaches for the development of allosteric modulators are traditionally serendipitous. Recently, the reversed allosteric communication theory has been proposed, providing a feasible tool for the unbiased detection of allosteric sites. Herein, we review the latest research on the reversed allosteric communication effect using the examples of sirtuin 6, epidermal growth factor receptor, 3-phosphoinositide-dependent protein kinase 1, and Related to A and C kinases (RAC) serine/threonine protein kinase B and recapitulate the methodologies of reversed allosteric communication strategy. The novel reversed allosteric communication strategy greatly expands the horizon of allosteric site identification and allosteric mechanism exploration and is expected to accelerate an end-to-end framework for drug discovery.
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Affiliation(s)
- Jigang Fan
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Zhiyuan Innovative Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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