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Olotu F, Tali MBT, Chepsiror C, Sheik Amamuddy O, Boyom FF, Tastan Bishop Ö. Repurposing DrugBank compounds as potential Plasmodium falciparum class 1a aminoacyl tRNA synthetase multi-stage pan-inhibitors with a specific focus on mitomycin. Int J Parasitol Drugs Drug Resist 2024; 25:100548. [PMID: 38805932 PMCID: PMC11152978 DOI: 10.1016/j.ijpddr.2024.100548] [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: 03/10/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
Plasmodium falciparum aminoacyl tRNA synthetases (PfaaRSs) are potent antimalarial targets essential for proteome fidelity and overall parasite survival in every stage of the parasite's life cycle. So far, some of these proteins have been singly targeted yielding inhibitor compounds that have been limited by incidences of resistance which can be overcome via pan-inhibition strategies. Hence, herein, for the first time, we report the identification and in vitro antiplasmodial validation of Mitomycin (MMC) as a probable pan-inhibitor of class 1a (arginyl(A)-, cysteinyl(C), isoleucyl(I)-, leucyl(L), methionyl(M), and valyl(V)-) PfaaRSs which hypothetically may underlie its previously reported activity on the ribosomal RNA to inhibit protein translation and biosynthesis. We combined multiple in silico structure-based discovery strategies that first helped identify functional and druggable sites that were preferentially targeted by the compound in each of the plasmodial proteins: Ins1-Ins2 domain in Pf-ARS; anticodon binding domain in Pf-CRS; CP1-editing domain in Pf-IRS and Pf-MRS; C-terminal domain in Pf-LRS; and CP-core region in Pf-VRS. Molecular dynamics studies further revealed that MMC allosterically induced changes in the global structures of each protein. Likewise, prominent structural perturbations were caused by the compound across the functional domains of the proteins. More so, MMC induced systematic alterations in the binding of the catalytic nucleotide and amino acid substrates which culminated in the loss of key interactions with key active site residues and ultimate reduction in the nucleotide-binding affinities across all proteins, as deduced from the binding energy calculations. These altogether confirmed that MMC uniformly disrupted the structure of the target proteins and essential substrates. Further, MMC demonstrated IC50 < 5 μM against the Dd2 and 3D7 strains of parasite making it a good starting point for malarial drug development. We believe that findings from our study will be important in the current search for highly effective multi-stage antimalarial drugs.
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Affiliation(s)
- Fisayo Olotu
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Mariscal Brice Tchatat Tali
- Antimicrobial & Biocontrol Agents Unit, Laboratory for Phytobiochemistry & Medicinal Plants Studies, Department of Biochemistry, Faculty of Science-University of Yaounde 1, P.O. Box 812, Yaounde, Cameroon; Advanced Research and Health Innovation Hub (ARHIH), Magzi Street, P.O. Box 812, Yaounde, Cameroon
| | - Curtis Chepsiror
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Fabrice Fekam Boyom
- Antimicrobial & Biocontrol Agents Unit, Laboratory for Phytobiochemistry & Medicinal Plants Studies, Department of Biochemistry, Faculty of Science-University of Yaounde 1, P.O. Box 812, Yaounde, Cameroon; Advanced Research and Health Innovation Hub (ARHIH), Magzi Street, P.O. Box 812, Yaounde, Cameroon
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa.
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Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 2024; 67:8817-8835. [PMID: 38768084 DOI: 10.1021/acs.jmedchem.4c00149] [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: 05/22/2024]
Abstract
Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.
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Affiliation(s)
- Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brenson A Jassim
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yiming Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuan Ma
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianping Lin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
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Chatterjee A. Mycobacterium tuberculosis and its secreted tyrosine phosphatases. Biochimie 2023; 212:41-47. [PMID: 37059349 DOI: 10.1016/j.biochi.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
Tuberculosis is one of the most common infectious diseases and has been a major burden for a long time now. Increasing drug resistance in TB is slowing down the process of disease treatment. Mycobacterium tuberculosis, the causative agent of TB is known to have a cascade of virulence factors to fight with host's immune system. The phosphatases (PTPs) of Mtb plays a critical role as these are secretory in nature and help the survival of bacteria in host. Researchers have been trying to synthesize inhibitors against a lot of virulence factors of Mtb but recently the phosphatases have gained a lot of interest due to their secretory nature. This review gives a concise overview of virulence factors of Mtb with emphasis on mPTPs. Here we discuss the current scenario of drug development against mPTPs.
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Affiliation(s)
- Aditi Chatterjee
- University of Maryland Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
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Maccari R, Ottanà R. Can Allostery Be a Key Strategy for Targeting PTP1B in Drug Discovery? A Lesson from Trodusquemine. Int J Mol Sci 2023; 24:ijms24119621. [PMID: 37298571 DOI: 10.3390/ijms24119621] [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: 04/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an enzyme crucially implicated in aberrations of various signaling pathways that underlie the development of different human pathologies, such as obesity, diabetes, cancer, and neurodegenerative disorders. Its inhibition can prevent these pathogenetic events, thus providing a useful tool for the discovery of novel therapeutic agents. The search for allosteric PTP1B inhibitors can represent a successful strategy to identify drug-like candidates by offering the opportunity to overcome some issues related to catalytic site-directed inhibitors, which have so far hampered the development of drugs targeting this enzyme. In this context, trodusquemine (MSI-1436), a natural aminosterol that acts as a non-competitive PTP1B inhibitor, appears to be a milestone. Initially discovered as a broad-spectrum antimicrobial agent, trodusquemine exhibited a variety of unexpected properties, ranging from antidiabetic and anti-obesity activities to effects useful to counteract cancer and neurodegeneration, which prompted its evaluation in several preclinical and clinical studies. In this review article, we provide an overview of the main findings regarding the activities and therapeutic potential of trodusquemine and their correlation with PTP1B inhibition. We also included some aminosterol analogues and related structure-activity relationships that could be useful for further studies aimed at the discovery of new allosteric PTP1B inhibitors.
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Affiliation(s)
- Rosanna Maccari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosaria Ottanà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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Shukla S, Nishanth Rao R, Bhuktar H, Edwin RK, Jamma T, Medishetti R, Banerjee S, Giliyaru VB, Shenoy GG, Oruganti S, Misra P, Pal M. Wang resin catalysed sonochemical synthesis of pyrazolo[4,3-d]pyrimidinones and 2,3-dihydroquinazolin-4(1H)-ones: Identification of chorismate mutase inhibitors having effects on Mycobacterium tuberculosis cell viability. Bioorg Chem 2023; 134:106452. [PMID: 36889201 DOI: 10.1016/j.bioorg.2023.106452] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/15/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
The enzyme chorismate mutase (or CM that is vital for the survival of bacteria) is an interesting pharmacological target for the identification of new anti-tubercular agents. The 5,5-disibstituted pyrazolo[4,3-d]pyrimidinone derivatives containing the fragment based on 4-amino-1-methyl-3-propyl-1H-pyrazole-5-carboxamide were designed and explored as the potential inhibitors of chorismate mutase. Based on encouraging docking results of two representative molecules evaluated in silico against MtbCM (PDB: 2FP2) the Wang resin catalysed sonochemical synthesis of target N-heteroarenes were undertaken. The methodology involved the reaction of 4-amino-1-methyl-3-propyl-1H-pyrazole-5-carboxamide with the appropriate cyclic/acyclic ketones to afford the desired products in acceptable (51-94%) yields. The methodology was also extended successfully towards the synthesis of 2,2-disubstituted 2,3-dihydroquinazolin-4(1H)-ones in excellent (85-90%) yields. In vitro MTT assay against the RAW 264.7 cell line followed by enzymatic assay against MtbCM identified 3b and 3c as active compounds that showed two H-bonding via their NH (at position 6) and CO group with MtbCM in silico and encouraging (54-57%) inhibition at 30 µM in vitro. Notably, none of the 2,2-disubstituted 2,3-dihydroquinazolin-4(1H)-ones showed any significant inhibition of MtbCM suggesting the favourable role of the pyrazole moiety in case of pyrazolo[4,3-d]pyrimidinones. The favourable role of cyclopentyl ring attached to the pyrazolo[4,3-d]pyrimidinone moiety and that of two methyl groups in place of cyclopentyl ring was also indicated by the SAR study. Besides showing effects against MtbCM in the concentration response study, 3b and 3c showed little or no effects on mammalian cell viability up to 100 µM in an MTT assay but decreased the % Mtb cell viability at 10-30 µM with > 20% decrease at 30 µM in an Alamar Blue Assay. Moreover, no adverse effects were noted for these compounds when tested for teratogenicity and hepatotoxicity in zebrafish at various concentrations. Overall, being the only example of MtbCM inhibitors that showed effects on Mtb cell viability the compound 3b and 3c are of further interest form the view point of discovery and development of new anti-tubercular agents.
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Affiliation(s)
- Sharda Shukla
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - R Nishanth Rao
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Harshavardhan Bhuktar
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Rebecca Kristina Edwin
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Trinath Jamma
- Department of Biological Sciences, B-225, BITS Pilani-Hyderabad Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad 500 078, Telangana, India
| | - Raghavender Medishetti
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Varadaraj Bhat Giliyaru
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Gautham G Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Srinivas Oruganti
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Parimal Misra
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India
| | - Manojit Pal
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India; Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhav Nagar, Manipal 576 104, Karnataka, India.
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Govindaraj RG, Thangapandian S, Schauperl M, Denny RA, Diller DJ. Recent applications of computational methods to allosteric drug discovery. Front Mol Biosci 2023; 9:1070328. [PMID: 36710877 PMCID: PMC9877542 DOI: 10.3389/fmolb.2022.1070328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023] Open
Abstract
Interest in exploiting allosteric sites for the development of new therapeutics has grown considerably over the last two decades. The chief driving force behind the interest in allostery for drug discovery stems from the fact that in comparison to orthosteric sites, allosteric sites are less conserved across a protein family, thereby offering greater opportunity for selectivity and ultimately tolerability. While there is significant overlap between structure-based drug design for orthosteric and allosteric sites, allosteric sites offer additional challenges mostly involving the need to better understand protein flexibility and its relationship to protein function. Here we examine the extent to which structure-based drug design is impacting allosteric drug design by highlighting several targets across a variety of target classes.
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Affiliation(s)
- Rajiv Gandhi Govindaraj
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States,*Correspondence: Rajiv Gandhi Govindaraj,
| | | | - Michael Schauperl
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
| | | | - David J. Diller
- Computational Chemistry, HotSpot Therapeutics Inc., Boston, MA, United States
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Structure-based discovery and in vitro validation of inhibitors of chloride intracellular channel 4 protein. Comput Struct Biotechnol J 2022; 21:688-701. [PMID: 36659928 PMCID: PMC9826898 DOI: 10.1016/j.csbj.2022.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022] Open
Abstract
The use of computer-aided methods have continued to propel accelerated drug discovery across various disease models, interestingly allowing the specific inhibition of pathogenic targets. Chloride Intracellular Channel Protein 4 (CLIC4) is a novel class of intracellular ion channel highly implicated in tumor and vascular biology. It regulates cell proliferation, apoptosis and angiogenesis; and is involved in multiple pathologic signaling pathways. Absence of specific inhibitors however impedes its advancement to translational research. Here, we integrate structural bioinformatics and experimental research approaches for the discovery and validation of small-molecule inhibitors of CLIC4. High-affinity allosteric binders were identified from a library of 1615 Food and Drug Administration (FDA)-approved drugs via a high-performance computing-powered blind-docking approach, resulting in the selection of amphotericin B and rapamycin. NMR assays confirmed the binding and conformational disruptive effects of both drugs while they also reversed stress-induced membrane translocation of CLIC4 and inhibited endothelial cell migration. Structural and dynamics simulation studies further revealed that the inhibitory mechanisms of these compounds were hinged on the allosteric modulation of the catalytic glutathione (GSH)-like site loop and the extended catalytic β loop which may elicit interference with the catalytic activities of CLIC4. Structure-based insights from this study provide the basis for the selective targeting of CLIC4 to treat the associated pathologies.
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Key Words
- A9C, 9-Anthracenecarboxylic acid
- AMPhB, Amphotericin B
- Ad, Adenovirus
- Allosteric inhibition
- Bad, BCL2 associated agonist of cell death
- Bcl-2, B-cell lymphoma 2
- Bcl-xL, B-cell lymphoma-extra large
- CDK, Cyclin-dependent kinases
- CLIC, Chloride intracellular channel protein
- Chloride intracellular channel protein 4
- Computational high-throughput screening
- DAPI, 4′,6-diamidino-2-phenylindole
- DIDS, 4,4′-Diisothiocyano-2,2′-stilbenedisulfonic acid
- DMSO, Dimethyl sulfoxide
- DOPE, Discrete optimized protein energy
- GPU, Graphics Processing Unit
- GSH-like catalytic site
- GST, glutathione S-transferases
- GUI, Graphical User Interface
- HEPES, (4-(2-hydroxyethyl)− 1-piperazineethanesulfonic acid;
- HIF, Hypoxia-inducible factor
- HSQC, Heteronuclear single quantum coherence spectroscopy
- HUVEC, Human umbilical vein endothelial cells
- IKKβ, Inhibitor of nuclear kappa-B-kinase subunit beta
- JNK, c-Jun N-terminal kinase
- MKK6, Mitogen-activated protein kinase kinase-6
- MOI, Multiplicity of infection
- NF-κB, Nuclear factor kappa-light-chain-enhancer of activated B cells
- NMR, Nuclear magnetic resonance
- NPT, The constant-temperature, constant-pressure ensemble
- NaCL, Sodium chloride
- Nuclear magnetic resonance
- PAH, Pulmonary arterial hypertension
- RAPA, Rapamycin
- SASA, Solvent accessible surface area
- SEK1, Dual specificity mitogen-activated protein kinase kinase 4
- Smad, Suppressor of Mothers against Decapentaplegic
- Structure-based drug discovery
- TEV, Tobacco etch virus
- TIP3P, Transferable intermolecular potential 3 P
- TROSY, Transverse relaxation optimized spectroscopy
- UCSF, University of California, San Francisco
- VEGF, Vascular endothelial growth factor
- p38, Mitogen activated protein kinases
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Ryan A, Janosko CP, Courtney TM, Deiters A. Engineering SHP2 Phosphatase for Optical Control. Biochemistry 2022; 61:2687-2697. [DOI: 10.1021/acs.biochem.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chasity P. Janosko
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Fludarabine, a Potential DNA-Dependent RNA Polymerase Inhibitor, as a Prospective Drug against Monkeypox Virus: A Computational Approach. Pharmaceuticals (Basel) 2022; 15:ph15091129. [PMID: 36145351 PMCID: PMC9504824 DOI: 10.3390/ph15091129] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 12/16/2022] Open
Abstract
Monkeypox is a zoonotic contagious disease that has recently re-emerged in different countries worldwide. Due to the lack of an effective treatment that eliminates the virus, there is an urgent need to find effective drugs to stop the spread of the multi-country outbreak. The current study aimed to use computational methods to quickly identify potentially effective drugs against the Monkeypox virus (MPXV). Three MPXV proteins were targeted in this study due to their essential role in viral replication (a DNA-Dependent RNA Polymerase subunit (A6R)), a protein involved in cell entry (D8L), and a protein catalyzing the envelopment of intracellular mature virus particles (F13L). We virtually screened a library of 1615 FDA-approved compounds, utilizing different in-silico approaches including computational modeling, molecular docking, molecular dynamic (MD) simulation, and MM-GBSA. The compound Fludarabine was found to have the best docking score (−7.53 kcal/mol) in relation to the MPXV A6R protein. Additionally, Fludarabine showed in-silico activity on the D8L and F13L proteins. During the whole period of the 100 ns MD simulation, the complex of A6R and Fludarabine exhibited the best stability. This stability was reflected in a good score of MM-GBSA, with an average value of −44.62 kcal/mole in a range between −53.26 and −35.49 and a low value of standard deviation (3.76). Furthermore, Fludarabine blocked efficiently the Asn175 residue which has an important role in the attachment of the virus to a host cell. The results of this study recommend more in vitro studies on this compound, as a starting point to develop a novel treatment against MPXV.
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Behl T, Gupta A, Sehgal A, Albarrati A, Albratty M, Meraya AM, Najmi A, Bhatia S, Bungau S. Exploring protein tyrosine phosphatases (PTP) and PTP-1B inhibitors in management of diabetes mellitus. Biomed Pharmacother 2022; 153:113405. [DOI: 10.1016/j.biopha.2022.113405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/02/2022] Open
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Chitti S, Nandikolla A, Khetmalis YM, Van Calster K, Kumar BVS, Kumar BK, Murugesan S, Cappoen D, Kondapalli CSVG. Design, Synthesis and Biological Evaluation of Novel Spiro-[chroman-2,4'-piperidin]-4-one Analogues as Anti-Tubercular Agents. Chem Biodivers 2022; 19:e202200304. [PMID: 35821618 DOI: 10.1002/cbdv.202200304] [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: 04/01/2022] [Accepted: 07/12/2022] [Indexed: 11/06/2022]
Abstract
A series of novel spiro-[chromane-2,4'-piperidine]-4(3 H )-one derivatives were designed, synthesized and structures were confirmed by analytical methods viz., 1 H NMR, 13 C NMR and Mass spectrometry. Synthesized derivatives were evaluated for their anti-mycobacterial activity against Mycobacterium tuberculosis ( Mtb ) H37Ra strain. Among all the evaluated compounds, PS08 exhibited significant inhibition with MIC value of 3.72 μM while MIC values of the remaining compounds ranged from 7.68 to 230.42 μM in comparison to the standard drug INH (MIC 0.09 μM). The two most active compounds however showed acute cytotoxicity towards the human MRC-5 lung fibroblast cell line. The in-silico ADMET profiles of the titled compounds were predicted and found within the prescribed limits of the Lipinski and Jorgenson rules. Molecular docking study of the significantly active compound ( PS08 ) was also carried out after performing validation in order to understand the putative binding position of the test ligand at the active site of selected target protein Mtb tyrosine phosphatase (PtpB).
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Affiliation(s)
- Surendar Chitti
- Birla Institute of Technology & Science Pilani - Hyderabad Campus, Department of chemistry, Alwal, hyderabad, INDIA
| | - Adinarayana Nandikolla
- Birla Institute of Technology & Science Pilani - Hyderabad Campus, Department of chemistry, VYAS Bhavan, V169, Jawaha, 500078, Hyderabad, INDIA
| | - Yogesh Mahadu Khetmalis
- Birla Institute of Technology & Science Pilani - Hyderabad Campus, Department of chemistry, jawahar nagar, hyderabad, INDIA
| | - Kevin Van Calster
- University of Antwerp - City campus: Universiteit Antwerpen, Department of Pharmaceutical Sciences, Wilrijk, Wilrijk, BELGIUM
| | - Boddupalli Venkata Siva Kumar
- Birla Institute of Technology & Science Pilani - Hyderabad Campus, Department of chemistry, nacharam, hyderabad, INDIA
| | - Banoth Karan Kumar
- Birla Institute of Technology and Science - Pilani Campus: Birla Institute of Technology & Science Pilani, Department of Pharmacy, nacharam, hyderabad, INDIA
| | - Sankaranarayanan Murugesan
- Birla Institute of Technology and Science - Pilani Campus: Birla Institute of Technology & Science Pilani, Department of Pharmacy, pilani, Pilani, INDIA
| | - Davie Cappoen
- University of Antwerp - City campus: Universiteit Antwerpen, Department of Pharmaceutical Sciences, Wilrijk, Wilrijk, BELGIUM
| | - Chandra Sekhar Venkata Gowri Kondapalli
- Birla Institute of Technology & Science - Pilani, Hyderabad Campus, Chemistry Department, Jawahar Nagar, Shamirpet Mandal, Ranga Reddy District, 500 078, Hyderabad, INDIA
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Menegatti ACO. Targeting protein tyrosine phosphatases for the development of antivirulence agents: Yersinia spp. and Mycobacterium tuberculosis as prototypes. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140782. [PMID: 35470106 DOI: 10.1016/j.bbapap.2022.140782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
Protein phosphorylation mediated by protein kinases and phosphatases has a central regulatory function in many cellular processes in eukaryotes and prokaryotes. As a result, several diseases caused by imbalance in phosphorylation levels are known, especially due to protein tyrosine phosphatases (PTPs) activity, an important family of signaling enzymes. Furthermore, over the last decades several studies have shown the main role of PTPs in pathogenic bacteria: they are associated with growth, cell division, cell wall biosynthesis, biofilm formation, metabolic processes, as well as virulence factor. In this way, PTPs have ascended as targets for antibacterial drug design, particularly in view of the antibiotic resistance in pathogenic bacteria, which demands novel therapeutics strategies. Targeting secreted PTPs is an antivirulence strategy to combat the emergence of antimicrobial resistance (AMR). This review focuses on the recent advances in understanding the role of PTPs and the approaches to target them, with an emphasis in Yersinia spp. and Mycobacterium tuberculosis pathogenesis.
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Affiliation(s)
- Angela Camila Orbem Menegatti
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Paraíba, Brazil.
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13
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Prava J, Pan A. In silico analysis of Leishmania proteomes and protein-protein interaction network: Prioritizing therapeutic targets and drugs for repurposing to treat leishmaniasis. Acta Trop 2022; 229:106337. [PMID: 35134348 DOI: 10.1016/j.actatropica.2022.106337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/07/2022] [Accepted: 01/29/2022] [Indexed: 01/31/2023]
Abstract
Leishmaniasis is a serious world health problem and its current therapies have several limitations demanding to develop novel therapeutics for this disease. The present study aims to prioritize novel broad-spectrum targets using proteomics and protein-protein interaction network (PPIN) data for 11 Leishmania species. Proteome comparison and host non-homology analysis resulted in 3605 pathogen-specific conserved core proteins. Gene ontology analysis indicated their involvement in major molecular functions like DNA binding, transportation, dioxygenase, and catalytic activity. PPIN analysis of these core proteins identified eight hub proteins (viz., vesicle-trafficking protein (LBRM2903_190011800), ribosomal proteins S17 (LBRM2903_34004790) and L2 (LBRM2903_080008100), eukaryotic translation initiation factor 3 (LBRM2903_350086700), replication factor A (LBRM2903_150008000), U3 small nucleolar RNA-associated protein (LBRM2903_340025600), exonuclease (LBRM2903_200021800), and mitochondrial RNA ligase (LBRM2903_200074100)). Among the hub proteins, six were classified as drug targets and two as vaccine candidates. Further, druggability analysis indicated three hub proteins, namely eukaryotic translation initiation factor 3, ribosomal proteins S17 and L2 as druggable. Their three-dimensional structures were modelled and docked with the identified ligands (2-methylthio-N6-isopentenyl-adenosine-5'-monophosphate, artenimol and omacetaxine mepesuccinate). These ligands could be experimentally validated (in vitro and in vivo) and repurposed for the development of novel antileishmanial agents.
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Thirunavukkarasu MK, Suriya U, Rungrotmongkol T, Karuppasamy R. In Silico Screening of Available Drugs Targeting Non-Small Cell Lung Cancer Targets: A Drug Repurposing Approach. Pharmaceutics 2021; 14:59. [PMID: 35056955 PMCID: PMC8778223 DOI: 10.3390/pharmaceutics14010059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 01/03/2023] Open
Abstract
The RAS-RAF-MEK-ERK pathway plays a key role in malevolent cell progression in many tumors. The high structural complexity in the upstream kinases limits the treatment progress. Thus, MEK inhibition is a promising strategy since it is easy to inhibit and is a gatekeeper for the many malignant effects of its downstream effector. Even though MEK inhibitors are under investigation in many cancers, drug resistance continues to be the principal limiting factor to achieving cures in patients with cancer. Hence, we accomplished a high-throughput virtual screening to overcome this bottleneck by the discovery of dual-targeting therapy in cancer treatment. Here, a total of 11,808 DrugBank molecules were assessed through high-throughput virtual screening for their activity against MEK. Further, the Glide docking, MLSF and prime-MM/GBSA methods were implemented to extract the potential lead compounds from the database. Two compounds, DB012661 and DB07642, were outperformed in all the screening analyses. Further, the study results reveal that the lead compounds also have a significant binding capability with the co-target PIM1. Finally, the SIE-based free energy calculation reveals that the binding of compounds was majorly affected by the van der Waals interactions with MEK receptor. Overall, the in silico binding efficacy of these lead compounds against both MEK and PIM1 could be of significant therapeutic interest to overcome drug resistance in the near future.
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Affiliation(s)
- Muthu Kumar Thirunavukkarasu
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
| | - Utid Suriya
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ramanathan Karuppasamy
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India;
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Choudhry H. High-throughput screening to identify potential inhibitors of the Zα domain of the adenosine deaminase 1 (ADAR1). Saudi J Biol Sci 2021; 28:6297-6304. [PMID: 34759749 PMCID: PMC8568724 DOI: 10.1016/j.sjbs.2021.06.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 11/26/2022] Open
Abstract
Adenosine deaminases acting on RNA 1 (ADAR1) are enzymes involved in editing adenosine to inosine in the dsRNAs of cells associated with cancer development. The p150 isoform of ADAR1 is the only isoform containing the Zα domain that binds to both Z-DNA and Z-RNA. The Zα domain is suggested to modulate the immune response and could be a suitable target for antiviral treatment and cancer immunotherapy. In this study, we aimed to identify potential inhibitors for ADAR1 protein that bind the Zα domain using molecular docking and simulation tools. Virtual docking and molecular dynamics simulation approaches were used to screen the potential activity of 2115 FDA-approved compounds on the Zα domain of ADAR1 and filtered for to obtain the top-scoring hits. The top three compounds with the best XP Gscore—namely alendronate (−7.045), etidronate (−6.923), and zoledronate (−6.77)—were subjected to 50 ns simulations to characterize complex stability and identify the fundamental interactions that contribute to inhibition of the ADAR1 Zα domain. The three compounds were shown to interact with Lys169, Lys170, Asn173, and Tyr177 of the Zα domain-like helical backbone of Z-RNA. The study provides a comprehensive and novel insights of repurposes drugs for the inhibition of ADAR1 function.
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Affiliation(s)
- Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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Nayak C, Singh SK. In silico identification of natural product inhibitors against Octamer-binding transcription factor 4 (Oct4) to impede the mechanism of glioma stem cells. PLoS One 2021; 16:e0255803. [PMID: 34613998 PMCID: PMC8494328 DOI: 10.1371/journal.pone.0255803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 07/23/2021] [Indexed: 02/07/2023] Open
Abstract
Octamer-binding transcription factor 4 (Oct4) is a core regulator in the retention of stemness, invasive, and self-renewal properties in glioma initiating cells (GSCs) and its overexpression inhibits the differentiation of glioma cells promoting tumor cell proliferation. The Pit-Oct-Unc (POU) domain comprising POU-specific domain (POUS) and POU-type homeodomain (POUHD) subdomains is the most critical part of the Oct4 for the generation of induced pluripotent stem cells from somatic cells that lead to tumor initiation, invasion, posttreatment relapse, and therapeutic resistance. Therefore, the present investigation hunts for natural product inhibitors (NPIs) against the POUHD domain of Oct4 by employing receptor-based virtual screening (RBVS) followed by binding free energy calculation and molecular dynamics simulation (MDS). RBVS provided 13 compounds with acceptable ranges of pharmacokinetic properties and good docking scores having key interactions with the POUHD domain. More Specifically, conformational and interaction stability analysis of 13 compounds through MDS unveiled two compounds ZINC02145000 and ZINC32124203 which stabilized the backbone of protein even in the presence of linker and POUS domain. Additionally, ZINC02145000 and ZINC32124203 exhibited stable and strong interactions with key residues W277, R242, and R234 of the POUHD domain even in dynamic conditions. Interestingly, ZINC02145000 and ZINC32124203 established communication not only with the POUHD domain but also with the POUS domain indicating their incredible potency toward thwarting the function of Oct4. ZINC02145000 and ZINC32124203 also reduced the flexibility and escalated the correlations between the amino acid residues of Oct4 evidenced by PCA and DCCM analysis. Finally, our examination proposed two NPIs that can impede the Oct4 function and may help to improve overall survival, diminish tumor relapse, and achieve a cure not only in deadly disease GBM but also in other cancers with minimal side effects.
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Affiliation(s)
- Chirasmita Nayak
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer-Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi Tamil Nadu, India
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17
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Yang Y, Zhang L, Tian J, Ye F, Xiao Z. Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site. J Chem Inf Model 2021; 61:4720-4732. [PMID: 34521197 DOI: 10.1021/acs.jcim.1c00357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an intractable target for drug discovery due to its conservative and cationic catalytic site. Targeting alternative allosteric sites of PTP1B is a promising strategy to achieve specificity and bioavailability. A hierarchical virtual screening based on a previously identified allosteric site was applied to search for potential PTP1B inhibitors with better pharmacological profiles. Four potent PTP1B inhibitors (H1, H3, H7, and H9) with structures distinct from known inhibitors were identified. Among them, H3 and H9 demonstrated evident selectivity to PTP1B over homologous T-cell protein tyrosine phosphatase (TCPTP) and SHP2. Molecular dynamics simulations and molecular mechanics-generalized Born surface area (MM-GBSA) calculations recognized Phe280, Phe196, Leu192, and Asn193 as key residues responsible for potent allosteric inhibition and excellent PTP selectivity. The results not only expand the structural diversity but also aid the future molecular design of PTP1B allosteric inhibitors.
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Affiliation(s)
- Ying Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Lei Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jinying Tian
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P. R. China
| | - Fei Ye
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P. R. China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
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18
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MohammadiPeyhani H, Chiappino-Pepe A, Haddadi K, Hafner J, Hadadi N, Hatzimanikatis V. NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. eLife 2021; 10:e65543. [PMID: 34340747 PMCID: PMC8331181 DOI: 10.7554/elife.65543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/07/2021] [Indexed: 12/30/2022] Open
Abstract
The discovery of a drug requires over a decade of intensive research and financial investments - and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied their enzymatic metabolic targets, fate, and toxicity. NICEdrug.ch includes a unique fingerprint that identifies reactive similarities between drug-drug and drug-metabolite pairs. We validated the application, scope, and performance of NICEdrug.ch over similar methods in the field on golden standard datasets describing drugs and metabolites sharing reactivity, drug toxicities, and drug targets. We use NICEdrug.ch to evaluate inhibition and toxicity by the anticancer drug 5-fluorouracil, and suggest avenues to alleviate its side effects. We propose shikimate 3-phosphate for targeting liver-stage malaria with minimal impact on the human host cell. Finally, NICEdrug.ch suggests over 1300 candidate drugs and food molecules to target COVID-19 and explains their inhibitory mechanism for further experimental screening. The NICEdrug.ch database is accessible online to systematically identify the reactivity of small molecules and druggable enzymes with practical applications in lead discovery and drug repurposing.
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Affiliation(s)
- Homa MohammadiPeyhani
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Kiandokht Haddadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Jasmin Hafner
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Noushin Hadadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
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19
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Therapeutic Targeting of Protein Tyrosine Phosphatases from Mycobacterium tuberculosis. Microorganisms 2020; 9:microorganisms9010014. [PMID: 33374544 PMCID: PMC7822160 DOI: 10.3390/microorganisms9010014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is an airborne infectious disease caused by Mycobacterium tuberculosis (Mtb). According to the World Health Organization, an estimated 10 million people developed TB in 2018. The occurrence of drug-resistant TB demands therapeutic agents with novel mechanisms of action. Antivirulence is an alternative strategy that targets bacterial virulence factors instead of central growth pathways to treat disease. Mycobacterium protein tyrosine phosphatases, mPTPA and mPTPB, are secreted by Mtb into the cytoplasm of macrophages and are required for survival and growth of infection within the host. Here we present recent advances in understanding the roles of mPTPA and mPTPB in the pathogenesis of TB. We also focus on potent, selective, and well-characterized small molecule inhibitors reported in the last decade for mPTPA and mPTPB.
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20
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García‐Marín J, Griera M, Sánchez‐Alonso P, Di Geronimo B, Mendicuti F, Rodríguez‐Puyol M, Alajarín R, Pascual‐Teresa B, Vaquero JJ, Rodríguez‐Puyol D. Pyrrolo[1,2‐
a
]quinoxalines: Insulin Mimetics that Exhibit Potent and Selective Inhibition against Protein Tyrosine Phosphatase 1B. ChemMedChem 2020; 15:1788-1801. [DOI: 10.1002/cmdc.202000446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/29/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Javier García‐Marín
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805 Alcalá de Henares Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Instituto de Investigación Química Andrés M. del Río Facultad de Farmacia Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Mercedes Griera
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Departamento de Biología de Sistemas Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Patricia Sánchez‐Alonso
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Bruno Di Geronimo
- Departamento de Química y Bioquímica Facultad de Farmacia Universidad San Pablo CEU 28925 Alcorcón Spain
| | - Francisco Mendicuti
- Departamento de Química Analítica Química Física e Ingeniería Química Universidad de Alcalá 28805 Alcalá de Henares Spain
- Instituto de Investigación Química Andrés M. del Río Facultad de Farmacia Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Manuel Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Departamento de Biología de Sistemas Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Ramón Alajarín
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805 Alcalá de Henares Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Instituto de Investigación Química Andrés M. del Río Facultad de Farmacia Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Beatriz Pascual‐Teresa
- Departamento de Química y Bioquímica Facultad de Farmacia Universidad San Pablo CEU 28925 Alcorcón Spain
| | - Juan J. Vaquero
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805 Alcalá de Henares Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Instituto de Investigación Química Andrés M. del Río Facultad de Farmacia Universidad de Alcalá 28805 Alcalá de Henares Spain
| | - Diego Rodríguez‐Puyol
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS) Ctra. Colmenar Viejo, km. 9100 28034 Madrid Spain
- Departamento de Biología de Sistemas Universidad de Alcalá 28805 Alcalá de Henares Spain
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21
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In silico and saturation transfer difference NMR approaches to unravel the binding mode of an andrographolide derivative to K-Ras oncoprotein. Future Med Chem 2020; 12:1611-1631. [PMID: 32892640 DOI: 10.4155/fmc-2020-0104] [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] [Indexed: 11/17/2022] Open
Abstract
Background: Andrographolide and its benzylidene derivatives, SRJ09 and SRJ23, potentially bind oncogenic K-Ras to exert anticancer activity. Their molecular interactions with K-Ras oncoproteins that lead to effective biological activity are of major interest. Methods & results: In silico docking and molecular dynamics simulation were performed using Glide and Desmond, respectively; while saturation transfer difference NMR was performed using GDP-bound K-RasG12V. SRJ23 was found to bind strongly and selectively to K-RasG12V, by anchoring to a binding pocket (namely p2) principally via hydrogen bond and hydrophobic interactions. The saturation transfer difference NMR analysis revealed the proximity of protons of functional moieties in SRJ23 to K-RasG12V, suggesting positive binding. Conclusion: SRJ23 binds strongly and interacts stably with K-RasG12V to exhibit its inhibitory activity.
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22
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de Souza AC, Mori M, Sens L, Rocha RF, Tizziani T, de Souza LF, Domeneghini Chiaradia-Delatorre L, Botta M, Nunes RJ, Terenzi H, Menegatti AC. A chalcone derivative binds a putative allosteric site of YopH: Inhibition of a virulence factor of Yersinia. Bioorg Med Chem Lett 2020; 30:127350. [DOI: 10.1016/j.bmcl.2020.127350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023]
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23
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Recent advance on PTP1B inhibitors and their biomedical applications. Eur J Med Chem 2020; 199:112376. [DOI: 10.1016/j.ejmech.2020.112376] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022]
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24
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Ghattas MA, Al Rawashdeh S, Atatreh N, Bryce RA. How Do Small Molecule Aggregates Inhibit Enzyme Activity? A Molecular Dynamics Study. J Chem Inf Model 2020; 60:3901-3909. [PMID: 32628846 DOI: 10.1021/acs.jcim.0c00540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Small molecule compounds which form colloidal aggregates in solution are problematic in early drug discovery; adsorption of the target protein by these aggregates can lead to false positives in inhibition assays. In this work, we probe the molecular basis of this inhibitory mechanism using molecular dynamics simulations. Specifically, we examine in aqueous solution the adsorption of the enzymes β-lactamase and PTP1B onto aggregates of the drug miconazole. In accordance with experiment, molecular dynamics simulations observe formation of miconazole aggregates as well as subsequent association of these aggregates with β-lactamase and PTP1B. When complexed with aggregate, the proteins do not exhibit significant alteration in protein tertiary structure or dynamics on the microsecond time scale of the simulations, but they do indicate persistent occlusion of the protein active site by miconazole molecules. MD simulations further suggest this occlusion can occur via surficial interactions of protein with miconazole but also potentially by envelopment of the protein by miconazole. The heterogeneous polarity of the miconazole aggregate surface seems to underpin its activity as an invasive and nonspecific inhibitory agent. A deeper understanding of these protein/aggregate systems has implications not only for drug design but also for their exploitation as tools in drug delivery and analytical biochemistry.
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Affiliation(s)
| | - Sara Al Rawashdeh
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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25
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Zhang Y, Roos M, Himburg H, Termini CM, Quarmyne M, Li M, Zhao L, Kan J, Fang T, Yan X, Pohl K, Diers E, Jin Gim H, Damoiseaux R, Whitelegge J, McBride W, Jung ME, Chute JP. PTPσ inhibitors promote hematopoietic stem cell regeneration. Nat Commun 2019; 10:3667. [PMID: 31413255 PMCID: PMC6694155 DOI: 10.1038/s41467-019-11490-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 07/18/2019] [Indexed: 01/08/2023] Open
Abstract
Receptor type protein tyrosine phosphatase-sigma (PTPσ) is primarily expressed by adult neurons and regulates neural regeneration. We recently discovered that PTPσ is also expressed by hematopoietic stem cells (HSCs). Here, we describe small molecule inhibitors of PTPσ that promote HSC regeneration in vivo. Systemic administration of the PTPσ inhibitor, DJ001, or its analog, to irradiated mice promotes HSC regeneration, accelerates hematologic recovery, and improves survival. Similarly, DJ001 administration accelerates hematologic recovery in mice treated with 5-fluorouracil chemotherapy. DJ001 displays high specificity for PTPσ and antagonizes PTPσ via unique non-competitive, allosteric binding. Mechanistically, DJ001 suppresses radiation-induced HSC apoptosis via activation of the RhoGTPase, RAC1, and induction of BCL-XL. Furthermore, treatment of irradiated human HSCs with DJ001 promotes the regeneration of human HSCs capable of multilineage in vivo repopulation. These studies demonstrate the therapeutic potential of selective, small-molecule PTPσ inhibitors for human hematopoietic regeneration.
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Affiliation(s)
- Yurun Zhang
- Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - Martina Roos
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
| | - Heather Himburg
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Christina M Termini
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Mamle Quarmyne
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Michelle Li
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Liman Zhao
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Jenny Kan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Tiancheng Fang
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Xiao Yan
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
| | - Katherine Pohl
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Emelyne Diers
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Hyo Jin Gim
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Robert Damoiseaux
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, 90095, USA
- California Nanosystems Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Julian Whitelegge
- Department of Psychiatry and Behavioral Sciences, UCLA, Los Angeles, CA, 90095, USA
| | - William McBride
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Department of Radiation Oncology, UCLA, Los Angeles, CA, 90095, USA
| | - Michael E Jung
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- California Nanosystems Institute, UCLA, Los Angeles, CA, 90095, USA
| | - John P Chute
- Division of Hematology/Oncology, Department of Medicine, UCLA, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA.
- Department of Radiation Oncology, UCLA, Los Angeles, CA, 90095, USA.
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26
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Docking- and pharmacophore-based virtual screening for the identification of novel Mycobacterium tuberculosis protein tyrosine phosphatase B (MptpB) inhibitor with a thiobarbiturate scaffold. Bioorg Chem 2019; 85:229-239. [DOI: 10.1016/j.bioorg.2018.12.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/23/2018] [Accepted: 12/29/2018] [Indexed: 01/15/2023]
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27
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Tang Y, Zhang X, Chen Z, Yin W, Nan G, Tian J, Ye F, Xiao Z. Novel benzamido derivatives as PTP1B inhibitors with anti-hyperglycemic and lipid-lowering efficacy. Acta Pharm Sin B 2018; 8:919-932. [PMID: 30505661 PMCID: PMC6251817 DOI: 10.1016/j.apsb.2018.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/10/2018] [Accepted: 04/17/2018] [Indexed: 11/16/2022] Open
Abstract
Based on a non-competitive and selective PTP1B inhibitor reported by us previously, thirty-nine benzamido derivatives were designed and synthesized as novel PTP1B inhibitors. Among them, twelve compounds exhibited IC50 values at micromolar level against human recombinant PTP1B, and most of them exhibited significant selectivity to PTP1B over TC-PTP and CD45. Further evaluation of the most potent compound 27 on high-fat diet (HFD)-induced insulin-resistant (IR) obese mice indicated that 27 could modulate glucose metabolism and ameliorate dyslipidemia simultaneously.
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28
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Lountos GT, Raran-Kurussi S, Zhao BM, Dyas BK, Burke TR, Ulrich RG, Waugh DS. High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design. Acta Crystallogr D Struct Biol 2018; 74:1015-1026. [PMID: 30289412 PMCID: PMC6173050 DOI: 10.1107/s2059798318011919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/22/2018] [Indexed: 11/10/2022] Open
Abstract
Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPℇ), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPℇ D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPℇ D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPℇ D1 domain is also described.
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Affiliation(s)
- George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sreejith Raran-Kurussi
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Bryan M. Zhao
- The Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Beverly K. Dyas
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Robert G. Ulrich
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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29
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Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 2018; 7:36307. [PMID: 29877794 PMCID: PMC6039181 DOI: 10.7554/elife.36307] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022] Open
Abstract
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here, we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function. Proteins perform many important jobs in each of the cells in our bodies, such as transporting other molecules and helping chemical reactions to occur. The part of the protein directly involved in these tasks is called the active site. Other areas of the protein can communicate with the active site to switch the protein on or off. This method of control is known as allostery. Switching proteins on and off could help us to develop treatments for certain diseases. For example, a protein called PTP1B reduces how well cells can respond to insulin. Switching this protein off could therefore help to treat diabetes. However, much like it’s hard to guess how a light switch is wired to a light bulb without seeing behind the walls, it is hard to predict which remote areas of a protein are ‘wired’ to the active site. Keedy, Hill et al. have now used two complementary methods to examine the structure of PTP1B and find new allosteric sites. The first method captured a series of X-ray images from crystallized molecules of the protein held at different temperatures. This revealed areas of PTP1B that can move like windshield wipers to communicate with each other. The second method soaked PTP1B crystals in trays with hundreds of drug-sized molecules and assessed which sites on the protein the molecules bound to. The molecules generally bound to just a few sites of the protein. Further tests on one of these sites showed that it can communicate with the active site to turn the protein on or off. Further work will be needed to develop drugs that could treat diabetes by binding to the newly identified allosteric sites in PTP1B. More generally, the methods developed by Keedy, Hill et al. could be used to study allostery in other important proteins.
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Zachary B Hill
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Justin T Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Emily Kang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - T Justin Rettenmaier
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | | | - Nicholas M Pearce
- Crystal and Structural Chemistry Group, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Frank von Delft
- Diamond Light Source, Didcot, United Kingdom.,Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom.,Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.,Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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30
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Fan L, Wu X, Jin C, Li F, Xiong S, Dong Y. MptpB Promotes Mycobacteria Survival by Inhibiting the Expression of Inflammatory Mediators and Cell Apoptosis in Macrophages. Front Cell Infect Microbiol 2018; 8:171. [PMID: 29888212 PMCID: PMC5981270 DOI: 10.3389/fcimb.2018.00171] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/03/2018] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis is a severe contagious disease caused by Mycobacterium tuberculosis (Mtb). To develop new vaccines and medicine against TB, there is an urgent need to provide insights into the mechanisms by which Mtb induces tuberculosis. In this study, we found that secreted Mtb virulence factor MptpB significantly enhanced the survival of H37Rv in macrophages. MptpB suppressed the production of iNOS, the expression of inflammatory factors IL-1β and IL-6, as well as the apoptosis of the macrophage in Mtb infected RAW264.7 cells. Mechanism investigation showed that MptpB simultaneously hampered the NF-κB and MAPK signal pathways, evidenced by its blocking of p65, IKKα, Erk1/2, and p38 phosphorylation induced by Mtb infection. MptpB also inhibited host cell p53 expression. The results demonstrated that MptpB contributed to the survival of H37Rv by inhibiting host inflammatory responses and apoptosis through impeding the NF-κB and MAPK signal pathways and p53 expression in the macrophage.
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Affiliation(s)
- Lingbo Fan
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Xiaoyu Wu
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Chunyan Jin
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Fengge Li
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
| | - Yuanshu Dong
- Jiangsu Key Laboratory of Infection and Immunity, Institute of Biology and Medical Sciences, Suzhou, China
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31
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Kumar AP, Nguyen MN, Verma C, Lukman S. Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites. Proteins 2018; 86:301-321. [PMID: 29235148 DOI: 10.1002/prot.25440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/16/2017] [Accepted: 12/10/2017] [Indexed: 12/11/2022]
Abstract
Catalytic proteins such as human protein tyrosine phosphatase 1B (PTP1B), with conserved and highly polar active sites, warrant the discovery of druggable nonactive sites, such as allosteric sites, and potentially, therapeutic small molecules that can bind to these sites. Catalyzing the dephosphorylation of numerous substrates, PTP1B is physiologically important in intracellular signal transduction pathways in diverse cell types and tissues. Aberrant PTP1B is associated with obesity, diabetes, cancers, and neurodegenerative disorders. Utilizing clustering methods (based on root mean square deviation, principal component analysis, nonnegative matrix factorization, and independent component analysis), we have examined multiple PTP1B structures. Using the resulting representative structures in different conformational states, we determined consensus clustroids and used them to identify both known and novel binding sites, some of which are potentially allosteric. We report several lead compounds that could potentially bind to the novel PTP1B binding sites and can be further optimized. Considering the possibility for drug repurposing, we discovered homologous binding sites in other proteins, with ligands that could potentially bind to the novel PTP1B binding sites.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Minh N Nguyen
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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32
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Mascarello A, Orbem Menegatti AC, Calcaterra A, Martins PGA, Chiaradia-Delatorre LD, D'Acquarica I, Ferrari F, Pau V, Sanna A, De Logu A, Botta M, Botta B, Terenzi H, Mori M. Naturally occurring Diels-Alder-type adducts from Morus nigra as potent inhibitors of Mycobacterium tuberculosis protein tyrosine phosphatase B. Eur J Med Chem 2018; 144:277-288. [DOI: 10.1016/j.ejmech.2017.11.087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 12/18/2022]
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33
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LaRochelle JR, Fodor M, Ellegast JM, Liu X, Vemulapalli V, Mohseni M, Stams T, Buhrlage SJ, Stegmaier K, LaMarche MJ, Acker MG, Blacklow SC. Identification of an allosteric benzothiazolopyrimidone inhibitor of the oncogenic protein tyrosine phosphatase SHP2. Bioorg Med Chem 2017; 25:6479-6485. [DOI: 10.1016/j.bmc.2017.10.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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34
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Small molecule targeting of PTPs in cancer. Int J Biochem Cell Biol 2017; 96:171-181. [PMID: 28943273 DOI: 10.1016/j.biocel.2017.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 01/28/2023]
Abstract
Protein tyrosine phosphatases (PTPs) undeniably have a central role in the development and progression of human cancers. Historically, however, PTPs have not been viewed as privileged drug targets, and progress on identifying potent, selective, and cell-active small molecule PTP inhibitors has suffered accordingly. This situation is rapidly changing, however, due to biochemical advances in the study of PTPs and recent small molecule screening campaigns, which have identified potent and mechanistically diverse lead structures. These compounds are facilitating the exploration of the fundamental cellular processes controlled by PTPs in cancers, and could form the inflection point for new therapeutic paradigms for the treatment of a range of cancers. Herein, we review recent advances in the discovery and biological annotation of cancer-relevant small molecule PTP inhibitors.
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35
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Reisdorf WC, Chhugani N, Sanseau P, Agarwal P. Harnessing public domain data to discover and validate therapeutic targets. Expert Opin Drug Discov 2017; 12:687-693. [DOI: 10.1080/17460441.2017.1329296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- William C. Reisdorf
- Computational Biology, Target Sciences, GlaxoSmithKline R&D, King of Prussia, PA, USA
| | - Neha Chhugani
- Jacobs School of Engineering, University of California San Diego, Belle Mead, NJ, USA
| | - Philippe Sanseau
- Computational Biology, Target Sciences, GlaxoSmithKline R&D, Hertfordshire, UK
| | - Pankaj Agarwal
- Computational Biology, Target Sciences, GlaxoSmithKline R&D, King of Prussia, PA, USA
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