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Li N, Zheng G, Fu L, Liu N, Chen T, Lu S. Designed dualsteric modulators: A novel route for drug discovery. Drug Discov Today 2024; 29:104141. [PMID: 39168404 DOI: 10.1016/j.drudis.2024.104141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/01/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
Orthosteric and allosteric modulators, which constitute the majority of current drugs, bind to the orthosteric and allosteric sites of target proteins, respectively. However, the clinical efficacy of these agents is frequently compromised by poor selectivity or reduced potency. Dualsteric modulators feature two linked pharmacophores that bind to orthosteric and allosteric sites of the target proteins simultaneously, thereby offering a promising avenue to achieve both potency and specificity. In this review, we summarize recent structures available for dualsteric modulators in complex with their target proteins, elucidating detailed drug-target interactions and dualsteric action patterns. Moreover, we provide a design and optimization strategy for dualsteric modulators based on structure-based drug design approaches.
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Affiliation(s)
- Nuan Li
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guodong Zheng
- Department of VIP Clinic, Changhai Hospital, Affiliated to Naval Medical University, Shanghai 200433, China
| | - Lili Fu
- Department of Nephrology, People's Hospital of Pudong New Area, Shanghai University of Medicine & Health Sciences, Shanghai 201299, China
| | - Ning Liu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai 200003, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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2
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Sun H, Bai X, Zhang Y, Gao Y, Dai J, Xing P, Zhu J, Liu R, Wang Z, Li X. Small Molecule SHP2 Inhibitor LXQ-217 Affects Lung Cancer Cell Proliferation in Vitro and in Vivo. Chem Biodivers 2024; 21:e202301610. [PMID: 38379194 DOI: 10.1002/cbdv.202301610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND SHP2 is highly expressed in a variety of cancer and has emerged as a potential target for cancer therapeutic agents. The identification of uncharged pTyr mimics is an important direction for the development of SHP2 orthosteric inhibitors. METHODS Surface plasmon resonance analysis and cellular thermal shift assay were employed to verify the direct binding of LXQ-217 to SHP2. The inhibitory effect of LXQ-217 was characterized by linear Weaver-Burke enzyme kinetic analysis and BIOVIA Discovery Studio. The inhibition of tumor cell proliferation by LXQ-217 was characterized by cell viability assay, colony formation assays and hoechst 33258 staining. The inhibition of lung cancer proliferation in vivo was studied in nude mice after oral administration of LXQ-217. RESULTS An electroneutral bromophenol derivative, LXQ-217, was identified as a competitive SHP2 inhibitor. LXQ-217 induced apoptosis and inhibited growth of human pulmonary epithelial cells by affecting the RAS-ERK and PI3 K-AKT signaling pathways. Long-term oral administration of LXQ-217 significantly inhibited the proliferation ability of lung cancer cells in nude mice. Moreover, mice administered LXQ-217 orally at high doses exhibited no mortality or significant changes in vital signs. CONCLUSIONS Our findings on the uncharged orthosteric inhibitor provide a foundation for further development of a safe and effective anti-lung cancer drug.
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Affiliation(s)
- Hao Sun
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Xiaoyi Bai
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Yiting Zhang
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Yanan Gao
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Jiajia Dai
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, Shandong, China
| | - Pan Xing
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Jiqiang Zhu
- Shandong Linghai Biotechnology Co., Ltd., 250299, Jinan, Shandong, P. R. China
| | - Ruihua Liu
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Zemin Wang
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
| | - Xiangqian Li
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, Shandong, P. R. China
- Laboratory of Marine Drugs and Biological Products, National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, P. R. China
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3
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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4
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Xiang S, Lu X. Selective type II TRK inhibitors overcome xDFG mutation mediated acquired resistance to the second-generation inhibitors selitrectinib and repotrectinib. Acta Pharm Sin B 2024; 14:517-532. [PMID: 38322338 PMCID: PMC10840435 DOI: 10.1016/j.apsb.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/15/2023] [Accepted: 10/24/2023] [Indexed: 02/08/2024] Open
Abstract
Neurotrophic receptor kinase (NTRK) fusions are actionable oncogenic drivers of multiple pediatric and adult solid tumors, and tropomyosin receptor kinase (TRK) has been considered as an attractive therapeutic target for "pan-cancer" harboring these fusions. Currently, two generations TRK inhibitors have been developed. The representative second-generation inhibitors selitrectinib and repotrectinib were designed to overcome clinic acquired resistance of the first-generation inhibitors larotrectinib or entrectinib resulted from solvent-front and gatekeeper on-target mutations. However, xDFG (TRKAG667C/A/S, homologous TRKCG696C/A/S) and some double mutations still confer resistance to selitrectinib and repotrectinib, and overcoming these resistances represents a major unmet clinical need. In this review, we summarize the acquired resistance mechanism of the first- and second-generation TRK inhibitors, and firstly put forward the emerging selective type II TRK inhibitors to overcome xDFG mutations mediated resistance. Additionally, we concluded our perspectives on new challenges and future directions in this field.
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Affiliation(s)
- Shuang Xiang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
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5
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Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. J Am Chem Soc 2024; 146:2757-2768. [PMID: 38231868 PMCID: PMC10843641 DOI: 10.1021/jacs.3c12494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of cooperativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semiquantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different rescuabilities observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same noninducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscores the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions and therefore provides quantitative guidance to allostery modulation for therapeutic and engineering applications.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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6
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He J, Liu X, Zhu C, Zha J, Li Q, Zhao M, Wei J, Li M, Wu C, Wang J, Jiao Y, Ning S, Zhou J, Hong Y, Liu Y, He H, Zhang M, Chen F, Li Y, He X, Wu J, Lu S, Song K, Lu X, Zhang J. ASD2023: towards the integrating landscapes of allosteric knowledgebase. Nucleic Acids Res 2024; 52:D376-D383. [PMID: 37870448 PMCID: PMC10767950 DOI: 10.1093/nar/gkad915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct from the orthosteric site, is one of the most direct and efficient ways to fine-tune macromolecular function. The Allosteric Database (ASD; accessible online at http://mdl.shsmu.edu.cn/ASD) has been systematically developed since 2009 to provide comprehensive information on allosteric regulation. In recent years, allostery has seen sustained growth and wide-ranging applications in life sciences, from basic research to new therapeutics development, while also elucidating emerging obstacles across allosteric research stages. To overcome these challenges and maintain high-quality data center services, novel features were curated in the ASD2023 update: (i) 66 589 potential allosteric sites, covering > 80% of the human proteome and constituting the human allosteric pocketome; (ii) 748 allosteric protein-protein interaction (PPI) modulators with clear mechanisms, aiding protein machine studies and PPI-targeted drug discovery; (iii) 'Allosteric Hit-to-Lead,' a pioneering dataset providing panoramic views from 87 well-defined allosteric hits to 6565 leads and (iv) 456 dualsteric modulators for exploring the simultaneous regulation of allosteric and orthosteric sites. Meanwhile, ASD2023 maintains a significant growth of foundational allosteric data. Based on these efforts, the allosteric knowledgebase is progressively evolving towards an integrated landscape, facilitating advancements in allosteric target identification, mechanistic exploration and drug discovery.
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Affiliation(s)
- Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinyi Liu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chunhao Zhu
- College of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, China
| | - Jinyin Zha
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Li
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingzhu Zhao
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiacheng Wei
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Junyuan Wang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Yonglai Jiao
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shaobo Ning
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jiamin Zhou
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Yue Hong
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yonghui Liu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hongxi He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200011, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Feiying Chen
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanxiu Li
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinheng He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jing Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kun Song
- Nutshell Therapeutics, Shanghai 201210, 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 Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- College of Pharmacy, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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7
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Zhu C, Lan X, Wei Z, Yu J, Zhang J. Allosteric modulation of G protein-coupled receptors as a novel therapeutic strategy in neuropathic pain. Acta Pharm Sin B 2024; 14:67-86. [PMID: 38239234 PMCID: PMC10792987 DOI: 10.1016/j.apsb.2023.07.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 01/22/2024] Open
Abstract
Neuropathic pain is a debilitating pathological condition that presents significant therapeutic challenges in clinical practice. Unfortunately, current pharmacological treatments for neuropathic pain lack clinical efficacy and often lead to harmful adverse reactions. As G protein-coupled receptors (GPCRs) are widely distributed throughout the body, including the pain transmission pathway and descending inhibition pathway, the development of novel neuropathic pain treatments based on GPCRs allosteric modulation theory is gaining momentum. Extensive research has shown that allosteric modulators targeting GPCRs on the pain pathway can effectively alleviate symptoms of neuropathic pain while reducing or eliminating adverse effects. This review aims to provide a comprehensive summary of the progress made in GPCRs allosteric modulators in the treatment of neuropathic pain, and discuss the potential benefits and adverse factors of this treatment. We will also concentrate on the development of biased agonists of GPCRs, and based on important examples of biased agonist development in recent years, we will describe universal strategies for designing structure-based biased agonists. It is foreseeable that, with the continuous improvement of GPCRs allosteric modulation and biased agonist theory, effective GPCRs allosteric drugs will eventually be available for the treatment of neuropathic pain with acceptable safety.
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Affiliation(s)
- Chunhao Zhu
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
- School of Basic Medical Science, Ningxia Medical University, Yinchuan 750004, China
| | - Xiaobing Lan
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao 266100, China
| | - Jianqiang Yu
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Jian Zhang
- School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
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8
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Li M, Lan X, Lu X, Zhang J. A Structure-Based Allosteric Modulator Design Paradigm. HEALTH DATA SCIENCE 2023; 3:0094. [PMID: 38487194 PMCID: PMC10904074 DOI: 10.34133/hds.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 03/17/2024]
Abstract
Importance: Allosteric drugs bound to topologically distal allosteric sites hold a substantial promise in modulating therapeutic targets deemed undruggable at their orthosteric sites. Traditionally, allosteric modulator discovery has predominantly relied on serendipitous high-throughput screening. Nevertheless, the landscape has undergone a transformative shift due to recent advancements in our understanding of allosteric modulation mechanisms, coupled with a significant increase in the accessibility of allosteric structural data. These factors have extensively promoted the development of various computational methodologies, especially for machine-learning approaches, to guide the rational design of structure-based allosteric modulators. Highlights: We here presented a comprehensive structure-based allosteric modulator design paradigm encompassing 3 critical stages: drug target acquisition, allosteric binding site, and modulator discovery. The recent advances in computational methods in each stage are encapsulated. Furthermore, we delve into analyzing the successes and obstacles encountered in the rational design of allosteric modulators. Conclusion: The structure-based allosteric modulator design paradigm holds immense potential for the rational design of allosteric modulators. We hope that this review would heighten awareness of the use of structure-based computational methodologies in advancing the field of allosteric drug discovery.
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Affiliation(s)
- Mingyu Li
- College of Pharmacy,
Ningxia Medical University, Yinchuan, NingxiaHui Autonomous Region, China
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center,
Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaobin Lan
- College of Pharmacy,
Ningxia Medical University, Yinchuan, NingxiaHui Autonomous Region, China
- Medicinal Chemistry and Bioinformatics Center,
Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xun Lu
- College of Pharmacy,
Ningxia Medical University, Yinchuan, NingxiaHui Autonomous Region, China
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center,
Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- College of Pharmacy,
Ningxia Medical University, Yinchuan, NingxiaHui Autonomous Region, China
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital,
Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center,
Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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9
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Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555381. [PMID: 37905112 PMCID: PMC10614727 DOI: 10.1101/2023.08.29.555381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of co-operativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semi-quantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different degrees of rescuability observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same non-inducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscore the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions, and therefore provide quantitative guidance to allostery modulation for therapeutic and engineering applications.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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10
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Zha J, He J, Wu C, Zhang M, Liu X, Zhang J. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev 2023; 52:8651-8677. [PMID: 37990599 DOI: 10.1039/d3cs00650f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Traditionally, drugs are monovalent, targeting only one site on the protein surface. This includes orthosteric and allosteric drugs, which bind the protein at orthosteric and allosteric sites, respectively. Orthosteric drugs are good in potency, whereas allosteric drugs have better selectivity and are solutions to classically undruggable targets. However, it would be difficult to simultaneously reach high potency and selectivity when targeting only one site. Also, both kinds of monovalent drugs suffer from mutation-caused drug resistance. To overcome these obstacles, dualsteric modulators have been proposed in the past twenty years. Compared to orthosteric or allosteric drugs, dualsteric modulators are bivalent (or bitopic) with two pharmacophores. Each of the two pharmacophores bind the protein at the orthosteric and an allosteric site, which could bring the modulator with special properties beyond monovalent drugs. In this study, we comprehensively review the current development of dualsteric modulators. Our main effort reason and illustrate the aims to apply the dualsteric approach, including a "double win" of potency and selectivity, overcoming mutation-caused drug resistance, developments of function-biased modulators, and design of partial agonists. Moreover, the strengths of the dualsteric technique also led to its application outside pharmacy, including the design of highly sensitive fluorescent tracers and usage as molecular rulers. Besides, we also introduced drug targets, designing strategies, and validation methods of dualsteric modulators. Finally, we detail the conclusions and perspectives.
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Affiliation(s)
- Jinyin Zha
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jixiao He
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chengwei Wu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyang Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Liu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Yang J, Jiang C, Chen J, Qin L, Cheng G. Predicting GPR40 Agonists with A Deep Learning-Based Ensemble Model. ChemistryOpen 2023; 12:e202300051. [PMID: 37404062 PMCID: PMC10661831 DOI: 10.1002/open.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Recent studies have identified G protein-coupled receptor 40 (GPR40) as a promising target for treating type 2 diabetes mellitus, and GPR40 agonists have several superior effects over other hypoglycemic drugs, including cardiovascular protection and suppression of glucagon levels. In this study, we constructed an up-to-date GPR40 ligand dataset for training models and performed a systematic optimization of the ensemble model, resulting in a powerful ensemble model (ROC AUC: 0.9496) for distinguishing GPR40 agonists and non-agonists. The ensemble model is divided into three layers, and the optimization process is carried out in each layer. We believe that these results will prove helpful for both the development of GPR40 agonists and ensemble models. All the data and models are available on GitHub. (https://github.com/Jiamin-Yang/ensemble_model).
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Affiliation(s)
- Jiamin Yang
- School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhouP. R. China310053
| | - Chen Jiang
- School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhouP. R. China310053
| | - Jing Chen
- School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhouP. R. China310053
| | - Lu‐Ping Qin
- School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhouP. R. China310053
| | - Gang Cheng
- School of Pharmaceutical SciencesZhejiang Chinese Medical UniversityHangzhouP. R. China310053
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12
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Yu Z, He X, Wang R, Xu X, Zhang Z, Ding K, Zhang ZM, Tan Y, Li Z. Simultaneous Covalent Modification of K-Ras(G12D) and K-Ras(G12C) with Tunable Oxirane Electrophiles. J Am Chem Soc 2023; 145:20403-20411. [PMID: 37534597 DOI: 10.1021/jacs.3c05899] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Owing to their remarkable pharmaceutical properties compared to those of noncovalent inhibitors, the development of targeted covalent inhibitors (TCIs) has emerged as a powerful method for cancer treatment. The K-Ras mutant, which is prevalent in multiple cancers, has been confirmed to be a crucial drug target in the treatment of various malignancies. However, although the K-Ras(G12D) mutation is present in up to 33% of K-Ras mutations, no covalent inhibitors targeting K-Ras(G12D) have been developed to date. The relatively weak nucleophilicity of the acquired aspartic acid (12D) residue in K-Ras may be the reason for this. Herein, we present the first compound capable of covalently engaging both K-Ras(G12D) and K-Ras(G12C) mutants. Proteome profiling revealed that this compound effectively conjugates with G12C and G12D residues, modulating the protein functions in situ. These findings offer a unique pathway for the development of novel dual covalent inhibitors.
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Affiliation(s)
- Zhongtang Yu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xiaoqiang He
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ruiliu Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Xinxin Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhang Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- Guangzhou City Key Laboratory of Precision Chemical Drug Development, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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13
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Yang WC, Gong DH, Hong Wu, Gao YY, Hao GF. Grasping cryptic binding sites to neutralize drug resistance in the field of anticancer. Drug Discov Today 2023; 28:103705. [PMID: 37453458 DOI: 10.1016/j.drudis.2023.103705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Drug resistance is a significant obstacle to successful cancer treatment. The utilization and development of cryptic binding sites (CBSs) in proteins involved in cancer-related drug-resistance (CRDR) could help to overcome that drug resistance. However, there is no comprehensive review of the successful use of CBSs in addressing CRDR. Here, we have systematically summarized and analyzed the opportunities and challenges of using CBSs in addressing CRDR and revealed the key role that CBSs have in targeting CRDR. First, we have identified the CRDR targets and the corresponding CBSs. Second, we discuss the mechanisms by which CBSs can overcome CRDR. Finally, we have provided examples of successful CBS applications in addressing CRDR. We hope that this approach will provide guidance to biologists and chemists in effectively utilizing CBSs for the development of new drugs to alleviate CRDR.
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Affiliation(s)
- Wei-Cheng Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Dao-Hong Gong
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Hong Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China.
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China; National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, China.
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14
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Huth SW, Oakley JV, Seath CP, Geri JB, Trowbridge AD, Parker DL, Rodriguez-Rivera FP, Schwaid AG, Ramil C, Ryu KA, White CH, Fadeyi OO, Oslund RC, MacMillan DWC. μMap Photoproximity Labeling Enables Small Molecule Binding Site Mapping. J Am Chem Soc 2023; 145:16289-16296. [PMID: 37471577 PMCID: PMC10809032 DOI: 10.1021/jacs.3c03325] [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: 07/22/2023]
Abstract
The characterization of ligand binding modes is a crucial step in the drug discovery process and is especially important in campaigns arising from phenotypic screening, where the protein target and binding mode are unknown at the outset. Elucidation of target binding regions is typically achieved by X-ray crystallography or photoaffinity labeling (PAL) approaches; yet, these methods present significant challenges. X-ray crystallography is a mainstay technique that has revolutionized drug discovery, but in many cases structural characterization is challenging or impossible. PAL has also enabled binding site mapping with peptide- and amino-acid-level resolution; however, the stoichiometric activation mode can lead to poor signal and coverage of the resident binding pocket. Additionally, each PAL probe can have its own fragmentation pattern, complicating the analysis by mass spectrometry. Here, we establish a robust and general photocatalytic approach toward the mapping of protein binding sites, which we define as identification of residues proximal to the ligand binding pocket. By utilizing a catalytic mode of activation, we obtain sets of labeled amino acids in the proximity of the target protein binding site. We use this methodology to map, in vitro, the binding sites of six protein targets, including several kinases and molecular glue targets, and furthermore to investigate the binding site of the STAT3 inhibitor MM-206, a ligand with no known crystal structure. Finally, we demonstrate the successful mapping of drug binding sites in live cells. These results establish μMap as a powerful method for the generation of amino-acid- and peptide-level target engagement data.
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Affiliation(s)
- Sean W. Huth
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - James V. Oakley
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ciaran P. Seath
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jacob B. Geri
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Aaron D. Trowbridge
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Adam G. Schwaid
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Carlo Ramil
- Discovery Chemistry, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Cory H. White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Olugbeminiyi O. Fadeyi
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - Rob C. Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141, United States
| | - David W. C. MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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15
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Lu X, Shi X, Fan J, Li M, Zhang Y, Lu S, Xu G, Chen Z. Mechanistic Elucidation of Activation/Deactivation Signal Transduction within Neurotensin Receptor 1 Triggered by 'Driver Chemical Groups' of Modulators: A Comparative Molecular Dynamics Simulation. Pharmaceutics 2023; 15:2000. [PMID: 37514186 PMCID: PMC10385606 DOI: 10.3390/pharmaceutics15072000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Small-molecule modulators of neurotensin receptor 1 (NTSR1), a class A G-protein-coupled receptor (GPCR), has emerged as promising therapeutic agent for psychiatric disorders and cancer. Interestingly, a chemical group substitution in NTSR1 modulators can launch different types of downstream regulation, highlighting the significance of deciphering the internal fine-tuning mechanism. Here, we conducted a synergistic application of a Gaussian accelerated molecular dynamics simulation, a conventional molecular dynamics simulation, and Markov state models (MSM) to investigate the underlying mechanism of 'driver chemical groups' of modulators triggering inverse signaling. The results indicated that the flexibility of the leucine moiety in NTSR1 agonists contributes to the inward displacement of TM7 through a loosely coupled allosteric pathway, while the rigidity of the adamantane moiety in NTSR1 antagonists leads to unfavorable downward transduction of agonistic signaling. Furthermore, we found that R3226.54, Y3196.51, F3537.42, R1483.32, S3567.45, and S3577.46 may play a key role in inducing the activation of NTSR1. Together, our findings not only highlight the ingenious signal transduction within class A GPCRs but also lay a foundation for the development of targeted drugs harboring different regulatory functions of NTSR1.
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Affiliation(s)
- Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinchao Shi
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuxiang Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guanghuan Xu
- Department of VIP Clinic, Changhai Hospital, Affiliated to Navy Medical University, Shanghai 200433, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai 200433, China
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16
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Zheng X, Zheng D, Zhang C, Guo H, Zhang Y, Xue X, Shi Z, Zhang X, Zeng X, Wu Y, Gao W. A cuproptosis-related lncRNA signature predicts the prognosis and immune cell status in head and neck squamous cell carcinoma. Front Oncol 2023; 13:1055717. [PMID: 37538124 PMCID: PMC10394648 DOI: 10.3389/fonc.2023.1055717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 06/29/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction The incidence of head and neck squamous cell carcinoma (HNSCC), one of the most prevalent tumors, is increasing rapidly worldwide. Cuproptosis, as a new copper-dependent cell death form, was proposed recently. However, the prognosis value and immune effects of cuproptosis-related lncRNAs (CRLs) have not yet been elucidated in HNSCC. Methods In the current study, the expression pattern, differential profile, clinical correlation, DNA methylation, functional enrichment, univariate prognosis factor, and the immune effects of CRLs were analyzed. A four-CRL signature was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm. Results Results showed that 20 CRLs had significant effects on the stage progression of HNSCC. Sixteen CRLs were tightly correlated with the overall survival (OS) of HNSCC patients. Particularly, lnc-FGF3-4 as a single risk factor was upregulated in HNSCC tissues and negatively impacted the prognosis of HNSCC. DNA methylation probes of cg02278768 (MIR9-3HG), cg07312099 (ASAH1-AS1), and cg16867777 (TIAM1-AS1) were also correlated with the prognosis of HNSCC. The four-CRL signature that included MAP4K3-DT, lnc-TCEA3-1, MIR9-3HG, and CDKN2A-DT had a significantly negative effect on the activation of T cells follicular helper and OS probability of HNSCC. Functional analysis revealed that cell cycle, DNA replication, and p53 signal pathways were enriched. Discussion A novel CRL-related signature has the potential of prognosis prediction in HNSCC. Targeting CRLs may be a promising therapeutic strategy for HNSCC.
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Affiliation(s)
- Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Defei Zheng
- Department of Hematology/Oncology, Children’s Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huina Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuliang Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuting Xue
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhaohui Shi
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Xiangmin Zhang
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Xianhai Zeng
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Yongyan Wu
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
| | - Wei Gao
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen, Guangdong, China
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17
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Pandey P, Ghimire S, Wu B, Alexov E. On the linkage of thermodynamics and pathogenicity. Curr Opin Struct Biol 2023; 80:102572. [PMID: 36965249 PMCID: PMC10239362 DOI: 10.1016/j.sbi.2023.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/27/2023]
Abstract
This review outlines the effect of disease-causing mutations on proteins' thermodynamics. Two major thermodynamics quantities, which are essential for structural integrity, the folding and binding free energy changes caused by missense mutations, are considered. It is emphasized that disease effects in case of complex diseases may originate from several mutations over several genes, while monogenic diseases are caused by mutation is a single gene. Nevertheless, in both cases it is shown that pathogenic mutations cause larger perturbations of the above-mentioned thermodynamics quantities as compared with the benign mutations. Recent works demonstrating the effect of pathogenic mutations on the above-mentioned thermodynamics quantities, as well as on structural dynamics and allosteric pathways, are reviewed.
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Affiliation(s)
- Preeti Pandey
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Sanjeev Ghimire
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Bohua Wu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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18
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Kim C, Ludewig H, Hadzipasic A, Kutter S, Nguyen V, Kern D. A biophysical framework for double-drugging kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533217. [PMID: 36993258 PMCID: PMC10055307 DOI: 10.1101/2023.03.17.533217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as "double-drugging", has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Förster resonance energy transfer, coupled-enzyme assays, and X-ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a conformational equilibrium shift is the main principle governing this cooperative effect. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X-ray crystal structures of the doubledrugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe the first fully-closed conformation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light onto the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of doubledrugging strategies.
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Affiliation(s)
- C. Kim
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - H. Ludewig
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - A. Hadzipasic
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - S. Kutter
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - V. Nguyen
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
| | - D. Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA 02454, USA
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19
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Nussinov R, Zhang M, Maloney R, Liu Y, Tsai CJ, Jang H. Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs. J Mol Biol 2022; 434:167569. [PMID: 35378118 PMCID: PMC9398924 DOI: 10.1016/j.jmb.2022.167569] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/12/2023]
Abstract
Here, we discuss the principles of allosteric activating mutations, propagation downstream of the signals that they prompt, and allosteric drugs, with examples from the Ras signaling network. We focus on Abl kinase where mutations shift the landscape toward the active, imatinib binding-incompetent conformation, likely resulting in the high affinity ATP outcompeting drug binding. Recent pharmacological innovation extends to allosteric inhibitor (GNF-5)-linked PROTAC, targeting Bcr-Abl1 myristoylation site, and broadly, allosteric heterobifunctional degraders that destroy targets, rather than inhibiting them. Designed chemical linkers in bifunctional degraders can connect the allosteric ligand that binds the target protein and the E3 ubiquitin ligase warhead anchor. The physical properties and favored conformational state of the engineered linker can precisely coordinate the distance and orientation between the target and the recruited E3. Allosteric PROTACs, noncompetitive molecular glues, and bitopic ligands, with covalent links of allosteric ligands and orthosteric warheads, increase the effective local concentration of productively oriented and placed ligands. Through covalent chemical or peptide linkers, allosteric drugs can collaborate with competitive drugs, degrader anchors, or other molecules of choice, driving innovative drug discovery.
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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.
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Yonglan Liu
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - 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
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20
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Zhao JF, Wang RS, Lu SZ, Guo XJ, Chen Y, Li LH, Ding CH, Liu WS. Identification of the novel natural product inhibitors of SHP2 from the plant Toona sinensis: In vitro and in silico study. Int J Biol Macromol 2022; 221:679-690. [PMID: 36096249 DOI: 10.1016/j.ijbiomac.2022.09.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]
Abstract
In this study, we tested the inhibitory activity of 45 natural products extracted from the plant Toona sinensis on SHP2 protein, and identified four natural product inhibitors. The natural product 1,2,3,6-Tetragalloylglucose (A-1) was first reported as a competitive inhibitor of SHP2, with an IC50 value of 0.20 ± 0.029 μM and the selectivity of 1.8-fold and 4.35-fold to high homologous proteins SHP1 and PTP1B, respectively. Compound A-1 also showed high inhibitory activity on SHP2-E76K and SHP2-E76A mutants, with IC50 values of 0.95 ± 0.21 μM and 0.29 ± 0.045 μM, respectively. Cell viability assay showed that compound A-1 could inhibit the proliferation of a variety of cancer cells. Apoptosis assay showed that compound A-1 could effectively induce apoptosis of KRASG12C-mut NCI-H23 and KRASG12S-mut A549 cells. Western blot assay showed that compound A-1 could down regulate the phosphorylation levels of Erk1/2 and Akt in NCI-H23 and A549 cells. Molecular docking showed that compound A-1 could effectively dock to the catalytic active region of SHP2. Molecular dynamics simulation explored the effect of compound A-1 on SHP2, revealing the deep-seated binding mechanism. This study would provide valuable clues for the development of SHP2 and its mutant inhibitors.
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Affiliation(s)
- Ji-Feng Zhao
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Rong-Shen Wang
- School of Pharmacy, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Sheng-Ze Lu
- School of Pharmacy, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Xiao-Jing Guo
- Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China
| | - Ying Chen
- School of Pharmacy, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Li-Hua Li
- Eye Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China.
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China.
| | - Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China; Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261041, Shandong Province, China.
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21
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Ebrahim A, Riley BT, Kumaran D, Andi B, Fuchs MR, McSweeney S, Keedy DA. The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro). IUCRJ 2022; 9:682-694. [PMID: 36071812 PMCID: PMC9438506 DOI: 10.1107/s2052252522007497] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 05/12/2023]
Abstract
The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or Mpro, is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic tem-per-ature or room tem-per-ature only. Here we report a series of high-resolution crystal structures of unliganded Mpro across multiple tem-per-atures from cryogenic to physiological, and another at high humidity. We inter-rogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for Mpro, including a mobile zinc ion inter-leaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intra-molecular network bridging the active site and dimer inter-face. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.
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Affiliation(s)
- Ali Ebrahim
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, England, United Kingdom
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Babak Andi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
- National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Martin R. Fuchs
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Sean McSweeney
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA
- National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology, and Chemistry, The Graduate Center–City University of New York, New York, NY 10016, USA
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22
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Zhou S, Yang B, Xu Y, Gu A, Peng J, Fu J. Understanding gilteritinib resistance to FLT3-F691L mutation through an integrated computational strategy. J Mol Model 2022; 28:247. [PMID: 35932378 DOI: 10.1007/s00894-022-05254-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/31/2022] [Indexed: 11/25/2022]
Abstract
FMS-like tyrosine kinase 3 (FLT3) serves as an important drug target for acute myeloid leukemia (AML), and gene mutations of FLT3 have been closely associated with AML patients with an incidence rate of ~ 30%. However, the mechanism of the clinically relevant F691L gatekeeper mutation conferred resistance to the drug gilteritinib remained poorly understood. In this study, multiple microsecond molecular dynamics (MD) simulations, end-point free energy calculations, and dynamic correlated and network analyses were performed to investigate the molecular basis of gilteritinib resistance to the FLT3-F691L mutation. The simulations revealed that the resistant mutation largely induced the conformational changes of the activation loop (A-loop), the phosphate-binding loop, and the helix αC of the FLT3 protein. The binding abilities of the gilteritinib to the wild-type and the F691L mutant were different through the binding free energy prediction. The simulation results further indicated that the driving force to determine the binding affinity of gilteritinib was derived from the differences in the energy terms of electrostatic and van der Waals interactions. Moreover, the per-residue free energy decomposition suggested that the four residues (Phe803, Gly831, Leu832, and Ala833) located at the A-loop of FLT3 had a significant impact on the binding affinity of gilteritinib to the F691L mutant. This study may provide useful information for the design of novel FLT3 inhibitors specially targeting the F691L gatekeeper mutant.
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Affiliation(s)
- Shibo Zhou
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Bo Yang
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Yufeng Xu
- Department of Radiotherapy, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Aihua Gu
- Department of Medicine, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China
| | - Juan Peng
- Department of Ultrasonography, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Jinfeng Fu
- Department of Radiology, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, 210009, Jiangsu, China.
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23
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Ji M, Chai Z, Chen J, Li G, Li Q, Li M, Ding Y, Lu S, Ju G, Hou J. Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study. Molecules 2022; 27:4149. [PMID: 35807394 PMCID: PMC9268427 DOI: 10.3390/molecules27134149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 11/26/2022] Open
Abstract
Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1-SUMO1 complex.
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Affiliation(s)
- Mingfei Ji
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China;
| | - Jie Chen
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Gang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Qiang Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Miao Li
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
| | - Yelei Ding
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Shaoyong Lu
- Department of Bioinformatics and Medicinal Chemistry Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Guanqun Ju
- Department of Urology, Second Affiliated Hospital of Navy Medical University, Shanghai 200433, China; (J.C.); (Y.D.)
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China; (M.J.); (G.L.); (Q.L.); (M.L.)
- Department of Urology, Dushuhu Public Hospital Affiliated to Soochow University, Suzhou 215000, China
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24
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Wah Tan Z, Tee WV, Berezovsky IN. Learning about allosteric drugs and ways to design them. J Mol Biol 2022; 434:167692. [PMID: 35738428 DOI: 10.1016/j.jmb.2022.167692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/23/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022]
Abstract
While the accelerating quest for precision medicine requires new individually targeting and selective drugs, and the ability to work with so-called undruggable targets, the realm of allosteric drugs meeting this need remains largely uncharted. Generalizing the observations on two major drug targets with widely observed inherent allostery, GPCRs and kinases, we describe and discuss basic allosteric modes of action that are universally applicable in all types of structures and functions. Using examples of Class A GPCRs and CMGC protein kinases, we show how Allosteric Signalling and Probing Fingerprints can be used to identify potential allosteric sites and reveal effector-leads that may serve as a starting point for the development of allosteric drugs targeting these regulatory sites. A set of distinct characteristics of allosteric ligands was established, which highlights the versatility of their design and make them advantageous before their orthosteric counterparts in personalized medicine. We argue that rational design of allosteric drugs should begin with the search for latent sites or design of non-natural binding sites followed by fragment-based design of allosteric ligands and by the mutual adjustment of the site-ligand pair in order to achieve required effects. On the basis of the perturbative nature and reversibility of allosteric communication, we propose a generic protocol for computational design of allosteric effectors, enabling also the allosteric tuning of biologics, in obtaining allosteric control over protein functions.
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Wei-Ven Tee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671; Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, 117579, Singapore.
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25
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Mech-Warda P, Giełdoń A, Kawiak A, Maciejewska N, Olszewski M, Makowski M, Chylewska A. Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123704. [PMID: 35744829 PMCID: PMC9228100 DOI: 10.3390/molecules27123704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022]
Abstract
Pyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure of chlorohydrazinopyrazine, its physicochemical and cytotoxic properties, and the site and nature of interaction with DNA. The obtained results indicated that 2-chloro-3-hydrazinopyrazine (2Cl3HP) displayed the highest affinity to DNA. Cytotoxicity studies revealed that the compound did not exhibit toxicity toward human dermal keratinocytes, which supported the potential application of 2Cl3HP in clinical use. The study also attempted to establish the possible equilibria occurring in the aqueous solution and, using both theoretical and experimental methods, clearly showed the hydrophilic nature of the compound. The experimental and theoretical results of the study confirmed the quality of the compound, as well as the appropriateness of the selected set of methods for similar research.
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Affiliation(s)
- Paulina Mech-Warda
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.M.-W.); (M.M.)
| | - Artur Giełdoń
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland;
| | - Anna Kawiak
- Institute of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland;
| | - Natalia Maciejewska
- Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland; (N.M.); (M.O.)
| | - Mateusz Olszewski
- Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland; (N.M.); (M.O.)
| | - Mariusz Makowski
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.M.-W.); (M.M.)
| | - Agnieszka Chylewska
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (P.M.-W.); (M.M.)
- Correspondence:
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26
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Sun SL, Wu SH, Kang JB, Ma YY, Chen L, Cao P, Chang L, Ding N, Xue X, Li NG, Shi ZH. Medicinal Chemistry Strategies for the Development of Bruton's Tyrosine Kinase Inhibitors against Resistance. J Med Chem 2022; 65:7415-7437. [PMID: 35594541 DOI: 10.1021/acs.jmedchem.2c00030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Despite significant efficacy, one of the major limitations of small-molecule Bruton's tyrosine kinase (BTK) agents is the presence of clinically acquired resistance, which remains a major clinical challenge. This Perspective focuses on medicinal chemistry strategies for the development of BTK small-molecule inhibitors against resistance, including the structure-based design of BTK inhibitors targeting point mutations, e.g., (i) developing noncovalent inhibitors from covalent inhibitors, (ii) avoiding steric hindrance from mutated residues, (iii) making interactions with the mutated residue, (iv) modifying the solvent-accessible region, and (v) developing new scaffolds. Additionally, a comparative analysis of multi-inhibitions of BTK is presented based on cross-comparisons between 2916 unique BTK ligands and 283 other kinases that cover 7108 dual/multiple inhibitions. Finally, targeting the BTK allosteric site and uding proteolysis-targeting chimera (PROTAC) as two potential strategies are addressed briefly, while also illustrating the possibilities and challenges to find novel ligands of BTK.
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Affiliation(s)
- Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shi-Han Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ji-Bo Kang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yi-Yuan Ma
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lu Chen
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Peng Cao
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Liang Chang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhi-Hao Shi
- Department of Organic Chemistry, China Pharmaceutical University, Nanjing 211198, China
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27
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Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. Antibiotics (Basel) 2022; 11:antibiotics11050557. [PMID: 35625201 PMCID: PMC9138118 DOI: 10.3390/antibiotics11050557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic β subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the β subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase.
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28
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Tastan Bishop Ö, Mutemi Musyoka T, Barozi V. Allostery and missense mutations as intermittently linked promising aspects of modern computational drug discovery. J Mol Biol 2022; 434:167610. [DOI: 10.1016/j.jmb.2022.167610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
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29
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Xiao F, Zhou Z, Song X, Gan M, Long J, Verkhivker G, Hu G. Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation. PLoS Comput Biol 2022; 18:e1010009. [PMID: 35320273 PMCID: PMC8979438 DOI: 10.1371/journal.pcbi.1010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/04/2022] [Accepted: 03/10/2022] [Indexed: 11/18/2022] Open
Abstract
Hypophosphatasia (HPP) is a rare inherited disorder characterized by defective bone mineralization and is highly variable in its clinical phenotype. The disease occurs due to various loss-of-function mutations in ALPL, the gene encoding tissue-nonspecific alkaline phosphatase (TNSALP). In this work, a data-driven and biophysics-based approach is proposed for the large-scale analysis of ALPL mutations-from nonpathogenic to severe HPPs. By using a pipeline of synergistic approaches including sequence-structure analysis, network modeling, elastic network models and atomistic simulations, we characterized allosteric signatures and effects of the ALPL mutations on protein dynamics and function. Statistical analysis of molecular features computed for the ALPL mutations showed a significant difference between the control, mild and severe HPP phenotypes. Molecular dynamics simulations coupled with protein structure network analysis were employed to analyze the effect of single-residue variation on conformational dynamics of TNSALP dimers, and the developed machine learning model suggested that the topological network parameters could serve as a robust indicator of severe mutations. The results indicated that the severity of disease-associated mutations is often linked with mutation-induced modulation of allosteric communications in the protein. This study suggested that ALPL mutations associated with mild and more severe HPPs can exert markedly distinct effects on the protein stability and long-range network communications. By linking the disease phenotypes with dynamic and allosteric molecular signatures, the proposed integrative computational approach enabled to characterize and quantify the allosteric effects of ALPL mutations and role of allostery in the pathogenesis of HPPs.
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Affiliation(s)
- Fei Xiao
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xingyu Song
- Department of Chemistry, Multiscale Research Institute of Complex Systems and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mi Gan
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jie Long
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Gennady Verkhivker
- Department of Computational and Data Sciences, Chapman University, One University Drive, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University Pharmacy School 9401 Jeronimo Rd, Irvine, California, United States of America
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- * E-mail:
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Zhang H, Zhu M, Li M, Ni D, Wang Y, Deng L, Du K, Lu S, Shi H, Cai C. Mechanistic Insights Into Co-Administration of Allosteric and Orthosteric Drugs to Overcome Drug-Resistance in T315I BCR-ABL1. Front Pharmacol 2022; 13:862504. [PMID: 35370687 PMCID: PMC8971931 DOI: 10.3389/fphar.2022.862504] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm, driven by the BCR-ABL1 fusion oncoprotein. The discovery of orthosteric BCR-ABL1 tyrosine kinase inhibitors (TKIs) targeting its active ATP-binding pocket, such as first-generation Imatinib and second-generation Nilotinib (NIL), has profoundly revolutionized the therapeutic landscape of CML. However, currently targeted therapeutics still face considerable challenges with the inevitable emergence of drug-resistant mutations within BCR-ABL1. One of the most common resistant mutations in BCR-ABL1 is the T315I gatekeeper mutation, which confers resistance to most current TKIs in use. To resolve such conundrum, co-administration of orthosteric TKIs and allosteric drugs offers a novel paradigm to tackle drug resistance. Remarkably, previous studies have confirmed that the dual targeting BCR-ABL1 utilizing orthosteric TKI NIL and allosteric inhibitor ABL001 resulted in eradication of the CML xenograft tumors, exhibiting promising therapeutic potential. Previous studies have demonstrated the cooperated mechanism of two drugs. However, the conformational landscapes of synergistic effects remain unclear, hampering future efforts in optimizations and improvements. Hence, extensive large-scale molecular dynamics (MD) simulations of wide type (WT), WT-NIL, T315I, T315I-NIL, T315I-ABL001 and T315I-ABL001-NIL systems were carried out in an attempt to address such question. Simulation data revealed that the dynamic landscape of NIL-bound BCR-ABL1 was significantly reshaped upon ABL001 binding, as it shifted from an active conformation towards an inactive conformation. The community network of allosteric signaling was analyzed to elucidate the atomistic overview of allosteric regulation within BCR-ABL1. Moreover, binding free energy analysis unveiled that the affinity of NIL to BCR-ABL1 increased by the induction of ABL001, which led to its favorable binding and the release of drug resistance. The findings uncovered the in-depth structural mechanisms underpinning dual-targeting towards T315I BCR-ABL1 to overcome its drug resistance and will offer guidance for the rational design of next generations of BCR-ABL1 modulators and future combinatory therapeutic regimens.
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Affiliation(s)
- Hao Zhang
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Mingsheng Zhu
- Department of Anesthesiology, Huashan Hospital Affiliated to Fudan University, Shanghai, China
| | - Mingzi Li
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Duan Ni
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yuanhao Wang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Liping Deng
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
| | - Kui Du
- School of Chemistry and Chemical Engineering, Shaoxing University, Shaoxing, China
- *Correspondence: Shaoyong Lu, ; Kui Du, ; Hui Shi, ; Chen Cai,
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Kui Du, ; Hui Shi, ; Chen Cai,
| | - Hui Shi
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Navy Medical University, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Kui Du, ; Hui Shi, ; Chen Cai,
| | - Chen Cai
- Department of VIP Clinic, Changhai Hospital, Navy Medical University, Shanghai, China
- *Correspondence: Shaoyong Lu, ; Kui Du, ; Hui Shi, ; Chen Cai,
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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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32
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Nussinov R, Zhang M, Maloney R, Tsai C, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2022; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Chung‐Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of InformaticsMiddle East Technical UniversityAnkaraTurkey
- Department of Chemical and Biological Engineering, College of EngineeringKoc UniversityIstanbulTurkey
- Koc University Research Center for Translational Medicine, School of MedicineKoc UniversityIstanbulTurkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer ImmunometabolismNational Cancer InstituteFrederickMarylandUSA
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Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J. Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. J Med Chem 2021; 64:17728-17743. [PMID: 34878270 DOI: 10.1021/acs.jmedchem.1c01695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a fundamental and extensive mechanism of intramolecular signal transmission. Allosteric drugs possess several unique pharmacological advantages over traditional orthosteric drugs, including greater selectivity, better physicochemical properties, and lower off-target toxicity. However, owing to the complexity of allosteric regulation, experimental approaches for the development of allosteric modulators are traditionally serendipitous. Recently, the reversed allosteric communication theory has been proposed, providing a feasible tool for the unbiased detection of allosteric sites. Herein, we review the latest research on the reversed allosteric communication effect using the examples of sirtuin 6, epidermal growth factor receptor, 3-phosphoinositide-dependent protein kinase 1, and Related to A and C kinases (RAC) serine/threonine protein kinase B and recapitulate the methodologies of reversed allosteric communication strategy. The novel reversed allosteric communication strategy greatly expands the horizon of allosteric site identification and allosteric mechanism exploration and is expected to accelerate an end-to-end framework for drug discovery.
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Affiliation(s)
- Jigang Fan
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Zhiyuan Innovative Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China.,State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China.,School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
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Das R, Choithramani A, Shard A. A molecular perspective for the use of type IV tyrosine kinase inhibitors as anticancer therapeutics. Drug Discov Today 2021; 27:808-821. [PMID: 34920095 DOI: 10.1016/j.drudis.2021.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/21/2021] [Accepted: 12/10/2021] [Indexed: 11/03/2022]
Abstract
Tyrosine kinases are enzymes that can transfer a phosphate group from ATP to a specific protein tyrosine, serine or threonine residue within a cell, operating as a switch that can turn 'on' and 'off' causing different physiological alterations in the body. Mutated kinases have been shown to display an equilibrium shift toward the activated state. Types I-III have been studied intensively leading to drugs like imatinib (type II), cobimetinib (type III), among others. It is the same scenario for types V-VII; however, there is a lacuna in information regarding type IV inhibitors, although recently some advances have surfaced. This review aims to accumulate the knowledge gained so far about type IV inhibitors.
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Affiliation(s)
- Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Asmita Choithramani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 380054, India.
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Liu M, Gao S, Elhassan RM, Hou X, Fang H. Strategies to overcome drug resistance using SHP2 inhibitors. Acta Pharm Sin B 2021; 11:3908-3924. [PMID: 35024315 PMCID: PMC8727779 DOI: 10.1016/j.apsb.2021.03.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/17/2022] Open
Abstract
Encoded by PTPN11, the SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is widely recognized as a carcinogenic phosphatase. As a promising anti-cancer drug target, SHP2 regulates many signaling pathways such as RAS-RAF-ERK, PI3K-AKT and JAK-STAT. Meanwhile, SHP2 plays a significant role in regulating immune cell function in the tumor microenvironment. Heretofore, five SHP2 allosteric inhibitors have been recruited in clinical studies for the treatment of cancer. Most recently, studies have proved the therapeutic potential of SHP2 inhibitor in overcoming drug resistance of kinase inhibitors and programmed cell death-1 (PD-1) blockade. Herein, we review the structure, function and small molecular inhibitors of SHP2, and highlight recent progress in overcoming drug resistance using SHP2 inhibitor. We hope this review would facilitate the future clinical development of SHP2 inhibitors.
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Affiliation(s)
| | | | | | - Xuben Hou
- Corresponding author. Tel./fax: +86 531 88381168.
| | - Hao Fang
- Corresponding author. Tel./fax: +86 531 88381168.
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS‐CoV‐2 and Fragment‐Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Lucile Brier
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Sandrine Belouzard
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Valérie Landry
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Florence Leroux
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
| | - Jean Dubuisson
- Univ. Lille CNRS INSERM, CHU Lille Institut Pasteur de Lille U1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille 1 rue du Professeur Calmette F-59019 Lille France
| | - Benoit Deprez
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Julie Charton
- Univ. Lille INSERM Institut Pasteur de Lille U1177—Drugs and Molecules for Living Systems F-59000 Lille France
- European Genomic Institute for Diabetes EGID University of Lille 3 rue du Professeur Laguesse F-59006 Lille France
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology 50 avenue Halley F-59658 Villeneuve d'Ascq Lille France
- Univ. Lille INSERM CHU Lille Institut Pasteur de Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 1 rue du Professeur Calmette F-59019 Lille France
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Cantrelle F, Boll E, Brier L, Moschidi D, Belouzard S, Landry V, Leroux F, Dewitte F, Landrieu I, Dubuisson J, Deprez B, Charton J, Hanoulle X. NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment. Angew Chem Int Ed Engl 2021; 60:25428-25435. [PMID: 34570415 PMCID: PMC8653025 DOI: 10.1002/anie.202109965] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Indexed: 11/17/2022]
Abstract
The main protease (3CLp) of the SARS-CoV-2, the causative agent for the COVID-19 pandemic, is one of the main targets for drug development. To be active, 3CLp relies on a complex interplay between dimerization, active site flexibility, and allosteric regulation. The deciphering of these mechanisms is a crucial step to enable the search for inhibitors. In this context, using NMR spectroscopy, we studied the conformation of dimeric 3CLp from the SARS-CoV-2 and monitored ligand binding, based on NMR signal assignments. We performed a fragment-based screening that led to the identification of 38 fragment hits. Their binding sites showed three hotspots on 3CLp, two in the substrate binding pocket and one at the dimer interface. F01 is a non-covalent inhibitor of the 3CLp and has antiviral activity in SARS-CoV-2 infected cells. This study sheds light on the complex structure-function relationships of 3CLp and constitutes a strong basis to assist in developing potent 3CLp inhibitors.
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Affiliation(s)
- François‐Xavier Cantrelle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Emmanuelle Boll
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Lucile Brier
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Danai Moschidi
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Sandrine Belouzard
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Valérie Landry
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Florence Leroux
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Frédérique Dewitte
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Isabelle Landrieu
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
| | - Jean Dubuisson
- Univ. LilleCNRSINSERM, CHU LilleInstitut Pasteur de LilleU1019-UMR 9017—CIIL—Center for Infection and Immunity of Lille1 rue du Professeur CalmetteF-59019LilleFrance
| | - Benoit Deprez
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Julie Charton
- Univ. LilleINSERMInstitut Pasteur de LilleU1177—Drugs and Molecules for Living SystemsF-59000LilleFrance
- European Genomic Institute for DiabetesEGIDUniversity of Lille3 rue du Professeur LaguesseF-59006LilleFrance
| | - Xavier Hanoulle
- CNRS ERL9002—BSI—Integrative Structural Biology50 avenue HalleyF-59658 Villeneuve d'AscqLilleFrance
- Univ. LilleINSERMCHU LilleInstitut Pasteur de LilleU1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases1 rue du Professeur CalmetteF-59019LilleFrance
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How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations. J Mol Model 2021; 27:337. [PMID: 34725737 DOI: 10.1007/s00894-021-04964-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/22/2021] [Indexed: 12/16/2022]
Abstract
Targeted drug therapies represent a therapeutic breakthrough in the treatment of human cancer. However, the emergence of acquired resistance inevitably compromises therapeutic drugs. Rearranged during transfection (RET) proto-oncogene, which encodes a receptor tyrosine kinase, is a target for several kinds of human cancer such as thyroid, breast, and colorectal carcinoma. A single mutation L881V at the RET kinase domain was found in familial medullary thyroid carcinoma. Nintedanib can effectively inhibit the RET L881V mutant, whereas its analog compound 1 is unable to combat this mutant. However, the underlying mechanism was still unexplored. Here, molecular dynamics (MD) simulations, binding free energy calculations, and structural analysis were performed to uncover the mechanism of overcoming the resistance of RET L881V mutant to nintedanib. Energetic analysis revealed that the L881V mutant remained sensitive to the treatment of nintedanib, whereas it was insensitive to the compound 1. Structural analysis further showed that the distribution of K758, D892, and N879 network had a detrimental effect on the binding of compound 1 to the L881V mutant. The obtained results may provide insight into the mechanism of overcoming resistance in the RET kinase.
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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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Adeleke BS, Babalola OO. The plant endosphere-hidden treasures: a review of fungal endophytes. Biotechnol Genet Eng Rev 2021; 37:154-177. [PMID: 34666635 DOI: 10.1080/02648725.2021.1991714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The endosphere represents intracellular regions within plant tissues colonize by microbial endophytes without causing disease symptoms to host plants. Plants harbor one or two endophytic microbes capable of synthesizing metabolite compounds. Environmental factors determine the plant growth and survival as well as the kind of microorganisms associated with them. Some fungal endophytes that symbiotically colonize the endosphere of medicinal plants with the potential of producing biological products have been employed in traditional and modern medicine. The bioactive resources from endophytic fungi are promising; biotechnologically to produce cheap and affordable commercial bioactive products as alternatives to chemical drugs and other compounds. The exploration of bioactive metabolites from fungal endophytes has been found applicable in agriculture, pharmaceutical, and industries. Thus, fungal endophytes can be engineered to produce a substantive quantity of pharmacological drugs through the biotransformation process. Hence, this review shall provide an overview of fungal endophytes, ecology, their bioactive compounds, and exploration with the biosystematics approach.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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Synthesis and biological evaluation of 2,5-diaryl-1,3,4-oxadiazole derivatives as novel Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) inhibitors. Bioorg Chem 2021; 116:105384. [PMID: 34601294 DOI: 10.1016/j.bioorg.2021.105384] [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: 06/02/2021] [Revised: 08/16/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
The Src homology-2 domain containing-protein tyrosine phosphatase-2 (SHP2) is a convergent node for oncogenic cell-signaling cascades including the PD-L1/PD-1 pathway. As an oncoprotein as well as a potential immunomodulator, SHP2 has now emerged as an attractive target for novel anti-cancer agents. Although significant progress has been made in identifying chemotypes of SHP2 inhibitors, these specific compounds might not be clinically useful to inhibit frequently encountered mutated SHP2 variants. Consequently, it is highly desirable to develop chemically different SHP2 inhibitors sensitive to SHP2 mutants. This work developed a new type of SHP2 inhibitors with 2,5-diaryl-1,3,4-oxadiazole scaffold. The representative compound 6l exhibited SHP2 inhibitory activity with IC50 of 2.73 ± 0.20 µM, showed about 1.56-fold, 5.26-fold, and 7.36-fold selectivity for SHP2 over SHP1, PTP1B and TCPTP respectively. Further investigations confirmed that 6l behaved as mixed-type inhibitor sensitive to leukemia cell TF-1 and inhibited SHP2 mediated cell signaling and proliferation. Molecular dynamics simulation provided more detailed information on the binding modes of compounds and SHP2 protein. These preliminary results could provide a possible opportunity for the development of novel SHP2 inhibitors sensitive to SHP2 mutants with optimal potency and improved pharmacological properties.
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Recent advances in the design and discovery of synthetic tyrosinase inhibitors. Eur J Med Chem 2021; 224:113744. [PMID: 34365131 DOI: 10.1016/j.ejmech.2021.113744] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Tyrosinase is a copper-containing metalloenzyme that is responsible for the rate-limiting catalytic step in the melanin biosynthesis and enzymatic browning. As a promising target, tyrosinase inhibitors can be used as skin whitening agents and food preservatives, thus having broad potential in the fields of food, cosmetics, agriculture and medicine. From 2015 to 2020, numerous synthetic inhibitors of tyrosinase have been developed to overcome the challenges of low efficacy and side effects. This review summarizes the enzyme structure and biological functions of tyrosinase and demonstrates the recent advances of synthetic tyrosinase inhibitors from the perspective of medicinal chemistry, providing a better understanding of the catalytic mechanisms and more effective tyrosinase inhibitors.
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Wu J, Zhang H, Zhao G, Wang R. Allosteric Inhibitors of SHP2: An Updated Patent Review (2015-2020). Curr Med Chem 2021; 28:3825-3842. [PMID: 32988341 DOI: 10.2174/1568011817666200928114851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 11/22/2022]
Abstract
Srchomology-2-domain-containing PTP 2 (SHP2) is a nonreceptor phosphatase encoded by the PTPN11 gene. Over expression of SHP2 is associated with various human diseases, such as Noonan syndrome, LEOPARD syndrome, and cancers. To overcome the shortcomings of existing orthosteric inhibitors, novel inhibitors targeting the allosteric site of SHP2 with high selectivity and low toxicity are under development. This paper reviews allosteric inhibitors of SHP2 published in patents from 2015 to 2020. The molecules are classified according to the chemical structure of the central core. SHP2 has long been considered as an 'undruggable' protein. Fortunately, a critical breakthrough was made by researchers from Novartis AG Ltd., who identified SHP099 as a highly potent, selective, soluble, and orally bioavailable SHP2 allosteric inhibitor. Currently, there are several allosteric inhibitors of SHP2 in clinical development. However, drug resistance is still a major challenge. The combination of SHP2 allosteric inhibitors and immunotherapy drugs or molecular targeted drugs is emerging as a promising therapeutic strategy against drug resistance.
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Affiliation(s)
- Jingwei Wu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
| | - Huan Zhang
- Department of Pharmacy, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Guilong Zhao
- The Institute of Drug Discovery and Development, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Runling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, No. 22, Qixiangtai Road, Heping District, Tianjin 300070, China
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Du X, Yang B, An Q, Assaraf YG, Cao X, Xia J. Acquired resistance to third-generation EGFR-TKIs and emerging next-generation EGFR inhibitors. Innovation (N Y) 2021; 2:100103. [PMID: 34557754 PMCID: PMC8454558 DOI: 10.1016/j.xinn.2021.100103] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/01/2021] [Indexed: 12/19/2022] Open
Abstract
The discovery that mutations in the EGFR gene are detected in up to 50% of lung adenocarcinoma patients, along with the development of highly efficacious epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs), has revolutionized the treatment of this frequently occurring lung malignancy. Indeed, the clinical success of these TKIs constitutes a critical milestone in targeted cancer therapy. Three generations of EGFR-TKIs are currently approved for the treatment of EGFR mutation-positive non-small cell lung cancer (NSCLC). The first-generation TKIs include erlotinib, gefitinib, lapatinib, and icotinib; the second-generation ErbB family blockers include afatinib, neratinib, and dacomitinib; whereas osimertinib, approved by the FDA on 2015, is a third-generation TKI targeting EGFR harboring specific mutations. Compared with the first- and second-generation TKIs, third-generation EGFR inhibitors display a significant advantage in terms of patient survival. For example, the median overall survival in NSCLC patients receiving osimertinib reached 38.6 months. Unfortunately, however, like other targeted therapies, new EGFR mutations, as well as additional drug-resistance mechanisms emerge rapidly after treatment, posing formidable obstacles to cancer therapeutics aimed at surmounting this chemoresistance. In this review, we summarize the molecular mechanisms underlying resistance to third-generation EGFR inhibitors and the ongoing efforts to address and overcome this chemoresistance. We also discuss the current status of fourth-generation EGFR inhibitors, which are of great value in overcoming resistance to EGFR inhibitors that appear to have greater therapeutic benefits in the clinic. EGFR gene mutations are detected in about 50% of non-small cell lung cancer (NSCLC) patients worldwide The three generations of EGFR tyrosine kinase inhibitors (TKIs) are critical milestones for NSCLC patients Like other targeted therapies, new EGFR mutations and coupled drug resistances emerge rapidly after TKI treatment, posing formidable obstacles to cancer management The investigational fourth-generation EGFR inhibitors are of great promise, through a number of novel mechanisms, in overcoming these resistances after third-generation TKI treatment, and will bring more benefits to NSCLC patients
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Affiliation(s)
- Xiaojing Du
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, China
| | - Biwei Yang
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Quanlin An
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Lab, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200000, Israel
| | - Xin Cao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jinglin Xia
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Institute of Fudan-Minhang Academic Health System, Minhang Hospital, Fudan University, Shanghai 201199, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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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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Kakarala KK, Jamil K. Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach. J Biomol Struct Dyn 2021; 40:6889-6909. [PMID: 33682622 DOI: 10.1080/07391102.2021.1891140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
EGFR1, VEGFR2, Bcr-Abl and Src kinases are key drug targets in non-small cell lung cancer (NSCLC), bladder cancer, pancreatic cancer, CML, ALL, colorectal cancer, etc. The available drugs targeting these kinases have limited therapeutic efficacy due to novel mutations resulting in drug resistance and toxicity, as they target ATP binding site. Allosteric drugs have shown promising results in overcoming drug resistance, but the discovery of allosteric drugs is challenging. The allosteric binding pockets are difficult to predict, as they are generally associated with high energy conformations and regulate protein function in yet unknown mechanisms. In addition, the discovery of drugs using conventional methods takes long time and goes through several challenges, putting the lives of many cancer patients at risk. Therefore, the aim of the present work was to apply the most successful, drug repurposing approach in combination with computational methods to identify kinase inhibitors targeting novel allosteric sites on protein structure and assess their potential multi-kinase binding affinity. Multiple crystal structures belonging to EGFR1, VEGFR2, Bcr-Abl and Src tyrosine kinases were selected, including mutated, inhibitor bound and allosteric conformations to identify potential leads, close to physiological conditions. Interestingly the potential inhibitors identified were peptides. The drugs identified in this study could be used in therapy as a single multi-kinase inhibitor or in a combination of single kinase inhibitors after experimental validation. In addition, we have also identified new hot spots that are likely to be druggable allosteric sites for drug discovery of kinase-specific drugs in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Kaiser Jamil
- Bhagwan Mahavir Medical Research Center, Hyderabad, Telangana, India
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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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Adeleke BS, Babalola OO. Pharmacological Potential of Fungal Endophytes Associated with Medicinal Plants: A Review. J Fungi (Basel) 2021; 7:147. [PMID: 33671354 PMCID: PMC7922420 DOI: 10.3390/jof7020147] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Endophytic microbes are microorganisms that colonize the intracellular spaces within the plant tissues without exerting any adverse or pathological effects. Currently, the world population is facing devastating chronic diseases that affect humans. The resistance of pathogens to commercial antibiotics is increasing, thus limiting the therapeutic potential and effectiveness of antibiotics. Consequently, the need to search for novel, affordable and nontoxic natural bioactive compounds from endophytic fungi in developing new drugs with multifunction mechanisms to meet human needs is essential. Fungal endophytes produce invaluable bioactive metabolic compounds beneficial to humans with antimicrobial, anticancer, antidiabetic, anti-inflammatory, antitumor properties, etc. Some of these bioactive compounds include pestacin, taxol, camptothecin, ergoflavin, podophyllotoxin, benzopyran, isopestacin, phloroglucinol, tetrahydroxy-1-methylxanthone, salidroside, borneol, dibenzofurane, methyl peniphenone, lipopeptide, peniphenone etc. Despite the aforementioned importance of endophytic fungal metabolites, less information is available on their exploration and pharmacological importance. Therefore, in this review, we shall elucidate the fungal bioactive metabolites from medicinal plants and their pharmacological potential.
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Affiliation(s)
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa;
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Targeting SHP2 as a therapeutic strategy for inflammatory diseases. Eur J Med Chem 2021; 214:113264. [PMID: 33582386 DOI: 10.1016/j.ejmech.2021.113264] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022]
Abstract
With the change of lifestyle and the acceleration of aging process, inflammatory diseases have increasingly become one of the most vital threats to global human health. SHP2 protein is a non-receptor tyrosine phosphatase encoded by PTPN11 gene, and it is widely expressed in various tissues and cells. Numerous studies have shown that SHP2 plays important roles in the regulation of inflammatory diseases, including cancer-related inflammation, neurodegenerative diseases and metabolic diseases. In this paper, the roles of SHP2 in inflammatory diseases of various physiological systems were reviewed. At the same time, the latest SHP2 inhibitors were summarized, which will hold a promise for the therapeutic potential in future.
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Li M, Guo J. Deciphering the T790M/L858R-Selective Inhibition Mechanism of an Allosteric Inhibitor of EGFR: Insights from Molecular Simulations. ACS Chem Neurosci 2021; 12:462-472. [PMID: 33435671 DOI: 10.1021/acschemneuro.0c00633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Allosteric inhibitors have lately received great attention because of their unique advantages, representing a more suitable choice for combinatory therapeutics targeting resistance-relevant signaling cascades. Among the various inhibitors, an allosteric small-molecule inhibitor, JBJ-04-125-02, has been proven to be effective against EGFRT790M/L858R mutant in vivo and in vitro. Herein, an in silico approach was adopted to shed light on the deep understanding of the higher selectivity of JBJ-04-125-02 against EGFRT790M/L858R mutant than wild-type EGFR. Our results indicate that JBJ-04-125-02 prefers to bind with the EGFRT790M/L858R mutant, stabilizes the inactive conformation, and further allosterically affects the conformations and dynamics of the interlobe cleft, including both the allosteric site and the ATP-binding site. Furthermore, docking results confirm that the binding of JBJ-04-125-02 at the allosteric site decreases the binding affinity of ANP (an ATP analogue) at the orthosteric site, especially for the Mut-holo one, which might further inhibit the function of EGFR. The present work provides a clear picture of the mutant-selective inhibition mechanism of an allosteric inhibitor of EGFR. The findings might pave the way for designing allosteric drugs targeting EGFR mutant lung cancer patients, which also takes a step forward in terms of drug resistance caused by protein mutations.
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Affiliation(s)
- Miaomiao Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Guo
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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