Protein Kinase Inhibitors: From Discovery to Therapeutics

Protein Kinase Inhibitors: From Discovery to Therapeutics offers a foundational, pragmatic overview of protein kinases inhibitors and their potential role in disease modulation and treatment. Here, international experts in the field offer an integrated discussion of kinase inhibitor biology, biomarker discovery, and methods for drug design and development. After a brief overview of kinases and kinase inhibitors, subsequent chapters discuss individual kinases that are representative of the wider kinases and kinase families, including their roles in disease pathogenesis, underlying mechanisms, potential inhibitors and their modes of action for therapeutic modulation.

Several potential drugs under different stages of clinical trials are discussed, including their relevance to cancer, diabetes, obesity, cardiovascular, neurological, and auto-immune and inflammatory disease, among other disorders. The book also addresses the challenges and opportunities for future kinase inhibitor development.

• Provides a thorough overview of kinase inhibitor biology and its role in disease progression and modulation
• Examines protein kinase inhibitor drugs in various stages of clinical trials and development
• Offers methods and protocols for protein kinase inhibitor research studies and drug design and development
• Includes chapter contributions from international leaders in the field

• Language: English
• Publisher: Academic Press
• Release date: May 19, 2022
• ISBN: 9780323913492

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Chapter 1: Kinase inhibitors: An overview

Sabeeha Ali; Manzar Alam; Md. Imtaiyaz Hassan    Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India

Abstract

The human kinome constitutes more than 500 protein kinases that cover about 2% of the proteome. The protein kinases are one of the critical and largest gene families. Kinases regulate most cellular and biochemical pathways, including the crucial growth, proliferation, survival, apoptosis, transcription, differentiation, and angiogenesis processes. Mutation and dysfunction of kinases have been correlated with different human diseases. Recent studies have shown kinases as drug targets and a therapeutic option for various cancers, neurodegenerative diseases, and other human disorders. Approximately 30% of research and development expenditure, as estimated, is being involved in kinase inhibitors development. At present, more than 80 kinase inhibitors have been clinically approved, and around 100 small-molecule kinase inhibitors have reached the later phases of the clinical development process. Many of them are expected to be approved in the upcoming times.

Keywords

Protein kinase; Kinase inhibitors; Human kinome; Cancer; Drug targets; Drug discovery; Targeted therapy

Acknowledgments

SA extends sincere thanks to the Indian Council of Medical Research for financial support.

Declaration of competing interest

The authors declare that they have no known competing interests or personal relationships that could have appeared to influence the work reported in this paper.

Funding

This work is funded by the Indian Council of Medical Research (ICMR) (BMI/11 (39)/2020).

1: Introduction

Protein kinases comprise one of the largest and crucial protein families of evolutionarily related proteins. The human genome encodes more than 500 different kinases accounting for around 2% of all the human genes (1). The kinases modulate the interaction, localization, and activity of around 30% of all cellular proteins by adding a phosphate group from ATP (adenosine triphosphate) to specific amino acids (Fig. 1). The phosphorylation of specific molecules alters several biological activities, including transcription and translation, and regulates important cellular processes, including cell growth, differentiation, and cell death (2–4). They are considering the importance of these cellular processes. The enzymatic activities of kinases in these pathways are tightly regulated.

Fig. 1

Fig. 1 An schematic presentation of kinase-mediated phosphate transfer to the hydroxyl group (OH) of a serine, threonine, or tyrosine residue of the targeted protein using adenosine triphosphate (ATP).

In the past few years, a mutation in the kinase genes was reported to underlie many human disorders and the cause of metabolic and developmental diseases. Additionally, the uncontrolled growth and proliferation due to mutated kinase enzymes cause certain human cancers (5). Therefore, the mutated kinase enzymes represent an attractive target for the treatment of several metabolic disorders and anticancer agents (6).

The human protein kinases can be categorized into three types based on their substrate specificity as tyrosine (Tyr) kinase, serine-threonine (Ser-Thr) kinase, and nonspecific. The kinase inhibitors are recently discovered molecules, and the tyrosine kinase receptor inhibitors are among the initially developed and best-characterized kinase inhibitors. Since discovering kinase inhibitors, a major advancement in cancer chemotherapy was observed (6,7). This chapter will provide an overview of human kinases and focus on the history and the clinical landscape of kinase inhibitors, including the recently FDA (Food and Drug Administration) approved drugs for use in humans.

2: Human kinome

The family of protein kinases comprises several 518 genes together with 106 pseudogenes in humans. Additionally, the crucial catalytic residues are absent in several gene products, approximately 50 out of 518, and those were named protein pseudokinases. Since the interaction of kinases and pseudokinases to other cellular molecules has added modulatory steps to several cellular and biochemical processes (8). Therefore, the kinases belonging to metazoans are compared and classified into families and subfamilies to better understand their function and evolution. Previously, Hanks and Hunter (9) have previously classified human kinases into 5 major groups consisting of 44 families and 51 subfamilies. Manning et al. (10) expanded the previous kinase classification by adding 4 new major groups, 90 families and 145 subfamilies. The major groups of human kinomes are AGC, CAMK, CK1, CMGC, STE, TK, TKL, RGC, and others (Fig. 2, Table 1).The classification of kinases was primarily based on comparing the catalytic motif sequences and further based on comparing the sequences and domain structures outside the catalytic motif, the functions it is involved in, and the previous classification of other metazoan kinomes.

Fig. 2

Fig. 2 A human kinome structure is showing the major groups with the representative members of each group.

Table 1

The comparison of metazoan kinomes that included human, fly, worm, and yeast validated that the kinase families are shared among these organisms. Furthermore, the phylogenetic analysis determined the categories which are extended in a particular lineage. The human kinome consists of 189 subfamilies. Out of it, 51 subfamilies were reported in all of the other 3 eukaryotic kinomes of fly, worm, and yeast, suggesting a possible involvement of a member of these 51 subfamilies in house-keeping functions that is crucial for eukaryotic cell existence. After that, some 93 subfamilies present in human kinome were also found in the other 2 metazoan kinomes of fly and worm, but not in yeast kinome, indicating their possible role in early metazoan evolution (1,34,35).

The human genome consists of double the number of kinases compared to the number of kinases present in fly or worms after subtracting the idiosyncratic worm-specific extensions (10). Therefore, the human kinome families comprise twice the number of kinases than worm or fly. However, it was found that the number of kinases is not consistent in each family or subfamilies. In particular, a total of 25 subfamilies together with CDK5, CDK9, and Erk7 constitute a single kinase in the eukaryotic kinomes, suggesting their crucial inequivalent roles (1,36).

On the contrary, several kinase families have expanded up to 14 members in a human kinase family, whereas only 1 member is present in their counterpart fly and worm kinase families such as Eph family receptor tyrosine kinases (RTKs). These human kinase families with multimembers, work primarily in more advanced pathways, particularly neural and immune processes, hemopoiesis, apoptosis, and cytokine-related signaling. Furthermore, 14 kinase families are present only in human kinomes, such as the Tie family, which plays a vital role in angiogenesis. The Axl family is involved in angiogenesis in hemopoietic and neural tissues. Following two families, the Trio and RIPK, function in muscle activity and apoptotic signaling. The function of other Lmr, NKF3, NKF4, NKF5, and HUNK families is majorly unidentified. Following it, the function of the next BCR, FAST, G11, H11, and DNAPK is divergent. The Chromosomal mapping of all kinase genes was studied using public genome databases and literature references to identify the expansion origins and to correlate known disease loci with the kinase map. However, the overall kinase gene arrangement is comparable to the other genes, closely related members of the same families found closer to each other, suggesting their origin due to local tandem duplications (1,37,38).

3: Kinase directed signaling networks

Protein kinases are involved in altering target substrate function by transferring a phosphate group to any Ser, Thr, or Tyr residue. The phosphorylation of protein by kinase enzymes results in conformational changes, modulation of interactions of the substrate with other proteins, and alteration in localization and activity of it. In general, the substrate molecule consists of multiple phosphorylation sites. Also, the protein kinase transfers a phosphate group to multiple residues of the same protein or a different protein. However, the kinase-substrate pair determined by multistep processes was found to be very specific and performs a particular biological activity (39–41). For instance, the disruption in cellular activities of phosphoinositide-3-kinase (PI3K), mitogen-activated protein kinase (MAPK), and AMP-activated protein kinase (AMPK) pathways that are involved in glucose homeostasis are mostly related to obesity and diabetes disorders (42).

The MAPK signaling pathways are crucial for critical biological activities such as proliferation, survival, and differentiation. The anomalies of MAPK signaling due to mutations are primarily associated with cancers and other human diseases. Therefore, the MAPK pathway, extracellular signal-regulated kinase (ERK), was an attractive target for cancer treatment. The ERK signaling was activated by Raf, which is a serine/threonine kinase. Mutation in the Raf kinase leads to human oncogenesis.

Furthermore, the Raf-ERK pathway is a downstream regulator of a GTPase, Ras. The mutation in the Ras gene is mainly found in human cancers. Eventually, Ras is involved in the activation of the epidermal growth factor receptor (EGFR). Overexpression of EGFR was reported in a wide variety of human cancers. The activation of ERK increases the expression of EGFR ligands creating an activation-expression loop critical for tumor growth. Thereby, it has been an area of intense research to identify the novel targets of the EGFR-Ras-Raf-MEK-ERK signaling cascades to develop the therapeutic intervention in human disease and cancer (43–46).

Necroptosis, an alternate apoptosis pathway, involves Receptor-interacting protein kinase 1 (RIPK1), RIPK3 and mixed lineage kinase domain-like (MLKL), as a critical player to regulate the necroptosis pathway. Necroptosis, recently found in different liver disease models, is observed in critical biological activities such as immune response, development, and metabolic disorders. The necroptosis signaling was initiated by intracellular adapter molecules FADD and TRADD, which subsequently recruit RIPK1. After that, RIPK1 undergoes a series of modifications before showing its RHIM-domain to recruit RIPK3 and induce the assembly of necrosome (47–49).

4: Kinase as a drug target

Recent advancements in molecular biotechniques have revealed the molecular basis of several human disorders, including various cancers, and indicated the critical role of protein kinases in these molecular pathways. Furthermore, deregulation of functional activities of kinases has been associated with various human cancers and immunological, neurological, and infectious diseases, making it an attractive target in clinical therapy (50–55).

The squamous cell carcinomas (HNSCC) are found in most head and neck cancers. In about 90% of the HNSCC cases, the PI3K/AKT/mTOR signaling is divergently active, accounting for varying aberrant activities such as activation of EGFR, overexpression of PI3K, a mutation in a kinase catalytic subunit alpha (PIK3CA), and in PTEN. Additionally, the most common mutation in these cancers is in the p16 oncogene that expresses cyclin-dependent kinase inhibitor 2A. Therefore, the role of PI3K/AKT/mTOR signaling in HNSCC was intensively studied, which has suggested it as a potential target for novel therapeutic options (56–58). Earlier, the functional role of glycogen synthase kinase-3 (GSK-3) has been very well documented in the modulation of the glucose metabolism pathway by phosphorylating glycogen synthase. However, presently the function of GSK-3 is reported in a wide array of cellular activities varying from transcription, translation, cytoskeletal arrangements, signal transduction to cell division and survival. GSK-3, a serine/threonine-protein kinase, was found pleiotropic but with unique activities and multiple cellular pathways. Therefore, it has been an attractive target for treating common human disorders; particularly type 2 diabetes and Alzheimer's disease (59–61). Recently, Flt3 receptor tyrosine kinase was intensively studied as a potential drug target in acute myeloid leukemia. A variety of mutations resulted in Flt3 activation, which initiates a cascade of signaling involving the RAS/MAP-Kinase and the PI3K/Akt pathways (62,63). A serine/threonine kinase, cyclin-dependent kinase (CDK), plays a vital role during the transcription elongation process. Apart from that, CDKs are also involved in various biological activities and were previously discovered as a switch to regulate the cell cycle system (63–65). CDKs belongs to a family of 13 protein kinases, and disruption in the functional activity of any of the CDKs was found to be correlated with many cancer types. A recent finding has suggested CDK9 as an attractive target for the development of anticancer agents (66–68).

5: Kinase inhibitors

Over few years, the protein kinases were studied intensively as an attractive target for several human diseases accounting for their key role in all aspects of biological processes and the well-established involvement of kinase dysfunction as the cause of several human disorders. The advancement of kinase inhibitors has emerged as an effective treatment option for several human diseases, especially for various cancers (69–73).

The Janus kinase (JAK) family consists of four members sharing a similar JAK homology. These JAK's activate the JAK-STAT signal transduction pathway and are involved in the regulation of inflammatory immune responses. The first JAK inhibitor was tofacitinib approved by the FDA to treat active rheumatic arthritis (69,74–79). Another kinase, RIPK1, is a vital regulator of the cell survival signaling pathway and apoptosis. The development of RIPK1 inhibitors was found effective in a variety of animal disease models. The first small-molecule inhibitor of RIPK1, Necrostatin-1s (Nec-1s), is investigated as a therapeutic option for treating neurodegenerative disorders and several other disorders (80–84).

Tyrosine kinase function inhibition was found effective in the target selective treatment of various malignancies. Imatinib is one of the first tyrosine kinase inhibitors (TKI) investigated in clinical cancer studies. Other TKIs reported are gefitinib, erlotinib, sorafenib, sunitinib, and dasatinib (85–88). The MEKK2 kinase (MAP3K2) that initiates the MEK5/ERK5 signaling cascade plays an essential role in tumor progression and oncogenesis. Ahmad et al. (89) screened a library of compounds to discover MEKK2 inhibitors, validated two compounds with validated structures, and confirmed their activity. The ERK5 pathway activation was inhibited by compound 1, which subsequently resulted in cell migration inhibition. A scaffold was reported with the potential to be developed into a target-specific and effective inhibitor against MEKK2 (89–92). Dysregulation of MAPK regulated Raf-MEK-ERK signaling contributes to several human disorders, including cancers. One of the Raf-inhibitor, RAF265, is currently being investigated in phase I clinical trials as a treatment option for local and advanced cancers. RAF265 was reported to inhibit all three isoforms of Raf kinase (27,44,93–95).

6: Structural features of kinase inhibitors

The human kinases are remarkably diverse in their primary amino acid sequence. Yet, a high level of identity in their 3D configuration was observed mainly in the kinase domain consisting of the ATP-binding pocket, which is made up of N-terminal β-sheet (N-lobe), connecting hinge site, and a C-terminal α-helix (C-lobe) (96). The ATP's binding governs the enzymatic activity in the aperture formed between N-terminal and C-terminal lobes. The interactions and binding of most kinase inhibitors to the ATP binding region between N-terminal and C-terminal lobes perturbed the functionality of the kinase molecule. A conserved activation loop composed of the amino acid sequence Asp-Phe-Gly (DFG) regulates the approach to the enzymatic catalytic site (97). Kinase inhibitors were classified into two main groups based on their binding mechanism as: (1) irreversible inhibitors and (2) reversible inhibitors. The irreversible kinase inhibitors block the ATP region by covalently binding with a reactive nucleophilic cysteine residue adjacent to the ATP-binding region resulting in an irreversible inhibition. However, the reversible inhibitors were further categorized into four major types depending on the DFG motif and the binding pocket configuration (98,99). The ATP-competitive inhibitors, or type I inhibitors, bind to the active forms of kinase, and the DFG motif aspartate residue face toward the active region of the kinase enzyme. The type II inhibitors target an inactive form of kinase and forms an aspartate DFG-outward conformation. Several type II inhibitors access and bind to specific regions close to the ATP-binding site accounting for the flexibility of the DFG motif (100). The type III inhibitors bind to specific allosteric pockets proximal to the ATP-binding pocket (101). The type IV inhibitors bind to the allosteric region outside the catalytic region (Fig. 3). Some kinase inhibitors exhibit more than one binding mechanism, such as bi-substrate and bivalent inhibitors classified as type V inhibitors (102).

Fig. 3

Fig. 3 Four types of reversible inhibitors (red) and their kinase (gray) binding mechanism are shown here. Type I inhibitors bind to the active form of the kinase, with the DFG loop motif facing inward. Type II inhibitors bind the inactive kinase form with the DFG loop pointing outside. Type III inhibitors bind to an allosteric pocket close to ATP binding pocket. Type IV inhibitors bind to an allosteric pocket located outside the ATP-binding pocket.

In multiple biological processes, small-molecule kinase inhibitors facilitated the analysis and investigation of kinase functions (103). Previously, the predominant conception about the conservation of kinase domain for the development of selective inhibitors was changed when the first instance of selective kinase inhibitors against the epidermal growth factor receptor (EGFR) was identified (74,104). Subsequently, several selective kinase inhibitors with a variety of inhibition profiles and structural features were reported (98,105,106), particularly the kinase-inhibitor complex investigated by high-resolution X-ray crystal structures (107–109).

7: History of kinase inhibitor

The discovery of kinase inhibitors dates back to the 1960s when the role of PKA in the signaling cascade was unraveled (110–112). In 1973, the first human oncogene was identified that expresses a fusion protein tyrosine kinase in chronic myelogenous leukemia (CML) (113). Furthermore, in 1980, following identifying the kinase signaling pathway in human cancer, polyphenols were reported as the first kinase inhibitors. In particular, bioflavonoid and quercetin were among the initially identified small-molecule kinase inhibitors. Previously, several other compounds such as phosphatidylinositol-4,5-bisphosphate 3-kinase, isoquinoline sulfonamides, alkaloid staurosporine were also identified as kinase inhibitors but reported with either low inhibitory potency or with target nonselectivity (114–118).

Over 20 years ago, Knighton and the group reported the PKA catalytic domain's crystal structure for the first time (96). Thus, the study laid the first stone for the development of structure-dependent kinase inhibitors. In 2001, the first FDA-approved and globally perceived kinase inhibitor was imatinib which inhibits the oncoprotein bcr-abl protein kinase and is used to treat CML (8). Subsequently, the FDA approved more than 25 protein kinase inhibitors since the first kinase inhibitor approval (103,119). In particular, MAPK/ERK inhibitors, CI-1040 in 2003 (120); dual tyrosine and serine/threonine kinase inhibitor sorafenib in 2005; bcr-abl inhibitor, GNF-2 and analogs in 2006 (121); trametinib in 2013; covalent kinase inhibitors, afatinib, and ibrutinib, in 2013; and PI3K inhibitor idelalisib in 2014 (122); are some of the recent key discoveries (Fig. 4).

Fig. 4

Fig. 4 Some of the important and FDA-approved small molecule kinase inhibitors.

8: Current scenario in kinase inhibitor development

Over the past 20 years, despite the emergence of various kinase inhibitors in oncology and other human diseases and facilitated by several important technical applications, kinase clinical and medicinal chemistry challenges remain. The emergence of drug resistance of tumor cells is a severe challenge that decreases the therapeutic response time and effectivity for many of the anticancer kinase inhibitors (123). The development of mutant-specific inhibitors suspending the resistance can be effective in long-term remission, but further resistance appears inexorably (124). In particular, EGFR C797S mutation reduces the effectivity of recently approved osimertinib, which was reported as an EGFR T790M inhibitor (125).

Additional processes conferring resistance include kinase upregulation. Like in the case of bcr-abl, it facilitates the imatinib resistance to CML. In another case of EGFR and mast/stem cell growth factor receptor (SCFR) upregulation, it acquired an anaplastic lymphoma kinase (ALK) translocation that confers crizotinib resistance in lung cancers (126–128). These resistance mechanisms are difficult to curb, demanding novel therapeutic options that are less frequent to resistance. Other than resistance, target selectivity remains a major hurdle in developing kinase inhibitor drugs (129).

Many of the identified SMKIs target multiple kinases by binding to the conserved ATP pocket of kinases. Kinase inhibitor selectivity analysis among reported kinase inhibitors was performed to measure the degree of target selectivity (130–132). Kinases with less closely related homologs or unique structural features could be a preferred target with high selectivity. Recent studies have shown the different strategies to develop inhibitors with improved selectivities, such as combining allosteric inhibition and covalent targeting to develop protein kinase B inhibitors (133).

Further, molecular structure-based drug design coupled with new crystallographic data and other biophysical techniques are subsequently improving the selectivity of kinase inhibitors (134). There have been some critical disease-associated protein kinases for which it was found impossible to develop an effective inhibitor accounting for an inability to achieve a successful treatment. Protein kinases function in the cell cycle pathway, such as aurora kinases, some cyclin-dependent kinases, and PLKs, are well-studied examples (135).

An ongoing and advanced medicinal chemistry approach is required to develop target selective inhibitors with improved suitability, for instance, in developing CDK4/CDK6 inhibitors (136). An alternative novel application presently undergoing clinical trial encapsulates aurora B kinase inhibitor within nanoparticles to upgrade its therapeutic index through selective delivery to the tumor (137). It would be interesting to observe further if the clinical benefit of approved kinase inhibitors also enhances with this approach.

9: Success stories

The last two decades witnessed exceptional success in the therapeutic interventions of clinically significant kinase inhibitors. The milestone was achieved with the approval of the first kinase inhibitor imatinib by the FDA that granted a revolutionary success in clinical and medicinal chemistry. A study on imatinib has provided an understanding and rationale to design and develop next-generation kinase inhibitors. Subsequently, the FDA approved many kinase inhibitors to treat various types of cancer and human diseases. Moreover, due to extensive research, our understanding of the molecular mechanism of kinase signaling pathways accompanied with disease pathology has improved. In 1999, Collin et al. (138) have designed a specialized database, KID (Kinase Inhibitor Database), which was dedicated to collecting all information related to protein kinase inhibitors. The KID comprises the inhibitors’ structural and bibliographic details gathered and deposited by researchers worldwide. A more advanced version of the kinase inhibitor database, KIDFamMap (http://gemdock.life.nctu.edu.tw/KIDFamMap/), was recently reported, which analyses the inhibitor families and inhibitor disease correlations for the selectivity and functions of the kinase inhibitors. KIDFamMap constitutes 1208 inhibitor families, 962 inhibitor disease, 55,603 kinase inhibitor interactions, 35,788 kinase inhibitors, 399 human protein kinases, 339 diseases, and 638 disease allelic variants (139). To give insights into the structural determinants of kinase-ligand selectivity and interaction, the KLIFS database (http://klifs.vu-compmedchem.nl) was designed and published in 2016. The database consists of kinase-ligand binding details gathered from more than 2900 catalytic domain structures of human and mouse kinases (140).

Some of the representative kinase inhibitors approved over the years and important in clinical and medicinal are discussed here. The first kinase inhibitor approved against bcr-abl was imatinib used successfully for CML treatment (141,142). Following imatinib, four more bcr-abl inhibitors were approved so far for the treatment of CML, and those are dasatinib, nilotinib, bosutinib, and ponatinib (143–145). The first JAK inhibitor approved was ruxolitinib which was used as a treatment option for myeloproliferative myelofibrosis disorder by inhibiting JAK1 and JAK2 kinases. Another JAK inhibitor approved, tofacitinib, was reported as a JAK3 inhibitor for rheumatoid arthritis treatment (77,146). The ERBB system is a family of RTKs comprising four receptors: ErbB1, ErbB2, ErbB3, and ErbB4, all activated by EGF ligands followed by a receptor dimer formation (75). The signaling through the ErbB cascade is one of the widely studied signaling networks and deregulation of this pathway is associated with human malignancies (147,148). The ErbB inhibitors belong to one of the largest classes of approved small-molecule kinase inhibitors. The five approved ErbB inhibitors are gefitinib, erlotinib, lapatinib, vandetanib, and afatinib (149–151).

Chromosomal rearrangements in anaplastic lymphoma kinase (ALK), an RTK, was reported in various human cancer (151,152). The first inhibitor approved against ALK was crizotinib to treat nonsmall cell lung carcinoma (NSCLC), nerve tissue cancer, and late-phase lung carcinoma (153). Afterward, a second-generation ALK inhibitor ceritinib was developed to overcome increasing crizotinib resistance due to L1196M, G1269A, I1171T, and S120Y mutations accounting for ALK gene rearrangements (154,155). Bruton's tyrosine kinase (BTK), a crucial component of the B-cell receptor signaling cascade, functions in the growth and survival of chronic lymphocytic leukemia (CLL) cells (156). In 2013, a BTK inhibitor, Ibrutinib, was approved as a treatment option for mantle cell lymphoma and then, in 2014, for CLL (157). In 2011, the first B-Raf inhibitor, vemurafenib, was approved to treat metastatic melanoma and thyroid tumors. The mutation Val600 with Glu600 in the activation loop of the B-Raf kinase domain increases cell survival and proliferation. Subsequently, after 2 years, dabrafenib was also approved as a B-Raf inhibitor in 2013 (95,158). The Cyclin-dependent kinases (CDKs) have been studied as critical therapeutic targets for multiple types of cancer and other proliferative disorders (159,160). In 2015, the first CDK inhibitor, palbociclib, which selectively inhibits CDK4 and CDK6, was approved to treat hormone-receptor-positive breast cancer. Other CDK4 and CDK6 inhibitors approved are abemaciclib and ribociclib (161). Idelalisib is the first lipid kinase PI3Kd inhibitor approved for combination therapy with monoclonal antibody rituximab for CLL treatment (162,163). Recently, last year in 2020, FDA approved nine small molecule kinase inhibitors and in the current year 2021, at the time of writing this chapter, two inhibitors have been approved for clinical use (Table 2).

Table 2

10: Conclusion and future prospect

The development of kinase inhibitors as a treatment option for diseases is among the most important and successful stories in drug discovery. Over the past 30 years, protein kinases have been analyzed widely as drug targets in various types of cancer. The intensive research studies on kinase inhibitors have revolutionized and expanded the number of therapeutic opportunities in oncology (164). Concurrently, the therapeutic interventions using kinase inhibitors as treatment options extend in inflammatory and autoimmune diseases (165–167). The role of kinases in other human diseases could not be neglected. However, understanding the molecular mechanism underlying infectious diseases and degenerative disorders is required to identify and validate the kinase targets. The future growth in these fields is anticipated based on the role of kinases in the disease mechanisms.

Furthermore, the future development of small-molecule kinase inhibitors depends on several criteria. Presently, the kinase inhibitors target only a small part of the human kinome and many of the kinases are not studies well. Therefore, novel techniques are needed to characterize the functionality of these abandoned kinases (168,169), which may increase the number of crucial targets for inhibitor development. Furthermore, lipid kinase inhibitor combined with other treatment agents was reported in successful cancer treatment, though only one lipid kinase inhibitor has been approved to date. Considering the crucial functions of lipid kinases in cellular processes, it could be a promising target for cancers and inflammation disease.

In conclusion, the identification and development of new kinase inhibitors are expanding swiftly. The excessive interventions in target confirmation preclinically, with novel computational, experimental technologies and medicinal chemistry, envisions this field to pursue through this expeditious growth trajectory.

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Chapter 2: Protein kinase inhibitors and cancer targeted therapy

Azadeh Hekmata; Ali Akbar Sabouryb    a Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran

b Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran

Abstract

Protein kinases, a large superfamily of ATP-dependent phosphotransferases, catalyze the reversible hydroxyl-phosphorylation of Tyr, Ser, or Thr residues of protein substrates, which signifies a major posttranslational signaling mechanism and a regulatory pathway that controls many cellular processes. Numerous kinases are discovered to be dysregulated in different types of cancers. The development of therapeutic inhibitors of protein kinases has discovered the most success in antitumor therapy. Till now, a large number of protein kinase inhibitors have been introduced by researchers. This chapter aims to provide insights into the molecular mechanism of protein kinases inhibition by chemical, herbal, and nanomaterial-based anticancer compounds.

Keywords

Chemical anticancer agents; Herbal anticancer agents; Enzyme inhibition; Enzyme kinetics; Nanomaterial-based anticancer agents

Abbreviations

AATK 

apoptosis-associated tyrosine kinase

ADR 

acquired drug resistance

ATP 

adenosine triphosphate

Au NPs gold nanoparticles

Au NRs gold nanorods

AURKA 

aurora kinase A

BSA 

bovine serum albumin

CAMK 

calcium/calmodulin-dependent protein kinase

CDKS 

cycle-dependent kinases

CHK2 

checkpoint kinase 2

CK1 

casein kinase 1

EGFR 

epidermal growth factor receptor

EML4-ALK 

echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase

ERK 

extracellular signal-regulated kinase

FLT3 

FMS-like receptor tyrosine kinase 3

GSK 

glycogen synthase kinases

HH 

Hedgehog signaling

HSA 

human serum albumin

JAK 

Janus kinase

JNK 

c-Jun N-terminal kinases

MAPK 

mitogen-activated protein kinase

MAPK/ERK 

mitogen-activated protein kinases/extracellular signal-regulated kinase

mTOR 

mechanistic target of rapamycin

NPs 

nanoparticles

NRY 

nonreceptor protein tyrosine kinases

NSCLC 

nonsmall-cell lung cancer

PAP 

phenylamino-pyrimidine

PEG 

polyethylene glycol

PEG-PLA 

polyethylene glycol-block-poly(d, l-lactic acid)

PI3K 

phosphatidylinositol-3 kinase

PKA 

protein kinase A

PKB 

protein kinase B

PKD1 

protein kinase D

RALs 

resorcylic acid lactones

RB 

retinoblastoma protein

RTKs 

receptor tyrosine kinases

RY 

receptor protein-tyrosine kinases

STAT 

signal transducers and activators of transcription

TGCT 

tensynovial giant cell tumor

TGF-β 

transforming growth factor-beta

TK 

tyrosine kinase

TKL 

tyrosine kinase-like

1: Introduction

Cancer is a source of mortality worldwide. Over the past 40 years, an enormous amount of data has been collected about the biology of cancer and the carcinogenic process. Cancer is not exactly one disease, but a common name above 200 diseases reveal common features. Malignant cells are described by their uncontrollable growth and spread of the malignant cells to organs and tissues beyond where the malignant tumor originated (metastasis) (1). In 2000, Hanahan and Weinberg distributed their concept of the hallmark of cancer (2). These hallmarks can offer a rational framework for identifying the remarkable diversity of neoplastic diseases. They suggested six hallmarks of cancer: persistent proliferative signaling, avoiding growth suppressors, initiating metastasis and invasion, facilitating replicative immortality, provoking angiogenesis, as well as resisting cell fatality. In 2011, they added two critical features for cells to obtain these features: tumor-promoting inflammation and genomic instability (3). Furthermore, they added two other features for identifying neoplastic diseases: preventing immune destruction and deregulating cellular energetics. In 2013, Vogelstein et al. proposed another model for detecting cancer cells and describing pathways and mechanisms relevant to several malignant cells (4). Consequently, tumor cells can be identified as highly specialized cells that can proliferate independently of extracellular mitotic signals, metastasize to distant sites, and induce angiogenesis. Regularly, these distinctive features of cancer cells are mediated through signaling pathways that have become deregulated. Twelve signaling pathways that perform an important function in cancer growth have been identified, including DNA damage control, transforming growth factor-beta (TGF-β), a mitogen-activated protein kinase (MAPK), APC, signal transducers and activators of transcription (STAT), phosphatidylinositol-3 kinase (PI3K), RAS, cell cycle apoptosis, Notch, Hedgehog signaling (HH), chromatin modification, and transcriptional regulation (Fig. 1). These 12 pathways are categorized into 3 cellular procedures underlying tumor growth: cell fate, genome maintenance, and cell survival. There are significant alterations in the signaling pathways across diverse cancer types. Even patients with similar cancer can have mutations on different signaling pathways, leading to heterogeneity in patients.

Fig. 1

Fig. 1 Twelve signaling pathways of cancer cells and the cellular processes that they regulate.

Consequently, these pathways could be promising targets for antitumor therapies. Although, it should be noted that both negative and positive regulatory factors are present in cells, therefore it is difficult to design oncogenic pathways inhibitors while leaving normal physiological pathways intact. Among these pathways, the connection between kinase pathways and cancer has attracted the attention of many scientists. Mutations in numerous genes encoding protein kinases and proteins involved in phosphorylation signaling pathways have been proved to be linked to cancer. Additionally, the most well-known oncogenes (a group of genes that generate cancer in humans or other animals when they are mutated) are the proteins, which belong to growth factor, transcription factor, GTPase, or protein kinase families. Hence, this chapter focuses on the protein kinase superfamily and their critical roles in cancer initiation and progression.

Protein kinases are a large family of enzymes; the second-largest enzyme family as well as the