1
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Lu J, Yu D, Li H, Qin P, Chen H, Chen L. Promising natural products targeting protein tyrosine phosphatase SHP2 for cancer therapy. Phytother Res 2024. [PMID: 38558278 DOI: 10.1002/ptr.8185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The development of Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) inhibitors is a hot spot in the research and development of antitumor drugs, which may induce immunomodulatory effects in the tumor microenvironment and participate in anti-tumor immune responses. To date, several SHP2 inhibitors have made remarkable progress and entered clinical trials for the treatment of patients with advanced solid tumors. Multiple compounds derived from natural products have been proved to influence tumor cell proliferation, apoptosis, migration and other cellular functions, modulate cell cycle and immune cell activation by regulating the function of SHP2 and its mutants. However, there is a paucity of information about their diversity, biochemistry, and therapeutic potential of targeting SHP2 in tumors. This review will provide the structure, classification, inhibitory activities, experimental models, and antitumor effects of the natural products. Notably, this review summarizes recent advance in the efficacy and pharmacological mechanism of natural products targeting SHP2 in inhibiting the various signaling pathways that regulate different cancers and thus pave the way for further development of anticancer drugs targeting SHP2.
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Affiliation(s)
- Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pengcheng Qin
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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2
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Liu Y, Zhang M, Jang H, Nussinov R. The allosteric mechanism of mTOR activation can inform bitopic inhibitor optimization. Chem Sci 2024; 15:1003-1017. [PMID: 38239681 PMCID: PMC10793652 DOI: 10.1039/d3sc04690g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024] Open
Abstract
mTOR serine/threonine kinase is a cornerstone in the PI3K/AKT/mTOR pathway. Yet, the detailed mechanism of activation of its catalytic core is still unresolved, likely due to mTOR complexes' complexity. Its dysregulation was implicated in cancer and neurodevelopmental disorders. Using extensive molecular dynamics (MD) simulations and compiled published experimental data, we determine exactly how mTOR's inherent motifs can control the conformational changes in the kinase domain, thus kinase activity. We also chronicle the critical regulation by the unstructured negative regulator domain (NRD). When positioned inside the catalytic cleft (NRD IN state), mTOR tends to adopt a deep and closed catalytic cleft. This is primarily due to the direct interaction with the FKBP-rapamycin binding (FRB) domain which restricts it, preventing substrate access. Conversely, when outside the catalytic cleft (NRD OUT state), mTOR favors an open conformation, exposing the substrate-binding site on the FRB domain. We further show how an oncogenic mutation (L2427R) promotes shifting the mTOR ensemble toward the catalysis-favored state. Collectively, we extend mTOR's "active-site restriction" mechanism and clarify mutation action. In particular, our mechanism suggests that RMC-5552 (RMC-6272) bitopic inhibitors may benefit from adjustment of the (PEG8) linker length when targeting certain mTOR variants. In the cryo-EM mTOR/RMC-5552 structure, the distance between the allosteric and orthosteric inhibitors is ∼22.7 Å. With a closed catalytic cleft, this linker bridges the sites. However, in our activation mechanism, in the open cleft it expands to ∼24.7 Å, offering what we believe to be the first direct example of how discovering an activation mechanism can potentially increase the affinity of inhibitors targeting mutants.
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Affiliation(s)
- Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute Frederick MD 21702 USA
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research Frederick MD 21702 USA +1-301-846-5579
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University Tel Aviv 69978 Israel
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3
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Šeflová J, Cruz-Cortés C, Guerrero-Serna G, Robia SL, Espinoza-Fonseca LM. Mechanisms for cardiac calcium pump activation by its substrate and a synthetic allosteric modulator using fluorescence lifetime imaging. PNAS NEXUS 2024; 3:pgad453. [PMID: 38222469 PMCID: PMC10785037 DOI: 10.1093/pnasnexus/pgad453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
The discovery of allosteric modulators is an emerging paradigm in drug discovery, and signal transduction is a subtle and dynamic process that is challenging to characterize. We developed a time-correlated single photon-counting imaging approach to investigate the structural mechanisms for small-molecule activation of the cardiac sarcoplasmic reticulum Ca2+-ATPase, a pharmacologically important pump that transports Ca2+ at the expense of adenosine triphosphate (ATP) hydrolysis. We first tested whether the dissociation of sarcoplasmic reticulum Ca2+-ATPase from its regulatory protein phospholamban is required for small-molecule activation. We found that CDN1163, a validated sarcoplasmic reticulum Ca2+-ATPase activator, does not have significant effects on the stability of the sarcoplasmic reticulum Ca2+-ATPase-phospholamban complex. Time-correlated single photon-counting imaging experiments using the nonhydrolyzable ATP analog β,γ-Methyleneadenosine 5'-triphosphate (AMP-PCP) showed ATP is an allosteric modulator of sarcoplasmic reticulum Ca2+-ATPase, increasing the fraction of catalytically competent structures at physiologically relevant Ca2+ concentrations. Unlike ATP, CDN1163 alone has no significant effects on the Ca2+-dependent shifts in the structural populations of sarcoplasmic reticulum Ca2+-ATPase, and it does not increase the pump's affinity for Ca2+ ions. However, we found that CDN1163 enhances the ATP-mediated modulatory effects to increase the population of catalytically competent sarcoplasmic reticulum Ca2+-ATPase structures. Importantly, this structural shift occurs within the physiological window of Ca2+ concentrations at which sarcoplasmic reticulum Ca2+-ATPase operates. We demonstrated that ATP is both a substrate and modulator of sarcoplasmic reticulum Ca2+-ATPase and showed that CDN1163 and ATP act synergistically to populate sarcoplasmic reticulum Ca2+-ATPase structures that are primed for phosphorylation. This study provides novel insights into the structural mechanisms for sarcoplasmic reticulum Ca2+-ATPase activation by its substrate and a synthetic allosteric modulator.
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Affiliation(s)
- Jaroslava Šeflová
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carlos Cruz-Cortés
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guadalupe Guerrero-Serna
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL 60153, USA
| | - L Michel Espinoza-Fonseca
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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Chen J, Garcia EJ, Merritt CR, Zamora JC, Bolinger AA, Pazdrak K, Stafford SJ, Mifflin RC, Wold EA, Wild CT, Chen H, Anastasio NC, Cunningham KA, Zhou J. Discovery of Novel Oleamide Analogues as Brain-Penetrant Positive Allosteric Serotonin 5-HT 2C Receptor and Dual 5-HT 2C/5-HT 2A Receptor Modulators. J Med Chem 2023; 66:9992-10009. [PMID: 37462530 PMCID: PMC10853020 DOI: 10.1021/acs.jmedchem.3c00908] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The serotonin 5-HT2A receptor (5-HT2AR) and 5-HT2CR localize to the brain and share overlapping signal transduction facets that contribute to their roles in cognition, mood, learning, and memory. Achieving selective targeting of these receptors is challenged by the similarity in their 5-HT orthosteric binding pockets. A fragment-based discovery approach was employed to design and synthesize novel oleamide analogues as selective 5-HT2CR or dual 5-HT2CR/5-HT2AR positive allosteric modulators (PAMs). Compound 13 (JPC0323) exhibited on-target properties, acceptable plasma exposure and brain penetration, as well as negligible displacement to orthosteric sites of ∼50 GPCRs and transporters. Furthermore, compound 13 suppressed novelty-induced locomotor activity in a 5-HT2CR-dependent manner, suggesting 5-HT2CR PAM, but not 5-HT2AR, activity at the level of the whole organism at the employed doses of 13. We discovered new selective 5-HT2CR PAMs and first-in-class 5-HT2CR/5-HT2AR dual PAMs that broaden the pharmacological toolbox to explore the biology of these vital receptors.
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Affiliation(s)
- Jianping Chen
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Erik J. Garcia
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Christina R. Merritt
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Joshua C. Zamora
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Andrew A. Bolinger
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Konrad Pazdrak
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Susan J. Stafford
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Randy C. Mifflin
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Eric A. Wold
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Christopher T. Wild
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Haiying Chen
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Noelle C. Anastasio
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Kathryn A. Cunningham
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Jia Zhou
- Center for Addiction Sciences and Therapeutics and Chemical Biology Program and Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
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5
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Lu L, Sun N, Wang Y. Development and therapeutic potential of allosteric retinoic acid receptor-related orphan receptor γt (RORγt) inverse agonists for autoimmune diseases. Eur J Med Chem 2023; 258:115574. [PMID: 37336069 DOI: 10.1016/j.ejmech.2023.115574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
The transcription factor retinoic acid receptor-related orphan receptor γt (RORγt) is an attractive drug target for some autoimmune diseases owing to its roles in the differentiation of human T helper 17 (Th17) cells which produce pro-inflammatory cytokine interleukin (IL)-17. RORγt agonists and inverse agonists are classically targeted to the hydrophobic and highly conserved orthosteric binding pocket of RORγt ligand binding domain (LBD). Although successful, this approach also brings some challenges, including off-target effects due to lack of selectivity over other nuclear receptors (NRs). Allosteric regulation of RORγt by synthetic small molecules has recently emerged as novel research interests for its interesting modes of action (MOA), satisfying bioactivity profile and improved selectivity. In this review, we delineated the discovery and identification of the allosteric pocket of RORγt. Subsequently, we focused on examples of small molecules that allosterically inhibit RORγt, with a central attention on structural-activity-relationship (SAR) information, biological activity, pharmacokinetic (PK) property, and the ligand binding mode of these compounds. We also discussed the potential role of RORγt allosteric inverse agonists as small molecule therapeutics for autoimmune diseases.
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Affiliation(s)
- Lixue Lu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China
| | - Nannan Sun
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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Luo ML, Zhao Q, He XH, Xie X, Zhu HP, You FM, Peng C, Zhan G, Huang W. Research progress of indole-fused derivatives as allosteric modulators: Opportunities for drug development. Biomed Pharmacother 2023; 162:114574. [PMID: 36996677 DOI: 10.1016/j.biopha.2023.114574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Allosteric modulation is a direct and effective method for regulating the function of biological macromolecules, which play vital roles in various cellular activities. Unlike orthosteric modulators, allosteric modulators bind to sites distant from the protein's orthosteric/active site and can have specific effects on the protein's function or activity without competing with endogenous ligands. Compared to traditional orthosteric modulators, allosteric modulators offer several advantages, including reduced side effects, greater specificity, and lower toxicity, making them a promising strategy for developing novel drugs. Indole-fused architectures are widely distributed in natural products and bioactive drug leads, displaying diverse biological activities that attract the interest of both chemists and biologists in drug discovery. Currently, an increasing number of indole-fused compounds have exhibited potent activities in allosteric modulation. In this review, we provide a brief summary of examples of allosteric modulators based on the indole-fused complex architecture, highlighting the strategies for drug design/discovery and the structure-activity relationships of allosteric modulators from the perspective of medicinal chemistry.
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7
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Sato S, Yamamoto K, Ito M, Nishino K, Otsuka T, Irie K, Nagao M. Enhancement of Inhibitory Activity by Combining Allosteric Inhibitors Putatively Binding to Different Allosteric Sites on Cathepsin K. Molecules 2023; 28:molecules28104197. [PMID: 37241936 DOI: 10.3390/molecules28104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Cathepsin K, which is involved in bone resorption, is a good target for treating osteoporosis, but no clinically approved medicine has been developed. Recently, allosteric inhibitors with high specificity and few side effects have been attracting attention for use in new medicines. METHODS Cathepsin K inhibitors were isolated from the methanol extract of Chamaecrista nomame (Leguminosae) using cathepsin K inhibition activity-assisted multi-step chromatography. Standard kinetic analysis was employed to examine the mechanism of cathepsin K inhibition when an isolated inhibitor and its derivative were used. The allosteric binding of these cathepsin K inhibitors was supported by a docking study using AutoDock vina. Combinations of allosteric cathepsin K inhibitors expected to bind to different allosteric sites were examined by means of cathepsin K inhibition assay. RESULTS Two types of cathepsin K inhibitors were identified in the methanol extract of Chamaecrista nomame. One type consisted of cassiaoccidentalin B and torachrysone 8-β-gentiobioside, and inhibited both cathepsin K and B with similar inhibitory potential, while the other type of inhibitor consisted of pheophytin a, and inhibited cathepsin K but not cathepsin B, suggesting that pheophytin a binds to an allosteric site of cathepsin K. Kinetic analysis of inhibitory activity suggested that pheophytin a and its derivative, pheophorbide b, bind allosterically to cathepsin K. This possibility was supported by a docking study on cathepsin K. The cathepsin K inhibitory activity of pheophytin a and pheophorbide b was enhanced by combining them with the allosteric inhibitors NSC 13345 and NSC94914, which bind to other allosteric sites on cathepsin K. CONCLUSIONS Different allosteric inhibitors that bind to different sites in combination, as shown in this study, may be useful for designing new allosteric inhibitory drugs with high specificity and few side effects.
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Affiliation(s)
- Shun Sato
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Kana Yamamoto
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Moeno Ito
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Takanao Otsuka
- Department of Applied Chemistry and Biotechnology, Okayama University of Science, Okayama 700-0005, Japan
| | - Kazuhiro Irie
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masaya Nagao
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
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8
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Baby K, Maity S, Mehta CH, Nayak UY, Shenoy GG, Pai KSR, Harikumar KB, Nayak Y. Computational drug repurposing of Akt-1 allosteric inhibitors for non-small cell lung cancer. Sci Rep 2023; 13:7947. [PMID: 37193898 DOI: 10.1038/s41598-023-35122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
Non-small cell lung carcinomas (NSCLC) are the predominant form of lung malignancy and the reason for the highest number of cancer-related deaths. Widespread deregulation of Akt, a serine/threonine kinase, has been reported in NSCLC. Allosteric Akt inhibitors bind in the space separating the Pleckstrin homology (PH) and catalytic domains, typically with tryptophan residue (Trp-80). This could decrease the regulatory site phosphorylation by stabilizing the PH-in conformation. Hence, in this study, a computational investigation was undertaken to identify allosteric Akt-1 inhibitors from FDA-approved drugs. The molecules were docked at standard precision (SP) and extra-precision (XP), followed by Prime molecular mechanics-generalized Born surface area (MM-GBSA), and molecular dynamics (MD) simulations on selected hits. Post XP-docking, fourteen best hits were identified from a library of 2115 optimized FDA-approved compounds, demonstrating several beneficial interactions such as pi-pi stacking, pi-cation, direct, and water-bridged hydrogen bonds with the crucial residues (Trp-80 and Tyr-272) and several amino acid residues in the allosteric ligand-binding pocket of Akt-1. Subsequent MD simulations to verify the stability of chosen drugs to the Akt-1 allosteric site showed valganciclovir, dasatinib, indacaterol, and novobiocin to have high stability. Further, predictions for possible biological interactions were performed using computational tools such as ProTox-II, CLC-Pred, and PASSOnline. The shortlisted drugs open a new class of allosteric Akt-1 inhibitors for the therapy of NSCLC.
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Affiliation(s)
- Krishnaprasad Baby
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Usha Y Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Gautham G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
| | - Karkala Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kuzhuvelil B Harikumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Abram M, Jakubiec M, Reeb K, Cheng MH, Gedschold R, Rapacz A, Mogilski S, Socała K, Nieoczym D, Szafarz M, Latacz G, Szulczyk B, Kalinowska-Tłuścik J, Gawel K, Esguerra CV, Wyska E, Müller CE, Bahar I, Fontana ACK, Wlaź P, Kamiński RM, Kamiński K. Discovery of ( R)- N-Benzyl-2-(2,5-dioxopyrrolidin-1-yl)propanamide [ (R)-AS-1], a Novel Orally Bioavailable EAAT2 Modulator with Drug-like Properties and Potent Antiseizure Activity In Vivo. J Med Chem 2022; 65:11703-11725. [PMID: 35984707 PMCID: PMC9469208 DOI: 10.1021/acs.jmedchem.2c00534] [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] [Indexed: 11/30/2022]
Abstract
(R)-7 [(R)-AS-1] showed broad-spectrum antiseizure activity across in vivo mouse seizure models: maximal electroshock (MES), 6 Hz (32/44 mA), acute pentylenetetrazol (PTZ), and PTZ-kindling. A remarkable separation between antiseizure activity and CNS-related adverse effects was also observed. In vitro studies with primary glia cultures and COS-7 cells expressing the glutamate transporter EAAT2 showed enhancement of glutamate uptake, revealing a stereoselective positive allosteric modulator (PAM) effect, further supported by molecular docking simulations. (R)-7 [(R)-AS-1] was not active in EAAT1 and EAAT3 assays and did not show significant off-target activity, including interactions with targets reported for marketed antiseizure drugs, indicative of a novel and unprecedented mechanism of action. Both in vivo pharmacokinetic and in vitro absorption, distribution, metabolism, excretion, toxicity (ADME-Tox) profiles confirmed the favorable drug-like potential of the compound. Thus, (R)-7 [(R)-AS-1] may be considered as the first-in-class small-molecule PAM of EAAT2 with potential for further preclinical and clinical development in epilepsy and possibly other CNS disorders.
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Affiliation(s)
- Michał Abram
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Marcin Jakubiec
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Katelyn Reeb
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania19102, United States
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15213, United States
| | - Robin Gedschold
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Anna Rapacz
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Szczepan Mogilski
- Department of Pharmacodynamics, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Katarzyna Socała
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Dorota Nieoczym
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Małgorzata Szafarz
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Bartłomiej Szulczyk
- Department of Pharmacodynamics, Centre for Preclinical Research and Technology, Medical University of Warsaw, Banacha 1B, 02-097Warsaw, Poland
| | - Justyna Kalinowska-Tłuścik
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387Krakow, Poland
| | - Kinga Gawel
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego 8B, 20-090Lublin, Poland
| | - Camila V Esguerra
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway, University of Oslo, Gaustadalléen 21, Forskningsparken, 0349Oslo, Norway
| | - Elżbieta Wyska
- Department of Pharmacokinetics and Physical Pharmacy, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121Bonn, Germany
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania15213, United States
| | - Andréia C K Fontana
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania19102, United States
| | - Piotr Wlaź
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033Lublin, Poland
| | - Rafał M Kamiński
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
| | - Krzysztof Kamiński
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688Krakow, Poland
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10
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Qiu Q, Abis G, Mattingly-Peck F, Lynham S, Fraternali F, Conte MR. Allosteric regulation of the soluble epoxide hydrolase by nitro fatty acids using a combined experimental and computational approach. J Mol Biol 2022; 434:167600. [PMID: 35460669 DOI: 10.1016/j.jmb.2022.167600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/31/2022] [Accepted: 04/17/2022] [Indexed: 11/18/2022]
Abstract
The human soluble epoxide hydrolase (hsEH) is a key regulator of epoxy fatty acid (EpFA) metabolism. Inhibition of sEH can maintain endogenous levels of beneficial EpFAs and reduce the levels of their corresponding diol products, thus ameliorating a variety of pathological conditions including cardiovascular, central nervous system and metabolic diseases. The quest for orthosteric drugs that bind directly to the catalytic crevice of hsEH has been prolonged and sustained over the past decades, but the disappointing outcome of clinical trials to date warrants alternative pharmacological approaches. Previously, we have shown that hsEH can be allosterically inhibited by the endogenous electrophilic lipid 15-deoxy-Δ12,14-Prostaglandin-J2, via covalent adduction to two cysteines, C423 and C522. In this study, we explore the properties and behaviour of three electrophilic lipids belonging to the class of the nitro fatty acids, namely 9- and 10-nitrooleate and 10-nitrolinoleate. Biochemical and biophysical investigations revealed that, in addition to C423 and C522, nitro fatty acids can covalently bind to additional nucleophilic residues in hsEH C-terminal domain (CTD), two of which predicted in this study to be latent allosteric sites. Systematic mapping of the protein mutational space and evaluation of possible propagation pathways delineated selected residues, both in the allosteric patches and in other regions of the enzyme, envisaged to play a role on allosteric signalling. The responses elicited by the ligands on the covalent adduction sites supports future fragment-based design studies of new allosteric effectors for hsEH with increased efficacy and selectivity.
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Affiliation(s)
- Qiongju Qiu
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Florence Mattingly-Peck
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, The James Black Centre, King's College London, London SE5 9NU, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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11
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SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations. PLoS One 2022; 17:e0265194. [PMID: 35298511 PMCID: PMC8929561 DOI: 10.1371/journal.pone.0265194] [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: 07/16/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet (“Structure ENSEmble NETworks”) framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology.
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12
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Ni D, Liu Y, Kong R, Yu Z, Lu S, Zhang J. Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discov Today 2022; 27:2226-2234. [DOI: 10.1016/j.drudis.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/22/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
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13
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Tze-Yang Ng J, Tan YS. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. J Chem Theory Comput 2022; 18:1969-1981. [PMID: 35175753 DOI: 10.1021/acs.jctc.1c01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The identification and characterization of binding sites is a critical component of structure-based drug design (SBDD). Probe-based/cosolvent molecular dynamics (MD) methods that allow for protein flexibility have been developed to predict ligand binding sites. However, cryptic pockets that appear only upon ligand binding and occluded binding sites with no access to the solvent pose significant challenges to these methods. Here, we report the development of accelerated ligand-mapping MD (aLMMD), which combines accelerated MD with LMMD, for the detection of these challenging binding sites. The method was validated on five proteins with what we term "recalcitrant" cryptic pockets, which are deeply buried pockets that require extensive movement of the protein backbone to expose, and three proteins with occluded binding sites. In all the cases, aLMMD was able to detect and sample the binding sites. Our results suggest that aLMMD could be used as a general approach for the detection of such elusive binding sites in protein targets, thus providing valuable information for SBDD.
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Affiliation(s)
- Justin Tze-Yang Ng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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14
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Rehman AU, Lu S, Khan AA, Khurshid B, Rasheed S, Wadood A, Zhang J. Hidden allosteric sites and De-Novo drug design. Expert Opin Drug Discov 2021; 17:283-295. [PMID: 34933653 DOI: 10.1080/17460441.2022.2017876] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Hidden allosteric sites are not visible in apo-crystal structures, but they may be visible in holo-structures when a certain ligand binds and maintains the ligand intended conformation. Several computational and experimental techniques have been used to investigate these hidden sites but identifying them remains a challenge. AREAS COVERED This review provides a summary of the many theoretical approaches for predicting hidden allosteric sites in disease-related proteins. Furthermore, promising cases have been thoroughly examined to reveal the hidden allosteric site and its modulator. EXPERT OPINION In the recent past, with the development in scientific techniques and bioinformatics tools, the number of drug targets for complex human diseases has significantly increased but unfortunately most of these targets are undruggable due to several reasons. Alternative strategies such as finding cryptic (hidden) allosteric sites are an attractive approach for exploitation of the discovery of new targets. These hidden sites are difficult to recognize compared to allosteric sites, mainly due to a lack of visibility in the crystal structure. In our opinion, after many years of development, MD simulations are finally becoming successful for obtaining a detailed molecular description of drug-target interaction.
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Affiliation(s)
- Ashfaq Ur Rehman
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Abdul Aziz Khan
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Institute of Psychology and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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15
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Ni D, Chai Z, Wang Y, Li M, Yu Z, Liu Y, Lu S, Zhang J. Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Duan Ni
- College of Pharmacy Ningxia Medical University Yinchuan China
- The Charles Perkins Centre University of Sydney Sydney New South Wales Australia
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital Second Military Medical University Shanghai China
| | - Ying Wang
- 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 China
| | - Mingyu Li
- 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 China
| | | | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Shaoyong Lu
- College of Pharmacy Ningxia Medical University Yinchuan 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 China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jian Zhang
- College of Pharmacy Ningxia Medical University Yinchuan 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 China
- Medicinal Chemistry and Bioinformatics Center Shanghai Jiao Tong University School of Medicine Shanghai China
- School of Pharmaceutical Sciences Zhengzhou University Zhengzhou China
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16
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Lu S, He X, Yang Z, Chai Z, Zhou S, Wang J, Rehman AU, Ni D, Pu J, Sun J, Zhang J. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nat Commun 2021; 12:4721. [PMID: 34354057 PMCID: PMC8342441 DOI: 10.1038/s41467-021-25020-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 07/17/2021] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the most common proteins targeted by approved drugs. A complete mechanistic elucidation of large-scale conformational transitions underlying the activation mechanisms of GPCRs is of critical importance for therapeutic drug development. Here, we apply a combined computational and experimental framework integrating extensive molecular dynamics simulations, Markov state models, site-directed mutagenesis, and conformational biosensors to investigate the conformational landscape of the angiotensin II (AngII) type 1 receptor (AT1 receptor) - a prototypical class A GPCR-activation. Our findings suggest a synergistic transition mechanism for AT1 receptor activation. A key intermediate state is identified in the activation pathway, which possesses a cryptic binding site within the intracellular region of the receptor. Mutation of this cryptic site prevents activation of the downstream G protein signaling and β-arrestin-mediated pathways by the endogenous AngII octapeptide agonist, suggesting an allosteric regulatory mechanism. Together, these findings provide a deeper understanding of AT1 receptor activation at an atomic level and suggest avenues for the design of allosteric AT1 receptor modulators with a broad range of applications in GPCR biology, biophysics, and medicinal chemistry.
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Affiliation(s)
- Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, 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, China.
| | - Xinheng He
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Material Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhao Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shuhua Zhou
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Junyan Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Ashfaq Ur Rehman
- 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, China
| | - Duan Ni
- 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, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jinpeng Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China.
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, 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, China.
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
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17
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Wei S, Zhao T, Wang J, Zhai X. Approach in Improving Potency and Selectivity of Kinase Inhibitors: Allosteric Kinase Inhibitors. Mini Rev Med Chem 2021; 21:991-1003. [PMID: 33355051 DOI: 10.2174/1389557521666201222144355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have a distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for the treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structure-activity relationships, ligand-protein interactions, and in vitro and in vivo activity. Additionally, challenges, as well as opportunities, are also presented.
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Affiliation(s)
- Shangfei Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianming Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jie Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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18
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Huang Q, Song P, Chen Y, Liu Z, Lai L. Allosteric Type and Pathways Are Governed by the Forces of Protein-Ligand Binding. J Phys Chem Lett 2021; 12:5404-5412. [PMID: 34080881 DOI: 10.1021/acs.jpclett.1c01253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Allostery is central to many cellular processes, by up- or down-regulating target function. However, what determines the allosteric type remains elusive and currently it is impossible to predict whether the allosteric compounds would activate or inhibit target function before experimental studies. We demonstrated that the allosteric type and allosteric pathways are governed by the forces imposed by ligand binding to target protein using the anisotropic network model and developed an allosteric type prediction method (AlloType). AlloType correctly predicted 13 of the 16 allosteric systems in the data set with experimentally determined protein and complex structures as well as verified allosteric types, which was also used to identify allosteric pathways. When applied to glutathione peroxidase 4, a protein with no complex structure information, AlloType could still be able to predict the allosteric type of the recently reported allosteric activators, demonstrating its potential application in designing specific allosteric drugs and uncovering allosteric mechanisms.
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Affiliation(s)
- Qiaojing Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Pengbo Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yixin Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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19
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Qiu Y, Yin X, Li X, Wang Y, Fu Q, Huang R, Lu S. Untangling Dual-Targeting Therapeutic Mechanism of Epidermal Growth Factor Receptor (EGFR) Based on Reversed Allosteric Communication. Pharmaceutics 2021; 13:747. [PMID: 34070173 PMCID: PMC8158526 DOI: 10.3390/pharmaceutics13050747] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022] Open
Abstract
Dual-targeting therapeutics by coadministration of allosteric and orthosteric drugs is drawing increased attention as a revolutionary strategy for overcoming the drug-resistance problems. It was further observed that the occupation of orthosteric sites by therapeutics agents has the potential to enhance allosteric ligand binding, which leads to improved potency of allosteric drugs. Epidermal growth factor receptor (EGFR), as one of the most critical anti-cancer targets belonging to the receptor tyrosine kinase family, represents a quintessential example. It was revealed that osimertinib, an ATP-competitive covalent EGFR inhibitor, remarkably enhanced the affinity of a recently developed allosteric inhibitor JBJ-04-125-02 for EGFRL858R/T790M. Here, we utilized extensive large-scale molecular dynamics simulations and the reversed allosteric communication to untangle the detailed molecular underpinning, in which occupation of osimertinib at the orthosteric site altered the overall conformational ensemble of EGFR mutant and reshaped the allosteric site via long-distance signaling. A unique intermediate state resembling the active conformation was identified, which was further stabilized by osimertinib loading. Based on the allosteric communication pathway, we predicted a novel allosteric site positioned around K867, E868, H893, and K960 within the intermediate state. Its correlation with the orthosteric site was validated by both structural and energetic analysis, and its low sequence conservation indicated the potential for selective targeting across the human kinome. Together, these findings not only provided a mechanistic basis for future clinical application of the dual-targeting therapeutics, but also explored an innovative perception of allosteric inhibition of tyrosine kinase signaling.
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Affiliation(s)
- Yuran Qiu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (Y.Q.); (X.L.); (Y.W.)
| | - Xiaolan Yin
- Department of Radiotherapy, Changhai Hospital (Hongkou District), Naval Medical University, Shanghai 200081, China;
| | - Xinyi Li
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (Y.Q.); (X.L.); (Y.W.)
| | - Yuanhao Wang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (Y.Q.); (X.L.); (Y.W.)
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080, China
| | - Renhua Huang
- Department of Radiation, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (Y.Q.); (X.L.); (Y.W.)
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20
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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21
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Popova NV, Jücker M. The Role of mTOR Signaling as a Therapeutic Target in Cancer. Int J Mol Sci 2021; 22:ijms22041743. [PMID: 33572326 PMCID: PMC7916160 DOI: 10.3390/ijms22041743] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/30/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
The aim of this review was to summarize current available information about the role of phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling in cancer as a potential target for new therapy options. The mTOR and PI3K/AKT/mTORC1 (mTOR complex 1) signaling are critical for the regulation of many fundamental cell processes including protein synthesis, cell growth, metabolism, survival, catabolism, and autophagy, and deregulated mTOR signaling is implicated in cancer, metabolic dysregulation, and the aging process. In this review, we summarize the information about the structure and function of the mTOR pathway and discuss the mechanisms of its deregulation in human cancers including genetic alterations of PI3K/AKT/mTOR pathway components. We also present recent data regarding the PI3K/AKT/mTOR inhibitors in clinical studies and the treatment of cancer, as well the attendant problems of resistance and adverse effects.
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Affiliation(s)
- Nadezhda V. Popova
- Laboratory of Receptor Cell Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia;
| | - Manfred Jücker
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
- Correspondence: ; Tel.: +49-(0)-40-7410-56339
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22
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Das N, Benko C, Gill SE, Dufour A. The Pharmacological TAILS of Matrix Metalloproteinases and Their Inhibitors. Pharmaceuticals (Basel) 2020; 14:ph14010031. [PMID: 33396445 PMCID: PMC7823758 DOI: 10.3390/ph14010031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 01/07/2023] Open
Abstract
Matrix metalloproteinases (MMPs) have been demonstrated to have both detrimental and protective functions in inflammatory diseases. Several MMP inhibitors, with the exception of Periostat®, have failed in Phase III clinical trials. As an alternative strategy, recent efforts have been focussed on the development of more selective inhibitors or targeting other domains than their active sites through specific small molecule inhibitors or monoclonal antibodies. Here, we present some examples that aim to better understand the mechanisms of conformational changes/allosteric control of MMPs functions. In addition to MMP inhibitors, we discuss unbiased global approaches, such as proteomics and N-terminomics, to identify new MMP substrates. We present some examples of new MMP substrates and their implications in regulating biological functions. By characterizing the roles and substrates of individual MMP, MMP inhibitors could be utilized more effectively in the optimal disease context or in diseases never tested before where MMP activity is elevated and contributing to disease progression.
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Affiliation(s)
- Nabangshu Das
- Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 4N1, Canada;
- McCaig Institute for Bone and Join Healthy, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada;
| | - Colette Benko
- McCaig Institute for Bone and Join Healthy, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada;
- Department of Physiology and Pharmacology, Cumming School of Medicine, Foothills Hospital, 3330 Hospital Dr, Calgary, AB T2N 4N1, Canada
| | - Sean E. Gill
- Centre for Critical Illness Research, Victoria Research Labs, Lawson Health Research Institute, A6-134, London, ON N6A 5W9, Canada;
- Division of Respirology, Department of Medicine, Western University, London, ON N6A 5W9, Canada
| | - Antoine Dufour
- Faculty of Kinesiology, University of Calgary, Calgary, AB T2N 4N1, Canada;
- McCaig Institute for Bone and Join Healthy, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada;
- Department of Physiology and Pharmacology, Cumming School of Medicine, Foothills Hospital, 3330 Hospital Dr, Calgary, AB T2N 4N1, Canada
- Correspondence:
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23
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Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
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Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
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24
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Making NSCLC Crystal Clear: How Kinase Structures Revolutionized Lung Cancer Treatment. CRYSTALS 2020. [DOI: 10.3390/cryst10090725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The parallel advances of different scientific fields provide a contemporary scenario where collaboration is not a differential, but actually a requirement. In this context, crystallography has had a major contribution on the medical sciences, providing a “face” for targets of diseases that previously were known solely by name or sequence. Worldwide, cancer still leads the number of annual deaths, with 9.6 million associated deaths, with a major contribution from lung cancer and its 1.7 million deaths. Since the relationship between cancer and kinases was unraveled, these proteins have been extensively explored and became associated with drugs that later attained blockbuster status. Crystallographic structures of kinases related to lung cancer and their developed and marketed drugs provided insight on their conformation in the absence or presence of small molecules. Notwithstanding, these structures were also of service once the initially highly successful drugs started to lose their effectiveness in the emergence of mutations. This review focuses on a subclassification of lung cancer, non-small cell lung cancer (NSCLC), and major oncogenic driver mutations in kinases, and how crystallographic structures can be used, not only to provide awareness of the function and inhibition of these mutations, but also how these structures can be used in further computational studies aiming at addressing these novel mutations in the field of personalized medicine.
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25
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Al-Horani RA, Kar S. Factor XIIIa inhibitors as potential novel drugs for venous thromboembolism. Eur J Med Chem 2020; 200:112442. [PMID: 32502864 PMCID: PMC7513741 DOI: 10.1016/j.ejmech.2020.112442] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/11/2022]
Abstract
Human factor XIIIa (FXIIIa) is a multifunctional transglutaminase with a significant role in hemostasis. FXIIIa catalyzes the last step in the coagulation process. It stabilizes the blood clot by cross-linking the α- and γ-chains of fibrin. It also protects the newly formed clot from plasmin-mediated fibrinolysis, primarily by cross-linking α2-antiplasmin to fibrin. Furthermore, FXIIIa is a major determinant of clot size and clot's red blood cells content. Therefore, inhibitors targeting FXIIIa have been considered to develop a new generation of anticoagulants to prevent and/or treat venous thromboembolism. Several inhibitors of FXIIIa have been discovered or designed including active site and allosteric site small molecule inhibitors as well as natural and modified polypeptides. This work reviews the structural, biochemical, and pharmacological aspects of FXIIIa inhibitors so as to advance their molecular design to become more clinically relevant.
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Affiliation(s)
- Rami A Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, 70125, USA.
| | - Srabani Kar
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, 70125, USA
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26
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Liu X, Lu S, Song K, Shen Q, Ni D, Li Q, He X, Zhang H, Wang Q, Chen Y, Li X, Wu J, Sheng C, Chen G, Liu Y, Lu X, Zhang J. Unraveling allosteric landscapes of allosterome with ASD. Nucleic Acids Res 2020; 48:D394-D401. [PMID: 31665428 PMCID: PMC7145546 DOI: 10.1093/nar/gkz958] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/30/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022] Open
Abstract
Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an orthosteric site. The Allosteric Database (ASD, available online at http://mdl.shsmu.edu.cn/ASD) was developed ten years ago to provide comprehensive information related to allosteric regulation. In recent years, allosteric regulation has received great attention in biological research, bioengineering, and drug discovery, leading to the emergence of entire allosteric landscapes as allosteromes. To facilitate research from the perspective of the allosterome, in ASD 2019, novel features were curated as follows: (i) >10 000 potential allosteric sites of human proteins were deposited for allosteric drug discovery; (ii) 7 human allosterome maps, including protease and ion channel maps, were built to reveal allosteric evolution within families; (iii) 1312 somatic missense mutations at allosteric sites were collected from patient samples from 33 cancer types and (iv) 1493 pharmacophores extracted from allosteric sites were provided for modulator screening. Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future.
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Affiliation(s)
- Xinyi Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Shaoyong Lu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Kun Song
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Qiancheng Shen
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Duan Ni
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qian Li
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Xinheng He
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Hao Zhang
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Qi Wang
- China National Pharmaceutical Industry Information Center, Shanghai, 200040, China
| | - Yingyi Chen
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Xinyi Li
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jing Wu
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guoqiang Chen
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yaqin Liu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xuefeng Lu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Jian Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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27
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Tan ZW, Tee WV, Guarnera E, Booth L, Berezovsky IN. AlloMAPS: allosteric mutation analysis and polymorphism of signaling database. Nucleic Acids Res 2020; 47:D265-D270. [PMID: 30365033 PMCID: PMC6323965 DOI: 10.1093/nar/gky1028] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023] Open
Abstract
AlloMAPS database provides data on the causality and energetics of allosteric communication obtained with the structure-based statistical mechanical model of allostery (SBSMMA). The database contains data on allosteric signaling in three sets of proteins and protein chains: (i) 46 proteins with comprehensively annotated functional and allosteric sites; (ii) 1908 protein chains from PDBselect set of chains with low (<25%) sequence identity; (iii) 33 proteins with more than 50 known pathological SNPs in each molecule. In addition to energetics of allosteric signaling between known functional and regulatory sites, allosteric modulation caused by the binding to these sites, by SNPs, and by mutations designated by the user can be explored. Allosteric Signaling Maps (ASMs), which are produced via the exhaustive computational scanning for stabilizing and destabilizing mutations and for the modulation range caused by the sequence position are available for each protein/protein chain in the database. We propose to use this database for evaluating the effects of allosteric signaling in the search for latent regulatory sites and in the design of allosteric sites and effectors. The database is freely available at: http://allomaps.bii.a-star.edu.sg.
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore
| | - Wei-Ven Tee
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579 Singapore
| | - Enrico Guarnera
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore
| | - Lauren Booth
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore.,Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Igor N Berezovsky
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671 Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579 Singapore
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28
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Inhibitors of blood coagulation factor XIII. Anal Biochem 2020; 605:113708. [PMID: 32335064 DOI: 10.1016/j.ab.2020.113708] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
The blood coagulation factor XIII (FXIII) plays an essential role in the stabilization of fibrin clots. This factor, belonging to the class of transglutaminases, catalyzes the final step of secondary hemostasis, i.e. the crosslinking of fibrin polymers. These crosslinks protect the clots against premature fibrinolysis. Consequently, FXIII is an interesting target for the therapeutic treatment of cardiovascular diseases. In this context, inhibitors can influence FXIII in the activation process of the enzyme itself or in its catalytic activity. To date, there is no FXIII inhibitor in medical application, but several studies have been conducted in the past. These studies provided a better understanding of FXIII and identified new lead structures for FXIII inhibitors. Next to small molecule inhibitors, the most promising candidates for the development of clinically applicable FXIII inhibitors are the peptide inhibitors tridegin and transglutaminase-inhibiting Michael acceptors (TIMAs) due to their selectivity towards activated FXIII (FXIIIa). In this review, select FXIII inhibitors and their pharmacological potential are discussed.
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29
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Lake PT, Davidson RB, Klem H, Hocky GM, McCullagh M. Residue-Level Allostery Propagates through the Effective Coarse-Grained Hessian. J Chem Theory Comput 2020; 16:3385-3395. [PMID: 32251581 DOI: 10.1021/acs.jctc.9b01149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-ranged coupling between residues that gives rise to allostery in a protein is built up from short-ranged physical interactions. Computational tools used to predict this coupling and its functional relevance have relied on the application of graph theoretical metrics to residue-level correlations measured from all-atom molecular dynamics simulations. The short-ranged interactions that yield these long-ranged residue-level correlations are quantified by the effective coarse-grained Hessian. Here we compute an effective harmonic coarse-grained Hessian from simulations of a benchmark allosteric protein, IGPS, and demonstrate the improved locality of this graph Laplacian over two other connectivity matrices. Additionally, two centrality metrics are developed that indicate the direct and indirect importance of each residue at producing the covariance between the effector binding pocket and the active site. The residue importance indicated by these two metrics is corroborated by previous mutagenesis experiments and leads to unique functional insights; in contrast to previous computational analyses, our results suggest that fP76-hK181 is the most important contact for conveying direct allosteric paths across the HisF-HisH interface. The connectivity around fD98 is found to be important at affecting allostery through indirect means.
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Affiliation(s)
- Peter T Lake
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Russell B Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Heidi Klem
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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30
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Ni D, Li Y, Qiu Y, Pu J, Lu S, Zhang J. Combining Allosteric and Orthosteric Drugs to Overcome Drug Resistance. Trends Pharmacol Sci 2020; 41:336-348. [PMID: 32171554 DOI: 10.1016/j.tips.2020.02.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
Historically, most drugs target protein orthosteric sites. The gradual emergence of resistance hampers their therapeutic effectiveness, posing a challenge to drug development. Coadministration of allosteric and orthosteric drugs provides a revolutionary strategy to circumvent drug resistance, as drugs targeting the topologically distinct allosteric sites can restore or even enhance the efficacy of orthosteric drugs. Here, we comprehensively review the latest successful examples of such combination treatments against drug resistance, with a focus on their modes of action and the underlying structural mechanisms. Our work supplies an innovative insight into such promising methodology against the recalcitrant drug resistance conundrum and will be instructive for future clinical therapeutics.
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Affiliation(s)
- Duan Ni
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; The Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yun Li
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuran Qiu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jun Pu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Jian Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Medicinal Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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31
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The past, present and future perspectives of matrix metalloproteinase inhibitors. Pharmacol Ther 2020; 207:107465. [DOI: 10.1016/j.pharmthera.2019.107465] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
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32
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Protein-protein complexes as targets for drug discovery against infectious diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:237-251. [PMID: 32312423 DOI: 10.1016/bs.apcsb.2019.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Antibiotics are therapeutic agents against bacterial infections, however, the emergence of multiple and extremely drug-resistant microbes (Multi-Drug Resistant and Extremely Drug-Resistant) are compromising the effectiveness of the currently available treatment options. The drug resistance is not a novel crisis, the current pace of drug discovery has failed to compete with the growth of MDR and XDR pathogenic strains and therefore, it is highly central to find out novel antimicrobial drugs with unique mechanisms of action which may reduce the burden of MDR and XDR pathogenic strains. Protein-protein interactions (PPIs) are involved in a countless of the physiological and cellular phenomena and have become an attractive target to treat the diseases. Therefore, targeting PPIs in infectious agents may offer a completely novel strategy of intervention to develop anti-infective drugs that may combat the ever-increasing rate of drug resistant strains. This chapter describes how small molecule candidate inhibitors that are capable of disrupting the PPIs in pathogenic microbes and it could be an alternative lead discovery strategy to obtain novel antibiotics. Over the last three decades, there has been increasing efforts focused on the manipulation of PPIs in order to develop novel therapeutic interventions. The diversity and complexity of such a complex and highly dynamic systems pose many challenges in targeting PPIs by drug-like molecules with necessary selectivity and potency. Traditional and novel drug discovery strategies have provided tools for designing and assessing PPI inhibitors against infectious diseases.
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33
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Xu X, Chen Y, Fu Q, Ni D, Zhang J, Li X, Lu S. The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. J Enzyme Inhib Med Chem 2019; 34:361-374. [PMID: 30734603 PMCID: PMC6327997 DOI: 10.1080/14756366.2018.1553167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/06/2023] Open
Abstract
Phosphoinositide-dependent protein kinase-1 (PDK1) is an important protein in mediating the PI3K-AKT pathway and is thus identified as a promising target. The catalytic activity of PDK1 is tightly regulated by allosteric modulators, which bind to the PDK1 Interacting Fragment (PIF) pocket of the kinase domain that is topographically distinct from the orthosteric, ATP binding site. Allosteric modulators by attaching to the less conserved PIF-pocket have remarkable advantages such as higher selectivity, less side effect, and lower toxicity. Targeting allosteric PIF-pocket of PDK1 has become the focus of recent attention. In this review, we summarise the current advances in the structure-based discovery of PDK1 allosteric modulators. We will first present the three-dimensional structure of PDK1 and illustrate the allosteric regulatory mechanism of PDK1 through the modulation of the PIF-pocket. Then, the recent advances of PDK1 allosteric modulators targeting the PIF-pocket will be recapitulated detailly according to the structural similarity of allosteric modulators.
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Affiliation(s)
- Xinyuan Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yingyi Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, 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
| | - Jian 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
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, 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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34
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Dynamic Protein Allosteric Regulation and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:25-43. [DOI: 10.1007/978-981-13-8719-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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35
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Musyoka T, Bishop ÖT. South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches. Molecules 2019; 24:E4036. [PMID: 31703388 PMCID: PMC6891524 DOI: 10.3390/molecules24224036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
The hemoglobin degradation process in Plasmodium parasites is vital for nutrient acquisition required for their growth and proliferation. In P. falciparum, falcipains (FP-2 and FP-3) are the major hemoglobinases, and remain attractive antimalarial drug targets. Other Plasmodium species also possess highly homologous proteins to FP-2 and FP-3. Although several inhibitors have been designed against these proteins, none has been commercialized due to associated toxicity on human cathepsins (Cat-K, Cat-L and Cat-S). Despite the two enzyme groups sharing a common structural fold and catalytic mechanism, distinct active site variations have been identified, and can be exploited for drug development. Here, we utilize in silico approaches to screen 628 compounds from the South African natural sources to identify potential hits that can selectively inhibit the plasmodial proteases. Using docking studies, seven abietane diterpenoids, binding strongly to the plasmodial proteases, and three additional analogs from PubChem were identified. Important residues involved in ligand stabilization were identified for all potential hits through binding pose analysis and their energetic contribution determined by binding free energy calculations. The identified compounds present important scaffolds that could be further developed as plasmodial protease inhibitors. Previous laboratory assays showed the effect of the seven diterpenoids as antimalarials. Here, for the first time, we demonstrate that their possible mechanism of action could be by interacting with falcipains and their plasmodial homologs. Dynamic residue network (DRN) analysis on the plasmodial proteases identified functionally important residues, including a region with high betweenness centrality, which had previously been proposed as a potential allosteric site in FP-2.
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Affiliation(s)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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36
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Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery. Drug Discov Today 2019; 25:177-184. [PMID: 31634592 DOI: 10.1016/j.drudis.2019.10.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/28/2019] [Accepted: 10/11/2019] [Indexed: 01/31/2023]
Abstract
Allosteric drugs have several significant advantages over traditional orthosteric drugs, encompassing higher selectivity and lower toxicity. Although allosteric drugs have potential advantages as therapeutic agents to treat human diseases, allosteric drug-resistance mutations still occur, rendering these drugs ineffective. Here, we review the emergence of allosteric drug-resistance mutations with an emphasis on examples covering clinically important therapeutic targets, including Breakpoint cluster region-Abelson tyrosine kinase (Bcr-Abl), Akt kinase [also called Protein Kinase B (PKB)], isocitrate dehydrogenase (IDH), MAPK/ERK kinase (MEK), and SRC homology 2 domain-containing phosphatase 2 (SHP2). We also discuss challenges associated with tackling allosteric drug resistance and the possible strategies to overcome this issue.
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Sakamoto S, Yamaura K, Numata T, Harada F, Amaike K, Inoue R, Kiyonaka S, Hamachi I. Construction of a Fluorescent Screening System of Allosteric Modulators for the GABA A Receptor Using a Turn-On Probe. ACS CENTRAL SCIENCE 2019; 5:1541-1553. [PMID: 31572781 PMCID: PMC6764212 DOI: 10.1021/acscentsci.9b00539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Indexed: 05/23/2023]
Abstract
γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system. The fast inhibitory actions of GABA are mainly mediated by GABAA receptors (GABAARs), which are widely recognized as clinically relevant drug targets. However, it remains difficult to create screening systems for drug candidates that act on GABAARs because of the existence of multiple ligand-binding sites and the delicate pentameric structures of GABAARs. We here developed the first turn-on fluorescent imaging probe for GABAARs, which can be used to quantitatively evaluate ligand-receptor interactions under live cell conditions. Using noncovalent labeling of GABAARs with this turn-on probe, a new imaging-based ligand assay system, which allows discovery of positive allosteric modulators (PAMs) for the GABAAR, was successfully constructed. Our system is applicable to high-throughput ligand screening, and we discovered new small molecules that function as PAMs for GABAARs. These results highlight the power of the use of a turn-on fluorescent probe to screen drugs for complicated membrane proteins that cannot be addressed by conventional methods.
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Affiliation(s)
- Seiji Sakamoto
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kei Yamaura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomohiro Numata
- Department
of Physiology, School of Medicine, Fukuoka
University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Fumio Harada
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuma Amaike
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ryuji Inoue
- Department
of Physiology, School of Medicine, Fukuoka
University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shigeki Kiyonaka
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO
Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST), Kyoto 615-8530, Japan
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38
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Huang M, Song K, Liu X, Lu S, Shen Q, Wang R, Gao J, Hong Y, Li Q, Ni D, Xu J, Chen G, Zhang J. AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Res 2019; 46:W451-W458. [PMID: 29757429 PMCID: PMC6030990 DOI: 10.1093/nar/gky374] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/28/2018] [Indexed: 01/07/2023] Open
Abstract
Allostery tweaks innumerable biological processes and plays a fundamental role in human disease and drug discovery. Exploration of allostery has thus been regarded as a crucial requirement for research on biological mechanisms and the development of novel therapeutics. Here, based on our previously developed allosteric data and methods, we present an interactive platform called AlloFinder that identifies potential endogenous or exogenous allosteric modulators and their involvement in human allosterome. AlloFinder automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator-protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. This web server exhibits prominent performance in the reemergence of allosteric metabolites and exogenous allosteric modulators in known allosteric proteins. Specifically, AlloFinder enables identification of allosteric metabolites for metabolic enzymes and screening of potential allosteric compounds for disease-related targets. Significantly, the feasibility of AlloFinder to discover allosteric modulators was tested in a real case of signal transduction and activation of transcription 3 (STAT3) and validated by mutagenesis and functional experiments. Collectively, AlloFinder is expected to contribute to exploration of the mechanisms of allosteric regulation between metabolites and metabolic enzymes, and to accelerate allosteric drug discovery. The AlloFinder web server is freely available to all users at http://mdl.shsmu.edu.cn/ALF/.
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Affiliation(s)
- Min Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Kun Song
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Xinyi Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, 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 (SJTU-SM), Shanghai 200025, China
| | - Qiancheng Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Renxiao Wang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingze Gao
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Yuanyuan Hong
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Qian Li
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, 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 (SJTU-SM), Shanghai 200025, China
| | - Jianrong Xu
- Department of Pharmacology, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Guoqiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
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Hernández González JE, Hernández Alvarez L, Pascutti PG, Leite VBP. Prediction of Noncompetitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2. J Phys Chem B 2019; 123:7327-7342. [DOI: 10.1021/acs.jpcb.9b05021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Lilian Hernández Alvarez
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
| | - Pedro Geraldo Pascutti
- Laboratório de Dinâmica e Modelagem Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Ave. Carlos
Chagas Filho, 373, CCS-Bloco D sala 30, Cidade Universitária
Ilha de Fundão, Rio de Janeiro, CEP 21941-902, Brazil
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo,
2265, Jardim Nazareth, São José do Rio Preto, São Paulo, CEP 15054-000, Brazil
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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40
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Revathidevi S, Munirajan AK. Akt in cancer: Mediator and more. Semin Cancer Biol 2019; 59:80-91. [PMID: 31173856 DOI: 10.1016/j.semcancer.2019.06.002] [Citation(s) in RCA: 379] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/29/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023]
Abstract
Akt is a serine/threonine kinase and it participates in the key role of the PI3K signaling pathway. The Akt can be activated by a wide range of growth signals and the biochemical mechanisms leading to Akt activation are well defined. Once activated, Akt modulates the function of many downstream proteins involved in cellular survival, proliferation, migration, metabolism, and angiogenesis. The Akt is a central node of many signaling pathways and it is frequently deregulated in many types of human cancers. In this review, we provide an overview of Akt function and its role in the hallmarks of human cancer. We also discussed various mechanisms of Akt dysregulation in cancers, including epigenetic modifications like methylation, post-transcriptional non-coding RNAs-mediated regulation, and the overexpression and mutation.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 113, Tamil Nadu, India
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 113, Tamil Nadu, India.
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41
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Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
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Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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42
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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43
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Li J, Fu Q, Liang Y, Cheng B, Li X. Microsecond molecular dynamics simulations and dynamic network analysis provide understanding of the allosteric inactivation of GSK3β induced by the L343R mutation. J Mol Model 2019; 25:111. [DOI: 10.1007/s00894-019-4003-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
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44
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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
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45
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Guarnera E, Berezovsky IN. Toward Comprehensive Allosteric Control over Protein Activity. Structure 2019; 27:866-878.e1. [PMID: 30827842 DOI: 10.1016/j.str.2019.01.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/23/2018] [Accepted: 01/25/2019] [Indexed: 01/14/2023]
Abstract
Universality of allosteric signaling in proteins, molecular machines, and receptors complemented by the great advantages of prospected allosteric drugs in the highly specific, non-competitive, and modulatory nature of their actions calls for deeper theoretical understanding of allosteric communication. We present a computational model that makes it possible to tackle the problem of modulating the energetics of protein allosteric communication. In the context of the energy landscape paradigm, allosteric signaling is always a result of perturbations, such as ligand binding, mutations, and intermolecular interactions. The calculation of local partition functions in the protein harmonic model with perturbations allows us to evaluate the energetics of allosteric communication at the single-residue level. In this framework, Allosteric Signaling Maps are proposed as a tool to exhaustively describe allosteric communication in the protein, to tune already existing signaling, and to design new elements of regulation for taking the protein activity under allosteric control.
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Affiliation(s)
- Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117579, Singapore.
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46
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Lu S, He X, Ni D, Zhang J. Allosteric Modulator Discovery: From Serendipity to Structure-Based Design. J Med Chem 2019; 62:6405-6421. [PMID: 30817889 DOI: 10.1021/acs.jmedchem.8b01749] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
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47
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Lu S, Shen Q, Zhang J. Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms. Acc Chem Res 2019; 52:492-500. [PMID: 30688063 DOI: 10.1021/acs.accounts.8b00570] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Allostery, or allosteric regulation, is the phenomenon in which protein functional activity is altered by the binding of an effector at an allosteric site that is topographically distinct from the orthosteric, active site. As one of the most direct and efficient ways to regulate protein function, allostery has played a fundamental role in innumerable biological processes of all living organisms, including enzyme catalysis, signal transduction, cell metabolism, and gene transcription. It is thus considered as "the second secret of life". The abnormality of allosteric communication networks between allosteric and orthosteric sites is associated with the pathogenesis of human diseases. Allosteric modulators, by attaching to structurally diverse allosteric sites, offer the potential for differential selectivity and improved safety compared with orthosteric drugs that bind to conserved orthosteric sites. Harnessing allostery has thus been regarded as a novel strategy for drug discovery. Despite much progress having been made in the repertoire of allostery since the turn of the millennium, the identification of allosteric drugs for therapeutic targets and the elucidation of allosteric mechanisms still present substantial challenges. These challenges are derived from the difficulties in the identification of allosteric sites and mutations, the assessment of allosteric protein-modulator interactions, the screening of allosteric modulators, and the elucidation of allosteric mechanisms in biological systems. To address these issues, we have developed a panel of allosteric services for specific allosteric applications over the past decade, including (i) the creation of the Allosteric Database, with the aim of providing comprehensive allosteric information such as allosteric proteins, modulators, sites, pathways, etc., (ii) the construction of the ASBench benchmark of high-quality allosteric sites for the development of computational methods for predicting allosteric sites, (iii) the development of Allosite and AllositePro for the prediction of the location of allosteric sites in proteins, (iv) the development of the Alloscore scoring function for the evaluation of allosteric protein-modulator interactions, (v) the development of Allosterome for evolutionary analysis of query allosteric sites/modulators within the human proteome, (vi) the development of AlloDriver for the prediction of allosteric mutagenesis, and (vii) the development of AlloFinder for the virtual screening of allosteric modulators and the investigation of allosteric mechanisms. Importantly, we have validated computationally predicted allosteric sites, mutations, and modulators in the real cases of sirtuin 6, casein kinase 2α, phosphodiesterase 10A, and signal transduction and activation of transcription 3. Furthermore, our developed allosteric methods have been widely exploited by other users around the world for allosteric research. Therefore, these allosteric services are expected to expedite the discovery of allosteric drugs and the investigation of allosteric mechanisms.
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Affiliation(s)
- 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 200025, China
| | - Qiancheng Shen
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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48
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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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49
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E-pharmacophore-based screening of mGluR5 negative allosteric modulators for central nervous system disorder. Comput Biol Chem 2019; 78:414-423. [DOI: 10.1016/j.compbiolchem.2018.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/25/2018] [Indexed: 01/01/2023]
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50
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Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PLoS One 2019; 14:e0211227. [PMID: 30682119 PMCID: PMC6347273 DOI: 10.1371/journal.pone.0211227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/09/2019] [Indexed: 02/08/2023] Open
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it can improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work, a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied to cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based criteria on trajectory snapshots, we predicted two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanisms exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation to the design of cruzain allosteric inhibitors and may serve for future pharmacological intervention. Here, no major effects on active site structure were observed due to compound binding (modification of distance and angles between catalytic residues), which indicates that allosteric regulation in cruzain might be mediated via alterations of its dynamical properties similarly to allosteric inhibition of human cathepsin K (HCatK). The current findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
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