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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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2
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Wei S, Zhao T, Wang J, Zhai X. Approach in Improving Potency and Selectivity of Kinase Inhibitors: Allosteric Kinase Inhibitors. Mini Rev Med Chem 2021; 21:991-1003. [PMID: 33355051 DOI: 10.2174/1389557521666201222144355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/21/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Allostery is an efficient and particular regulatory mechanism to regulate protein functions. Different from conserved orthosteric sites, allosteric sites have a distinctive functional mechanism to form the complex regulatory network. In drug discovery, kinase inhibitors targeting the allosteric pockets have received extensive attention for the advantages of high selectivity and low toxicity. The approval of trametinib as the first allosteric inhibitor validated that allosteric inhibitors could be used as effective therapeutic drugs for the treatment of diseases. To date, a wide range of allosteric inhibitors have been identified. In this perspective, we outline different binding modes and potential advantages of allosteric inhibitors. In the meantime, the research processes of typical and novel allosteric inhibitors are described briefly in terms of structure-activity relationships, ligand-protein interactions, and in vitro and in vivo activity. Additionally, challenges, as well as opportunities, are also presented.
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Affiliation(s)
- Shangfei Wei
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Tianming Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Jie Wang
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin Zhai
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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3
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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: 2] [Impact Index Per Article: 0.7] [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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4
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Manley PW, Barys L, Cowan-Jacob SW. The specificity of asciminib, a potential treatment for chronic myeloid leukemia, as a myristate-pocket binding ABL inhibitor and analysis of its interactions with mutant forms of BCR-ABL1 kinase. Leuk Res 2020; 98:106458. [DOI: 10.1016/j.leukres.2020.106458] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
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Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
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Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
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6
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Zanforlin E, Zagotto G, Ribaudo G. A Chemical Approach to Overcome Tyrosine Kinase Inhibitors Resistance: Learning from Chronic Myeloid Leukemia. Curr Med Chem 2019; 26:6033-6052. [PMID: 29874990 DOI: 10.2174/0929867325666180607092451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/03/2018] [Accepted: 05/15/2018] [Indexed: 01/02/2023]
Abstract
BACKGROUND The possibilities of treatment for oncological diseases are growing enormously in the last decades. Unfortunately, these developments have led to the onset of resistances with regards to the new treatments. This is particularly true if we face with the therapeutic field of Tyrosine Kinase Inhibitors (TKIs). This review gives an overview of possible TKI resistances that can occur during the treatment of an oncologic diesease and available strategies that can be adopted, taking cues from a successful example such as CML. METHODS We performed a literature search for peer-reviewed articles using different databases, such as PubMed and Scopus, and exploiting different keywords and different logical operators. RESULTS 68 papers were included in the review. Twenty-four papers give an overview of the causes of TKIs resistances in the wide oncologic field. The remaining papers deal CML, deeply analysing the TKIs Resistances present in this pathology and the strategies adopted to overcome them. CONCLUSION The aim of this review is to furnish an overview and a methodological guideline for the approach and the overcoming of TKIs Resistances.
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Affiliation(s)
- Enrico Zanforlin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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7
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Simpson GL, Bertrand SM, Borthwick JA, Campobasso N, Chabanet J, Chen S, Coggins J, Cottom J, Christensen SB, Dawson HC, Evans HL, Hobbs AN, Hong X, Mangatt B, Munoz-Muriedas J, Oliff A, Qin D, Scott-Stevens P, Ward P, Washio Y, Yang J, Young RJ. Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies. J Med Chem 2019; 62:2154-2171. [PMID: 30689376 DOI: 10.1021/acs.jmedchem.8b01872] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abelson kinase (c-Abl) is a ubiquitously expressed, nonreceptor tyrosine kinase which plays a key role in cell differentiation and survival. It was hypothesized that transient activation of c-Abl kinase via displacement of the N-terminal autoinhibitory "myristoyl latch", may lead to an increased hematopoietic stem cell differentiation. This would increase the numbers of circulating neutrophils and so be an effective treatment for chemotherapy-induced neutropenia. This paper describes the discovery and optimization of a thiazole series of novel small molecule c-Abl activators, initially identified by a high throughput screening. Subsequently, a scaffold-hop, which exploited the improved physicochemical properties of a dihydropyrazole analogue, identified through fragment screening, delivered potent, soluble, cell-active c-Abl activators, which demonstrated the intracellular activation of c-Abl in vivo.
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Affiliation(s)
- Graham L Simpson
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Sophie M Bertrand
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Jennifer A Borthwick
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Nino Campobasso
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Julien Chabanet
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | | | - Julia Coggins
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Josh Cottom
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | | | - Helen C Dawson
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Helen L Evans
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Andrew N Hobbs
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Xuan Hong
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Biju Mangatt
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Jordi Munoz-Muriedas
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Allen Oliff
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Donghui Qin
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Paul Scott-Stevens
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Paris Ward
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Yoshiaki Washio
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Jingsong Yang
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Robert J Young
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
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8
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Zhang H, He X, Ni D, Mou L, Chen X, Lu S. How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:89-100. [DOI: 10.1080/07391102.2019.1567390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hao Zhang
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xinheng He
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Duan Ni
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Linkai Mou
- Department of Urology, Affiliated Hospital of Weifang Medicinal University, Wei fang, Shandong, China
| | - Xiangyu Chen
- Department of Medicinal Laboratory, Weifang Medicinal University, Weifang, Shandong, China
| | - Shaoyong Lu
- Department of Pathophysiology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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9
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Wang J, Chen Q, Wang M, Zhong C. The opening/closure of the P-loop and hinge of BCR-ABL1 decodes the low/high bioactivities of dasatinib and axitinib. Phys Chem Chem Phys 2017; 19:22444-22453. [DOI: 10.1039/c7cp03443a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The open/closed conformations reveal the low/high bioactivities of the ligands.
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Affiliation(s)
- Jianyi Wang
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
| | - Qing Chen
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
| | - Mian Wang
- School of Chemistry and Chemical Engineering
- Guangxi University
- Nanning 530004
- China
- College of Life Science and Technology
| | - Cheng Zhong
- School of Computer
- Electronics and Information
- Guangxi University
- Nanning 530004
- China
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10
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La Sala G, Riccardi L, Gaspari R, Cavalli A, Hantschel O, De Vivo M. HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase. J Chem Theory Comput 2016; 12:5563-5574. [DOI: 10.1021/acs.jctc.6b00600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - Andrea Cavalli
- Department of Pharmacy & Biotechnology, Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Oliver Hantschel
- Swiss
Institute for Experimental Cancer Research (ISREC), School of Life
Sciences, École polytechnique fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- ISREC Foundation Chair in Translational Oncology, 1015 Lausanne, Switzerland
| | - Marco De Vivo
- IAS-S/INM-9 Computational Biomedicine Forschungszentrum, Jülich Wilhelm-Johnen-Staße, 52428 Jülich, Germany
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11
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Radi M, Schneider R, Fallacara AL, Botta L, Crespan E, Tintori C, Maga G, Kissova M, Calgani A, Richters A, Musumeci F, Rauh D, Schenone S. A cascade screening approach for the identification of Bcr-Abl myristate pocket binders active against wild type and T315I mutant. Bioorg Med Chem Lett 2016; 26:3436-40. [DOI: 10.1016/j.bmcl.2016.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 01/17/2023]
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12
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Singh VK, Chang HH, Kuo CC, Shiao HY, Hsieh HP, Coumar MS. Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors. J Biomol Struct Dyn 2016; 35:1833-1848. [DOI: 10.1080/07391102.2016.1196462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Vivek Kumar Singh
- School of Life Sciences, Centre for Bioinformatics, Pondicherry University, Kalapet, Puducherry 605014, India
| | - Hsin-Huei Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Institute of Clinical Pharmacy and Pharmaceutical Sciences, National Cheng Kung University Medical College, Tainan, Taiwan
- Graduate Program for Aging, China Medical University, Taichung, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 350, Taiwan, ROC
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- School of Life Sciences, Centre for Bioinformatics, Pondicherry University, Kalapet, Puducherry 605014, India
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Abstract
Small-molecule kinase inhibitors are invaluable targeted therapeutics for the treatment of various human diseases, especially cancers. While the majority of approved and developed preclinical small-molecule inhibitors are characterized as type I or type II inhibitors that target the ATP-binding pocket of kinases, the remarkable sequential and structural similarity among ATP pockets renders the selective inhibition of kinases a daunting challenge. Therefore, targeting allosteric pockets of kinases outside the highly conversed ATP pocket has been proposed as a promising alternative to overcome current barriers of kinase inhibitors, including poor selectivity and emergence of drug resistance. In spite of the small number of identified allosteric inhibitors in comparison with that of inhibitors targeting the ATP pocket, encouraging results, such as the FDA-approval of the first small-molecule allosteric inhibitor trametinib in 2013, the progress of more than 10 other allosteric inhibitors in clinical trials, and the emergence of a pipeline of highly selective and potent preclinical molecules, have been reported in the past decade. In this article, we present the current knowledge on allosteric inhibition in terms of conception, classification, potential advantages, and summarized debatable topics in the field. Recent progress and allosteric inhibitors that were identified in the past three years are highlighted in this paper.
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Affiliation(s)
- Peng Wu
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Mads H Clausen
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark; Center for Nanomedicine and Theranostics, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Thomas E Nielsen
- Protein and Peptide Chemistry, Novo Nordisk A/S, Måløv DK-2760, Denmark
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14
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Gonfloni S. Defying c-Abl signaling circuits through small allosteric compounds. Front Genet 2014; 5:392. [PMID: 25429298 PMCID: PMC4228975 DOI: 10.3389/fgene.2014.00392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 10/25/2014] [Indexed: 11/13/2022] Open
Abstract
Many extracellular and intracellular signals promote the c-Abl tyrosine kinase activity. c-Abl in turn triggers a multitude of changes either in protein phosphorylation or in gene expression in the cell. Yet, c-Abl takes part in diverse signaling routes because of several domains linked to its catalytic core. Complex conformational changes turn on and off its kinase activity. These changes affect surface features of the c-Abl kinase and likely its capability to bind actin and/or DNA. Two specific inhibitors (ATP-competitive or allosteric compounds) regulate the c-Abl kinase through different mechanisms. NMR studies show that a c-Abl fragment (SH3-SH2-linker-SH1) adopts different conformational states upon binding to each inhibitor. This supports an unconventional use for allosteric compounds to unraveling physiological c-Abl signaling circuits.
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15
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Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach. J Comput Aided Mol Des 2014; 29:69-78. [PMID: 25342515 DOI: 10.1007/s10822-014-9805-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/17/2014] [Indexed: 12/19/2022]
Abstract
Antibody drugs are very useful tools for the treatment of many chronic diseases. Recently, however, patients and doctors have encountered the problem of drug resistance. How to improve the affinity of antibody drugs has therefore become a pressing issue. Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1. This study investigates the mutation residues of the complementarity determining regions of Ibalizumab. We propose using the wild and mutations of Ibalizumab-human CD4 receptor complex structures, molecular dynamics techniques, alanine-scanning mutagenesis calculations and solvated interaction energies methods to predict the binding free energy of the Ibalizumab-human CD4 receptor complex structures. This work found that revealed three key positions (31th, 32th and 33th in HCDR-1) of the residues may play an important role in Ibalizumab-human CD4 receptor complex interactions. Therefore, bioengineering substitutions of the three key positions and increasing number of intermolecular interactions (HCDR-1 of Ibalizumab/human CD4 receptor) might improve the binding affinities of this complex structure.
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