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Wang S, Khan FI. Investigation of Molecular Interactions Mechanism of Pembrolizumab and PD-1. Int J Mol Sci 2023; 24:10684. [PMID: 37445859 DOI: 10.3390/ijms241310684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Human programmed cell death protein 1 (PD-1) is a checkpoint protein involved in the regulation of immune response. Antibodies are widely used as inhibitors that block the immune checkpoint, preventing strong immune responses. Pembrolizumab is an FDA-approved IgG4 antibody with PD-1 inhibitory ability for the treatment of melanoma. In this study, we investigated the effect of Pembrolizumab on the conformational changes in PD-1 using extensive molecular modeling and simulation approaches. Our study revealed that during the 200 ns simulation, the average values of the solvent accessible surface area, the radius of gyration, and internal hydrogen bonds of PD-1 were 64.46 nm2, 1.38 nm and 78, respectively, while these values of PD-1 in the PD-1/Pembrolizumab complex were 67.29 nm2, 1.39 nm and 76, respectively. The RMSD value of PD-1 gradually increased until 80 ns and maintained its stable conformation at 0.32 nm after 80 ns, while this value of PD-1 in the PD-1/Pembrolizumab complex maintained an increasing trend during 200 ns. The interaction between PD-1 and Pembrolizumab led to a flexible but stable structure of PD-1. PD-1 rotated around the rotation axis of the C'D loop and gradually approached Pembrolizumab. The number of hydrogen bonds involved in the interactions on the C and C' strands increased from 4 at 100 ns to 7 at 200 ns. The strong affinity of Pembrolizumab for the C'D and FG loops of PD-1 disrupted the interactions between PD-1 and PD-L1. Inhibition of the interaction between PD-1 and PD-L1 increased the T cell activity, and is effective in controlling and curing cancer. Further experimental work can be performed to support this finding.
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Affiliation(s)
- Simiao Wang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
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2
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Li L, Li J. Dimerization of Transmembrane Proteins in Cancer Immunotherapy. MEMBRANES 2023; 13:393. [PMID: 37103820 PMCID: PMC10143916 DOI: 10.3390/membranes13040393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
Transmembrane proteins (TMEMs) are integrated membrane proteins that span the entire lipid bilayer and are permanently anchored to it. TMEMs participate in various cellular processes. Some TMEMs usually exist and perform their physiological functions as dimers rather than monomers. TMEM dimerization is associated with various physiological functions, such as the regulation of enzyme activity, signal transduction, and cancer immunotherapy. In this review, we focus on the dimerization of transmembrane proteins in cancer immunotherapy. This review is divided into three parts. First, the structures and functions of several TMEMs related to tumor immunity are introduced. Second, the characteristics and functions of several typical TMEM dimerization processes are analyzed. Finally, the application of the regulation of TMEM dimerization in cancer immunotherapy is introduced.
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Affiliation(s)
- Lei Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Jingying Li
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
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3
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Xu D, Zheng QC. Theoretical investigations on the effects of mutations in important residues of NS1B on its RNA-binding using molecular dynamics simulations. Comput Biol Med 2022; 145:105412. [PMID: 35344866 DOI: 10.1016/j.compbiomed.2022.105412] [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: 02/21/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022]
Abstract
NS1B protein plays an important role in countering host antiviral defense and virulence of influenza virus B, considered as the promising target. The first experimental structure of the NS1B protein has recently been determined, was able to bind to double-stranded RNA (dsRNA). However, few studies attempt to investigate the RNA-binding mechanism of the NS1B. In this study, we provide our understanding of the structure-function relationship, dynamics and RNA-binding mechanism of the NS1B protein by performing molecular dynamics simulations combined and MM-GBSA calculations on the NS1B-dsRNA complex. 12 key residues are identified for RNA-binding by forming hydrogen bonds with the. Our results also demonstrate that mutations (R156A, K160A, R208A and K221A) can cause the local structure changes of NS1B CTD and the hydrogen bonds between NS1B CTD and RNA disappearance, which may be the main reasons for the decrease in RNA-binding affinity. These results mentioned will help us understanding the RNA-binding mechanism and could provide some medicinal chemistry insights chances for rational drug design targeting NS1B protein.
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Affiliation(s)
- Dan Xu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China
| | - Qing-Chuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, China.
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4
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Mittal L, Tonk RK, Awasthi A, Asthana S. Targeting cryptic-orthosteric site of PD-L1 for inhibitor identification using structure-guided approach. Arch Biochem Biophys 2021; 713:109059. [PMID: 34673001 DOI: 10.1016/j.abb.2021.109059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 09/30/2021] [Accepted: 10/10/2021] [Indexed: 12/23/2022]
Abstract
Approved mAbs that block the protein-protein interaction (PPI) interface of the PD-1/PD-L1 immune checkpoint axis have led to significant improvements in cancer treatment. Despite having drawbacks of mAbs only few a compounds are reported till date against this axis. Inhibiting PPIs using small molecules has emerged as a significant therapeutic opportunity, demanding for the identification of drug-like molecules at an accelerated pace under the hit-to-lead campaigns. Due to the PD-L1's cross-talk with PD-1/CD80 and its overexpression on cancer cells, as well as the availability of its crystal structures with small molecules, it is an enticing therapeutic target for structure-assisted small molecule design. Furthermore, the selection of chemical databases enriched with focused designing for PPI interfaces is crucial. Therefore, in this study we have utilized the Asinex signature library for structure-assisted virtual screening to find the potential PD-L1 inhibitors by targeting the cryptic PD-L1 interface, followed by induced fit docking for pose refinements in the pocket. The obtained hits were then subjected to interaction fingerprinting and ligand-based drug-likeness investigations in order to evaluate and analyze their drug-like qualities (ADME). Twelve compounds qualified for molecular dynamics simulations, followed by thermodynamic calculations for evaluation of their stability and energetics inside the pocket. Two novel compounds with different chemical moieties have been identified that are consistent throughout the simulation, mimicking the interactions and binding energies with BMS-1166. These compounds appear as potential therapeutic candidates to be explored experimentally, thereby paving the way for the development of novel leads as immunomodulators.
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Affiliation(s)
- Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India; Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Rajiv K Tonk
- Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, India
| | - Amit Awasthi
- 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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5
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Guo Y, Jin Y, Wang B, Liu B. Molecular Mechanism of Small-Molecule Inhibitors in Blocking the PD-1/PD-L1 Pathway through PD-L1 Dimerization. Int J Mol Sci 2021; 22:4766. [PMID: 33946261 PMCID: PMC8125578 DOI: 10.3390/ijms22094766] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/22/2023] Open
Abstract
Programmed cell death-1 (PD-1), which is a molecule involved in the inhibitory signal in the immune system and is important due to blocking of the interactions between PD-1 and programmed cell death ligand-1 (PD-L1), has emerged as a promising immunotherapy for treating cancer. In this work, molecular dynamics simulations were performed on complex systems consisting of the PD-L1 dimer with (S)-BMS-200, (R)-BMS-200 and (MOD)-BMS-200 (i.e., S, R and MOD systems) to systematically evaluate the inhibitory mechanism of BMS-200-related small-molecule inhibitors in detail. Among them, (MOD)-BMS-200 was modified from the original (S)-BMS-200 by replacing the hydroxyl group with a carbonyl to remove its chirality. Binding free energy analysis indicates that BMS-200-related inhibitors can promote the dimerization of PD-L1. Meanwhile, no significant differences were observed between the S and MOD systems, though the R system exhibited a slightly higher energy. Residue energy decomposition, nonbonded interaction, and contact number analyses show that the inhibitors mainly bind with the C, F and G regions of the PD-L1 dimer, while nonpolar interactions of key residues Ile54, Tyr56, Met115, Ala121 and Tyr123 on both PD-L1 monomers are the dominant binding-related stability factors. Furthermore, compared with (S)-BMS-200, (R)-BMS-200 is more likely to form hydrogen bonds with charged residues. Finally, free energy landscape and protein-protein interaction analyses show that the key residues of the PD-L1 dimer undergo remarkable conformational changes induced by (S)-BMS-200, which boosts its intimate interactions. This systematic investigation provides a comprehensive molecular insight into the ligand recognition process, which will benefit the design of new small-molecule inhibitors targeting PD-L1 for use in anticancer therapy.
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Affiliation(s)
| | - Yulong Jin
- Key Laboratory for Bio-Based Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510630, China; (Y.G.); (B.W.)
| | | | - Boping Liu
- Key Laboratory for Bio-Based Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou 510630, China; (Y.G.); (B.W.)
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6
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Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays. J Comput Aided Mol Des 2021; 35:679-694. [PMID: 33905074 DOI: 10.1007/s10822-021-00386-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 04/14/2021] [Indexed: 10/21/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-containing enzyme that catalyzes the first and rate-limiting step in catabolism of tryptophan via the kynurenine pathway, which plays a pivotal role in the proliferation and differentiation of T cells. IDO1 has been proven to be an attractive target for many diseases, such as breast cancer, lung cancer, colon cancer, prostate cancer, etc. In this study, docking-based virtual screening and bioassays were conducted to identify novel inhibitors of IDO1. The cellular assay demonstrated that 24 compounds exhibited potent inhibitory activity against IDO1 at micromolar level, including 8 compounds with IC50 values below 10 μM and the most potent one (compound 1) with IC50 of 1.18 ± 0.04 μM. Further lead optimization based on similarity searching strategy led to the discovery of compound 28 as an excellent inhibitor with IC50 of 0.27 ± 0.02 μM. Then, the structure-activity relationship of compounds 1, 2, 8 and 14 analogues is discussed. The interaction modes of two compounds against IDO1 were further explored through a Python Based Metal Center Parameter Builder (MCPB.py) molecular dynamics simulation, binding free energy calculation and electrostatic potential analysis. The novel IDO1 inhibitors of compound 1 and its analogues could be considered as promising scaffold for further development of IDO1 inhibitors.
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7
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Guardiola S, Varese M, Roig X, Sánchez-Navarro M, García J, Giralt E. Target-templated de novo design of macrocyclic d-/l-peptides: discovery of drug-like inhibitors of PD-1. Chem Sci 2021; 12:5164-5170. [PMID: 34163753 PMCID: PMC8179567 DOI: 10.1039/d1sc01031j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/22/2023] Open
Abstract
Peptides are a rapidly growing class of therapeutics with various advantages over traditional small molecules, especially for targeting difficult protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing bioactive cyclic topologies that go beyond natural l-amino acids. Here, we report a generalizable framework that exploits the computational power of Rosetta, in terms of large-scale backbone sampling, side-chain composition and energy scoring, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we developed two new inhibitors (PD-i3 and PD-i6) of programmed cell death 1 (PD-1), a key immune checkpoint in oncology. A comprehensive biophysical evaluation was performed to assess their binding to PD-1 as well as their blocking effect on the endogenous PD-1/PD-L1 interaction. Finally, NMR elucidation of their in-solution structures confirmed our de novo design approach.
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Affiliation(s)
- Salvador Guardiola
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Xavier Roig
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | | | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology Baldiri Reixac 10 08028 Barcelona Spain
- Department of Inorganic and Organic Chemistry, University of Barcelona Spain
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8
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Mittal L, Srivastava M, Kumari A, Tonk RK, Awasthi A, Asthana S. Interplay among Structural Stability, Plasticity, and Energetics Determined by Conformational Attuning of Flexible Loops in PD-1. J Chem Inf Model 2021; 61:358-384. [PMID: 33433201 DOI: 10.1021/acs.jcim.0c01080] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dynamics and plasticity of the PD-1/PD-L1 axis are the bottlenecks for the discovery of small-molecule antagonists to perturb this interaction interface significantly. Understanding the process of this protein-protein interaction (PPI) is of fundamental biological interest in structure-based drug designing. Food and Drug Administration (FDA)-approved anti-PD-1 monoclonal antibodies (mAbs) are the first-in-class with distinct binding modes to access this axis clinically; however, their mechanistic aspects remain elusive. Here, we have unveiled the interactive interfaces with PD-L1 and mAbs to investigate the native plasticity of PD-1 at global (structural and dynamical) and local (residue side-chain orientations) levels. We found that the structural stability and coordinated Cα movements are increased in the presence of PD-1's binding partners. The rigorous analysis of these PPIs using computational biophysical approaches revealed PD-1's intrinsic plasticity, its concerted loops' movement (BC, FG, and CC'), distal side-chain motions, and the thermodynamic landscape, which are perturbed remarkably from its unbound to bound states. Based on intra-/inter-residues' contact networks and energetics, the hot-spots have been identified that were found to be essential to arrest the dynamical motions of PD-1 significantly for the rational design of therapeutic agents by mimicking the mAbs mechanism.
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Affiliation(s)
- Lovika Mittal
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India.,Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Mitul Srivastava
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Anita Kumari
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Rajiv K Tonk
- Delhi Pharmaceutical Sciences and Research University (DPSRU), Delhi 110017, India
| | - Amit Awasthi
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Shailendra Asthana
- NCR Biotech Science Cluster, Translational Health Science and Technology Institute (THSTI), 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
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9
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Roither B, Oostenbrink C, Schreiner W. Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab. BMC Bioinformatics 2020; 21:557. [PMID: 33308148 PMCID: PMC7734776 DOI: 10.1186/s12859-020-03904-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cells upon interaction with programmed cell death protein ligand I (PD-L1). Various cancer types overexpress PD-L1 to evade the immune system by inducing apoptosis in tumor-specific CD8+ T cells. The clinically used blocking antibody nivolumab binds to PD-1 and inhibits the immunosuppressive interaction with PD-L1. Even though PD-1 is already used as a drug target, the exact mechanism of the receptor is still a matter of debate. For instance, it is hypothesized that the signal transduction is based on an active conformation of PD-1. RESULTS Here we present the results of the first molecular dynamics simulations of PD-1 with a complete extracellular domain with a focus on the role of the BC-loop of PD-1 upon binding PD-L1 or nivolumab. We could demonstrate that the BC-loop can form three conformations. Nivolumab binds to the BC-loop according to the conformational selection model whereas PD-L1 induces allosterically a conformational change of the BC-loop. CONCLUSION Due to the structural differences of the BC-loop, a signal transduction based on active conformation cannot be ruled out. These findings will have an impact on drug design and will help to refine immunotherapy blocking antibodies.
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Affiliation(s)
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Bernhard Roither
- Institute of Biosimulation and Bioinformatics, Medical University of Vienna, Spitalgasse 23/88.04.510, 1090 Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Science, Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Wolfgang Schreiner
- Institute of Biosimulation and Bioinformatics, Medical University of Vienna, Spitalgasse 23/88.04.510, 1090 Vienna, Austria
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10
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Probing the Molecular Mechanism of Rifampin Resistance Caused by the Point Mutations S456L and D441V on Mycobacterium tuberculosis RNA Polymerase through Gaussian Accelerated Molecular Dynamics Simulation. Antimicrob Agents Chemother 2020; 64:AAC.02476-19. [PMID: 32393493 DOI: 10.1128/aac.02476-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/06/2020] [Indexed: 01/08/2023] Open
Abstract
Rifampin is the first-line antituberculosis drug, with Mycobacterium tuberculosis RNA polymerase as the molecular target. Unfortunately, M. tuberculosis strains that are resistant to rifampin have been identified in clinical settings, which limits its therapeutic effects. In clinical isolates, S531L and D516V (in Escherichia coli) are two common mutated codons in the gene rpoB, corresponding to S456L and D441V in M. tuberculosis However, the resistance mechanism at the molecular level is still elusive. In this work, Gaussian accelerated molecular dynamics simulations were performed to uncover the resistance mechanism of rifampin due to S456L and D441V mutations at the atomic level. The binding free energy analysis revealed that the reduction in the ability of two mutants to bind rifampin is mainly due to a decrease in electrostatic interaction, specifically, a decrease in the energy contribution of the R454 residue. R454 acts as an anchor and forms stable hydrogen bond interaction with rifampin, allowing rifampin to be stably incorporated in the center of the binding pocket. However, the disappearance of the hydrogen bond between R454 and the mutated residues increases the flexibility of the side chain of R454. The conformation of R454 changes, and the hydrogen bond interaction between it and rifampin is disrupted. As result, the rifampin molecule moves to the outside of the pocket, and the binding affinity decreases. Overall, these findings can provide useful information for understanding the drug resistance mechanism of rifampin and also can give theoretical guidance for further design of novel inhibitors to overcome the drug resistance.
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11
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Paciotti R, Agamennone M, Coletti C, Storchi L. Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach. J Comput Aided Mol Des 2020; 34:897-914. [PMID: 32185582 DOI: 10.1007/s10822-020-00306-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
The programmed cell death protein 1 (PD-1) and its ligand, PD-L1, constitute an important co-inhibitory immune checkpoint leading to downregulation of immune system. Tumor cells developed a strategy to trigger PD-1/PD-L1 pathway reducing the T cell anticancer activity. Anti-PD-L1 small drugs, generally with improved pharmacokinetic and technological profiles than monoclonal antibodies, became an attractive research topic. Nevertheless, still few works have been published on the chemical features of possible binding sites. In this work, we applied a novel computational protocol based on the combination of the ab initio Fragment Molecular Orbital (FMO) method and a newly developed GRID-DRY approach in order to characterize the PD-L1 binding sites, starting from PD-1/PD-L1 and PD-L1/BMS-ligands (Bristol-Mayers Squibb ligands) complexes. The FMO method allows the calculation of the pair-residues as well as the ligand-residues interactions with ab initio accuracy, whereas the GRID-DRY approach is an effective tool to investigate hydrophobic interactions, not easily detectable by ab initio methods. The present GRID-DRY protocol is able to determine the energy contributions of each ligand atoms to each hydrophobic interaction, both qualitatively and quantitatively. We were also able to identify the three specific hot regions involved in PD-1/PD-L1 protein-protein interaction and in PD-L1/BMS-ligand interactions, in agreement with preceding theoretical/experimental results, and to suggest a specific pharmacophore for PD-L1 inhibitors.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy.
| | | | - Cecilia Coletti
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy
| | - Loriano Storchi
- Department of Pharmacy, Università "G. D'Annunzio" Di Chieti-Pescara, Chieti, Italy. .,Molecular Discovery Limited, Middlesex, London, UK.
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12
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Klyukin K, Alexandrov V. Kinetics of pH-dependent interactions between PD-1 and PD-L1 immune checkpoint proteins from molecular dynamics. Proteins 2020; 88:1162-1168. [PMID: 32105362 DOI: 10.1002/prot.25885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/05/2020] [Accepted: 02/23/2020] [Indexed: 12/17/2022]
Abstract
Immune checkpoint blockade of signaling pathways such as PD-1/PD-L1 has recently opened up a new avenue for highly efficient immunotherapeutic strategies to treat cancer. Since tumor microenvironments are characterized by lower pH (5.5-7.0), pH-dependent protein-ligand interactions can be exploited as efficient means to regulate drug affinity and specificity for a variety of malignancies. In this article, we investigate the mechanism and kinetics of pH-dependent binding and unbinding processes for the PD-1/PD-L1 checkpoint pair employing classical molecular dynamics simulations. Two representative pH levels corresponding to circumneutral physiological conditions of blood (pH 7.4) and acidic tumor microenvironment (pH 5.5) are considered. Our calculations demonstrate that pH plays a key role in protein-ligand interactions with small pH changes leading to several orders of magnitude increase in binding affinity. By identifying the binding pocket in the PD-1/PD-L1 complex, we show a pivotal role of the His68 protonation state of PD-1in the complex stabilization at low pH. The results on the reaction rate constants are in qualitative agreement with available experimental data. The obtained molecular details are important for further engineering of binding/unbinding kinetics to formulate more efficient immune checkpoint blockade strategies.
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Affiliation(s)
- Konstantin Klyukin
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Vitaly Alexandrov
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska.,Nebraska Center for Materials and Nanoscience, University of Nebraska-Lincoln, Lincoln, Nebraska
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13
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Lyu N, Wang K, Zhang F, Qin H, Zhao Y, Wu R, Si Y, Wang L. Recognition of PDL1/L2 by different induced-fit mechanisms of PD1: a comparative study of molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:1276-1287. [DOI: 10.1039/c9cp05531b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The different binding mechanism for PD1/PDL1 and PD1/PDL2 complexes.
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Affiliation(s)
- Nan Lyu
- School of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
| | - Kai Wang
- School of Agriculture and Biology
- Zhongkai University of Agriculture and Engineering
- Guangzhou 510000
- P. R. China
| | - Fan Zhang
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Haimei Qin
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Lab of Theoretical and Computational Chemistry, and Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- P. R. China
| | - Yubing Si
- College of Chemistry
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Laiyou Wang
- School of Pharmacy
- Guangdong Pharmaceutical University
- Guangzhou 510006
- P. R. China
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14
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Ji M, Ding Y, Li X, Mao N, Chen J. Computational investigation of a ternary model of SnoN-SMAD3-SMAD4 complex. Comput Biol Chem 2019; 83:107159. [PMID: 31743832 DOI: 10.1016/j.compbiolchem.2019.107159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/28/2019] [Accepted: 11/03/2019] [Indexed: 12/18/2022]
Abstract
The transforming growth factor β (TGFβ) plays an essential role in the regulation of cellular processes such as cell proliferation, migration, differentiation, and apoptosis by association with SMAD transcriptional factors that are regulated by the transcriptional regulator SnoN. The crystal structure of SnoN-SMAD4 reveals that SnoN can adopt two binding modes, the open and closed forms, at the interfaces of SMAD4 subunits. Accumulating evidence indicates that SnoN can interact with both SMAD3 and SMAD4 to form a ternary SnoN-SMAD3-SMAD4 complex in the TGFβ signaling pathway. However, how the interaction of SnoN with the SMAD3 and SMAD4 remains unclear. Here, molecular dynamics (MD) simulations and molecular modeling methods were performed to figure out this issue. The simulations reveal that SnoNopen exists in two, open and semi-closed, conformations. Molecular modeling and MD simulation studies suggest that the SnoNclosed form interferes with the SMAD3-SMAD4 protein; in contract, the SnoNopen can form a stable SnoN-SMAD3-SMAD4 complex. These mechanistic mechanisms may help elucidate the detailed engagement of SnoN with two SMAD3 and SMAD4 transcriptional factors in the regulation of TGFβ signaling pathway.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Yelei Ding
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Jie Chen
- Department of Urology, Changzheng Hospital, Naval Military Medical University, Shanghai, 200003, China.
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15
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Ding H, Liu H. Mapping the Binding Hot Spots on Human Programmed Cell Death 1 and Its Ligand with Free-Energy Simulations. J Chem Inf Model 2019; 59:4339-4349. [DOI: 10.1021/acs.jcim.9b00337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hanjing Ding
- School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning, Hubei 437100, China
| | - Hui Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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16
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Shen C, Liu H, Wang X, Lei T, Wang E, Xu L, Yu H, Li D, Yao X. Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I 1/2 NIK Inhibitors. Front Pharmacol 2019; 10:345. [PMID: 31024312 PMCID: PMC6465739 DOI: 10.3389/fphar.2019.00345] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/20/2019] [Indexed: 12/15/2022] Open
Abstract
NF-κB inducing kinase (NIK), which is considered as the central component of the non-canonical NF-κB pathway, has been proved to be an important target for the regulation of the immune system. In the past few years, NIK inhibitors with various scaffolds have been successively reported, among which type I1/2 inhibitors that can not only bind in the ATP-binding pocket at the DFG-in state but also extend into an additional back pocket, make up the largest proportion of the NIK inhibitors, and are worthy of more attention. In this study, an integration protocol that combines molecule docking, MD simulations, ensemble docking, MM/GB(PB)SA binding free energy calculations, and decomposition was employed to understand the binding mechanism of 21 tricyclic type I1/2 NIK inhibitors. It is found that the docking accuracy is largely dependent on the selection of docking protocols as well as the crystal structures. The predictions given by the ensemble docking based on multiple receptor conformations (MRCs) and the MM/GB(PB)SA calculations based on MD simulations showed higher linear correlations with the experimental data than those given by conventional rigid receptor docking (RRD) methods (Glide, GOLD, and Autodock Vina), highlighting the importance of incorporating protein flexibility in predicting protein–ligand interactions. Further analysis based on MM/GBSA demonstrates that the hydrophobic interactions play the most essential role in the ligand binding to NIK, and the polar interactions also make an important contribution to the NIK-ligand recognition. A deeper comparison of several pairs of representative derivatives reveals that the hydrophobic interactions are vitally important in the structural optimization of analogs as well. Besides, the H-bond interactions with some key residues and the large desolvation effect in the back pocket devote to the affinity distinction. It is expected that our study could provide valuable insights into the design of novel and potent type I1/2 NIK inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Huidong Yu
- Rongene Pharma Co., Ltd., Shenzhen, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
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17
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Zhang H, He X, Ni D, Mou L, Chen X, Lu S. How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:89-100. [DOI: 10.1080/07391102.2019.1567390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hao Zhang
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xinheng He
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Duan Ni
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medicinal University, Wei fang, Shandong, China
| | - Xiangyu Chen
- Department of Medicinal Laboratory, Weifang Medicinal University, Weifang, Shandong, China
| | - Shaoyong Lu
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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18
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Huang D, Wen W, Liu X, Li Y, Zhang JZH. Computational analysis of hot spots and binding mechanism in the PD-1/PD-L1 interaction. RSC Adv 2019; 9:14944-14956. [PMID: 35516311 PMCID: PMC9064197 DOI: 10.1039/c9ra01369e] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/05/2019] [Indexed: 12/14/2022] Open
Abstract
Programmed cell death protein-1 (PD-1) is an important immunological checkpoint and plays a vital role in maintaining the peripheral tolerance of the human body by interacting with its ligand PD-L1. The overexpression of PD-L1 in tumor cells induces local immune suppression and helps the tumor cells to evade the endogenous anti-tumor immunity. Developing monoclonal antibodies against the PD-1/PD-L1 protein–protein interaction to block the PD-1/PD-L1 signaling pathway has demonstrated superior anti-tumor efficacy in a variety of solid tumors and has made a profound impact on the field of cancer immunotherapy in recent years. Although the X-ray crystal structure of the PD-1/PD-L1 complex has been solved, the detailed binding mechanism of the PD-1/PD-L1 interaction is not fully understood from a theoretical point of view. In this study, we performed computational alanine scanning on the PD-1/PD-L1 complex to quantitatively identify the hot spots in the PD-1/PD-L1 interaction and characterize its binding mechanisms at the atomic level. To the best of our knowledge, this is the first time that theoretical calculations have been used to systematically and quantitatively predict the hot spots in the PD-1/PD-L1 interaction. We hope that the predicted hot spots and the energy profile of the PD-1/PD-L1 interaction presented in this work can provide guidance for the design of peptide and small molecule drugs targeting PD-1 or PD-L1. The hot spots quantitatively predicted by the recently developed MM/GBSA/IE method reveal a hydrophobic core in the PD-1/PD-L1 interaction.![]()
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Affiliation(s)
- Dading Huang
- State Key Laboratory for Precision Spectroscopy
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
| | - Wei Wen
- State Key Laboratory for Precision Spectroscopy
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
| | - Xiao Liu
- State Key Laboratory for Precision Spectroscopy
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
| | - Yang Li
- State Key Laboratory for Precision Spectroscopy
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
| | - John Z. H. Zhang
- State Key Laboratory for Precision Spectroscopy
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200062
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19
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Prediction of GluN2B-CT 1290-1310/DAPK1 Interaction by Protein⁻Peptide Docking and Molecular Dynamics Simulation. Molecules 2018; 23:molecules23113018. [PMID: 30463177 PMCID: PMC6278559 DOI: 10.3390/molecules23113018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 02/08/2023] Open
Abstract
The interaction of death-associated protein kinase 1 (DAPK1) with the 2B subunit (GluN2B) C-terminus of N-methyl-D-aspartate receptor (NMDAR) plays a critical role in the pathophysiology of depression and is considered a potential target for the structure-based discovery of new antidepressants. However, the 3D structures of C-terminus residues 1290⁻1310 of GluN2B (GluN2B-CT1290-1310) remain elusive and the interaction between GluN2B-CT1290-1310 and DAPK1 is unknown. In this study, the mechanism of interaction between DAPK1 and GluN2B-CT1290-1310 was predicted by computational simulation methods including protein⁻peptide docking and molecular dynamics (MD) simulation. Based on the equilibrated MD trajectory, the total binding free energy between GluN2B-CT1290-1310 and DAPK1 was computed by the mechanics generalized born surface area (MM/GBSA) approach. The simulation results showed that hydrophobic, van der Waals, and electrostatic interactions are responsible for the binding of GluN2B-CT1290⁻1310/DAPK1. Moreover, through per-residue free energy decomposition and in silico alanine scanning analysis, hotspot residues between GluN2B-CT1290-1310 and DAPK1 interface were identified. In conclusion, this work predicted the binding mode and quantitatively characterized the protein⁻peptide interface, which will aid in the discovery of novel drugs targeting the GluN2B-CT1290-1310 and DAPK1 interface.
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20
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Yang J, Hu L. Immunomodulators targeting the PD-1/PD-L1 protein-protein interaction: From antibodies to small molecules. Med Res Rev 2018; 39:265-301. [PMID: 30215856 DOI: 10.1002/med.21530] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 02/06/2023]
Abstract
Cancer immunotherapy has made great strides in the recent decade, especially in the area of immune checkpoint blockade. The outstanding efficacy, prolonged durability of effect, and rapid assimilation of anti-PD-1 and anti-PD-L1 monoclonal antibodies in clinical practice have been nothing short of a medical breakthrough in the treatment of numerous malignancies. The major advantages of these therapeutic antibodies over their small molecule counterparts have been their high binding affinity and target specificity. However, antibodies do have their flaws including immune-related toxicities, inadequate pharmacokinetics and tumor penetration, and high cost burden to manufacturers and consumers. These limitations hinder broader clinical applications of the antibodies and have heightened interests in developing the alternative small molecule platform that includes peptidomimetics and peptides to target the PD-1/PD-L1 immune checkpoint system. The progress on these small molecule alternatives has been relatively slow compared to that of the antibodies. Fortunately, recent structural studies of the interactions among PD-1, PD-L1, and their respective antibodies have revealed key hotspots on PD-1 and PD-L1 that may facilitate drug discovery efforts for small molecule immunotherapeutics. This review is intended to discuss key concepts in immuno-oncology, describe the successes and shortcomings of PD-1/PD-L1 antibody-based therapies, and to highlight the recent development of small molecule inhibitors of the PD-1/PD-L1 protein-protein interaction.
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Affiliation(s)
- Jeffrey Yang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey
| | - Longqin Hu
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey.,Cancer Pharmacology Program, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
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