key: cord-0022478-vl7a3g4o authors: Huang, Bo; Bai, Zhaoshi; Ye, Xinyue; Zhou, Chenyu; Xie, Xiaolin; Zhong, Yuejiao; Lin, Kejiang; Ma, Lingman title: Structural analysis and binding sites of inhibitors targeting the CD47/SIRPα interaction in anticancer therapy date: 2021-10-01 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2021.09.036 sha: 43fb519e9270448cbd7f53d845dd81699cc3ae9b doc_id: 22478 cord_uid: vl7a3g4o Cluster of differentiation 47 (CD47)/signal regulatory protein alpha (SIRPα) is a negative innate immune checkpoint signaling pathway that restrains immunosurveillance and immune clearance, and thus has aroused wide interest in cancer immunotherapy. Blockade of the CD47/SIRPα signaling pathway shows remarkable antitumor effects in clinical trials. Currently, all inhibitors targeting CD47/SIRPα in clinical trials are biomacromolecules. The poor permeability and undesirable oral bioavailability of biomacromolecules have caused researchers to develop small-molecule CD47/SIRPα pathway inhibitors. This review will summarize the recent advances in CD47/SIRPα interactions, including crystal structures, peptides and small molecule inhibitors. In particular, we have employed computer-aided drug discovery (CADD) approaches to analyze all the published crystal structures and docking results of small molecule inhibitors of CD47/SIRPα, providing insight into the key interaction information to facilitate future development of small molecule CD47/SIRPα inhibitors. Currently, the high morbidity and mortality of tumors remain a major challenge to the effectiveness of cancer treatment even though a series of anticancer drugs have been developed based on different treatment strategies [1] . Cancer immunotherapy, which aims to improve antitumor immune responses with fewer off-target effects than chemotherapies and other agents that directly kill cancer cells, provides an alternative strategy to treat cancer through the immune system rather than the tumor itself [2] and is an exciting area in current cancer research [3, 4] . This novel therapy, including immune checkpoint blockade, adoptive cellular therapy and cancer vaccinology [5] , has led to a growing number of immunotherapy drug approvals, with numerous treatments in clinical and preclinical development [3] . Herein, the immune checkpoint plays a central role in tissue homeostasis self-reactivity and autoimmunity, which targets the innate and adaptive immune systems [6] , and is the signal recognition factor for immunosurveillance in immune cells [7] . However, some tumor cells evade immune clearance by modulating signal recognition between immune cells and tumor cells; thus, immune checkpoint blockade is the main promising system in immunotherapy [8, 9] . To date, the blockade of two well-known adaptive immune system checkpoints, cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) and programmed cell death protein 1 (PD1), has led to the generation of several immune checkpoint inhibitors that have been used for treating multiple cancers [10] [11] [12] [13] ; however, an unsatisfactory overall response rate, tumor heterogeneity, drug resistance and rapid progression after therapy in patients are some of the challenges of inhibiting adaptive immune checkpoints [14] [15] [16] [17] . Interestingly, in addition to adaptive immunity, innate immune processes may also provide a good direction for cancer immunotherapy. Recently, CD47, which is one of the most attractive innate immune checkpoint regulators because of its inhibitory effect on the activation of macrophages and other myeloid cells against tumor, brings new hope to cancer patients. It belongs to the immunoglobulin (Ig) superfamily and is ubiquitouslyexpressed on all normal cells but overexpressed on hematological and solid malignancy cancer cell membranes [18] [19] [20] [21] . As a highly glycosylated transmembrane protein, CD47 consists of an extracellular amino terminal IgV-like domain, five membrane-spanning segments that are highly hydrophobic and a hydrophilic cytoplasmic C-terminus that is 3-6 amino acids long [22] , and it interacts with the NH 2 -terminal V-set domain of its ligand, SIRPa [23] . SIRPa is also known as CD172a or SHPS-1 and is highly expressed on the membrane of myeloid cells, such as monocytes, macrophages, neutrophils, and dendritic cells (DCs) [10, 24, 25] . CD47 interacts with SIRPa, tagging it with a ''self" or ''do not eat" signal, to trigger an inhibitory signaling cascade through the ITIM and ITSM motifs of SIRPa, inhibiting macrophage phagocytosis ( Fig. 1 ) [26] [27] [28] . Unfortunately, when overexpressed CD47 on the surface of solid malignancies binds to SIRPa on macrophages, this can suppress the phagocytic responses of macrophages [29] . Therefore, as a dominant macrophage checkpoint, disruption of the CD47/SIRPa pathway can induce macrophage-mediated phagocytosis of tumor cells and thus is employed when generating next-generation immunoregulatory drugs [30] [31] [32] . Currently, the gradual increase in patents with treatments targeting the CD47/SIRPa pathway clearly demonstrates the great effort being made to discover new inhibitors of this target. Consequently, some CD47/SIRPa pathway-targeting antibodies against various cancers (Table. 1), including acute myeloid leukemia (AML) [33, 34] , anaplastic thyroid carcinoma (ATC) [35] , lymphoma [36] [37] [38] , lung cancer [39, 40] and breast cancer [41] , have showed attractive results. For example, magrolimab (Hu5F9-G4) is an anti-CD47 monoclonal antibody that is currently undergoing phase III clinical trials, with an objective response rate of 75% in phase Ib clinical results during the treatment of myelodysplastic syndromes. ALX-148 is also a CD47 targeting antibody in phase II clinical trials whose objective responses could be observed in phase I clinical results for the treatment of patients with head and neck squamous cell carcinoma. It is undeniable that some adverse effects occur when using these antibodies therapeutically, such as the rapid target-mediated clearance, transient anemia, erythrocyte toxicity and infusion-related reactions [42] , which limit their rapid development. In addition, there are certain limitations of using these antibodies, including a long half-life, poor permeability and lacking oral availability. Thus, the development of low molecular-weight inhibitors with superb pharmacokinetics and druggability is an effective strategy and research focus to overcome the limitations of therapeutic antibodies [43] . Because the development of small molecule inhibitors of the CD47/SIRPa interaction has been slower than the development of antibody treatments, research on the CD47/SIRPa pathway is crucial. Currently, high-throughput screening and computer-aided drug design (CADD) are common approaches in the discovery of small molecule inhibitors [44] [45] [46] [47] [48] . CADD is a molecular design method based on computational chemistry [49, 50] and can help to produce valuable information on target proteins, lead compounds and protein-ligand interactions for rational drug design. Thus, CADD is used both to analyze hot spots of target proteins and protein-ligand interactions model for further drug discovery. In this review, we have employed the ''View Interactions" tool in CADD to analyze the hot spots of CD47 and SIRPa based on their cocrystal structures. Subsequently, ''LibDock" in CADD was further applied to predict the key interacting amino acids of CD47 and SIRPa from a small molecule inhibitor docking experiment. In addition, some of the peptides and small molecule inhibitors that have been reported to block the CD47/SIRPa interaction in fundamental research studies have been summarized, and their structure-activity relationships have been analyzed and compared to guide the discovery and design of new inhibitors blocking the CD47/SIRPa interaction with superb pharmacokinetics and druggability. The first high-resolution crystallographic structure of the CD47/ SIRPa d1 complex (the ligand-binding domain) was published by [54] , and CD47/C47B161 complex (PDB ID: 5TZT) [54] . Magrolimab, also known as Hu5F9-G4, is an IgG4 antibody and can form a Hu5F9-G4 diabody/CD47-ECD complex with the CD47 extracellular domain (CD47-ECD). Hu5F9-G4 employs VH and VL to cover the CD47-ECD surface area with 365 Å 2 and 310 Å 2 , respectively. Superposition of the CD47/magrolimab complex and CD47/SIRPa complex reveals that their surface interaction involves similar epitopes on CD47, including the BC and FG loops. Specifically, the CDR loops of magrolimab form 11 hydrogen bonds with the CD47-ECD surface (Fig. 3 , produced by Discovery Studio2019). Moreover, the crystal structures of the CD47-B6H12.2, CD47-C47B222, and CD47-C47B161 complexes demonstrate that the interaction interface of all three antibodies overlaps with the SIRPa binding epitope regions on the FG loop of CD47. Thus, these complex structures demonstrate that the FG loop of CD47 is a key component of the interaction, indicating that the FG loop may become a potential target for further structure-based drug design. Magrolimab mainly binds to N-terminal pyroglutamate of CD47 which is critical for CD47/SIRPa interaction and magrolimab binds to the BC and FG loops, which are highly overlapping epitopes with SIRPa [55, 56] . Analogously, the common binding area of B6H12.2, C47B161 and C47B222 is the CC 0 and FG loops on CD47. According to these findings, the N-terminal pyroglutamate and the BC, CC 0 and FG loops can be viewed as potential binding areas for subsequent structure-based drug design, and Tyr 37 , Asp 46 , Glu 97 , Glu 100 and Glu 106 may be developed into binding sites for inhibitors targeting CD47. Additionally, the loops of SIRPa undergo structural changes in the interaction with CD47, which indicates that C 0 D, DE, and FG loops may be possible targets. Among these loops, Glu 54 , Gly 55 , Ser 66 and Ser 98 undergo considerable movement, implying that these residues play crucial roles in the interaction and may act as binding sites for designing future SIRPa inhibitors. The development of non-antibodies with succinct synthesis and lower modification cost has led to the discovery of RS-17, Pep-20, Table 3 Sequences of bioactive peptides inhibitors blocking the CD47/SIRPa interaction. Code Name (Generic Name) Target Organization Sequence D4-2, and SP5. All four peptides, whose sequences are listed in [58, 59] . In addition, a human CD47/SIRPa blocking assay also revealed that pep-20 exhibited an IC 50 of 24.56 mM with the anti-CD47 antibody (B6H12), which served as a positive control. Pep-20 remarkably enhances the phagocytosis of MCF7 (human breast tumor cell lines), HT29 (human colon tumor cell lines) and Jurkat (human leukemia cell lines) and exhibits an enhancement of phagocytosis similar to that of the positive control (B6H12). Excitingly, the injection of pep-20 at a dose of 2 mg/kg daily in mice had no obvious influence on the reduction in the number of red blood cells, which is a common toxicity effect of CD47/SIRPa blockade [57] . Furthermore, after replacing three terminal residues of pep-20 with D-amino acids, the obtained peptide pep-20-D12 significantly improved stability without a functional decrease compared with pep-20, accompanied by an intravenous elimination T1/2 that increased by tenfold compared with pep-20. Pep-20-D12 remarkably slows tumor progression, and the combination treatment of pep-20-D12 and IR shows tumor growth regression in colon tumor (MC38 cells)-bearing mice [57] . A subsequent docking model and alanine substitution experiment of pep-20/CD47 revealed that Phe 4 , Glu 104 and Glu 106 of CD47 are key positions for inhibitors targeting CD47. These findings provide valuable information of CD47 binding sites and the key structure of pep-20 for small-molecule inhibitor design. Additionally, Xu et al. from China Pharmaceutical University discovered RS-17 in 2020 [60] . The K d value of RS-17 binding to the CD47 protein was 3.85 ± 0.79 nM. At a concentration of 20 lg/ml, RS-17 effectively binds to CD47 of SCC-13 (human epidermal squamous tumor cells) and HepG2 (human liver tumor cells) with corresponding binding rates of 55.5% and 71.2%, respectively; thus, the phagocytic efficiency of macrophages against HepG2 cells was greatly improved, showing a half phagocytic index of B6H12. Moreover, an in vivo assay demonstrated that the weight loss and tumor volume increase in liver tumorbearing mice were similar between RS-17 and B6H12 and that RS-17 effectively inhibited tumor growth in liver tumor-bearing mice. Hazama et al. utilized random nonstandard peptides integrated discovery (RaPID) system, which combines flexizyme-assisted genetic code reprogramming and mRNA display to obtain macrocyclic peptides of interest, to design and gain anti-SIRPa peptides L4-4, D4-1, D4-2 and D4-4 [61, 62] . Among these peptides, D4-2 shows comprehensive high binding affinity to SIRPa of C57BL/6 and NOD mouse strains with corresponding K d values of 10 nM and 8.22 nM, respectively. D4-2 evidently blocked the mCD47-Fc/NOD SIRPa interaction in a dose-dependent manner in HEK293A (human embryonic kidney cells) cells with an IC 50 value of 0.180 mM. The crystal structure of the D4-2/NOD SIRPa complex shows that the interaction area of D4-2/NOD SIRPa occupies 976.5 Å 2 . Arg 2 , Ser 4 , Ala 5 , Val 6 , IIe 9 , His 10 , Pro 11 , Ser 12 , Trp 13 and Gly 15 of D4-2 form hydrogen bonds with IgV-NOD SIRPa, and Arg 2 of D4-2 forms a salt bridge with Asp 84 of IgV-NOD SIRPa. Ala 5 and Pro 11 of D4-2 form hydrophobic interactions with Phe 51 and Phe 56 of IgV-NOD SIRPa. All these residues stabilize the cyclic structure of D4-2 and mediate the binding of D4-2 to IgV-NOD SIRPa. Further crystal structure comparison shows that the binding of D4-2 to Phe 56 and Ala 65 in the C'E loop of IgV-NOD SIRPa, which are key residues controlling the interaction with CD47, changes the conformation and induces the inhibition of the CD47/IgV-NOD SIRPa interaction [63] . In addition to D4-2, a series of macrocyclic peptides binding to SIRPa, including SP1 to SP6, were also developed in 2020 by Xu et al from Zhengzhou University [64] . Among these, SP4 and SP5 display higher affinity to SIRPa with K d values of 0.85 lM and 0.38 lM and block the SIRPɑ/CD47 interaction in a dosedependent manner in CHO-K1-hSirpɑ cells. SP5 (200 lM) not only effectively promotes the phagocytosis of HT29 (human colon tumor cells) by macrophages but also exhibits desirable in vivo efficacy by inhibiting tumor growth in colon tumor MC38 mouse model and melanoma B16-OVA mouse model. Analysis of the previously described peptides can lead to conclusions that these peptides share similar interaction areas that overlap with the epitopes in the CD47/SIRPa interaction area. For example, Pep-20 occupies Phe 4 , Glu 104 and Glu 106 of CD47 to block the D47-SIRPa interaction, and D4-2 binds to Phe 56 and Ala 65 of SIRPa to block the D47-SIRPa interaction. Moreover, these peptides mainly form hydrogen bonds with their receptor. Collectively, residues Phe 4 , Glu 104 and Glu 106 of CD47 and residues Phe 56 and Ala 65 of SIRPa may be developed into binding sites for structurebased CD47/SIRPa small molecule inhibitor design. Miller et al. utilized quantitative high-throughput screening (qHTS) assays to screen NCATS chemical libraries based on timeresolved Fö rster resonance energy transfer (TR-FRET) and beadbased luminescent oxygen channeling assay formats (AlphaScreen), resulting in the discovery of the parent compound NCGC00138783 [65, 66] whose scaffold is 2-((2-(2-(3,5-dimethyl-1H-pyrazol-4-yl) ethyl)-5,6-dihydro-[1,2,4] triazolo [1,5-c] quinazolin-5-yl) thio) butanal. This compound selectively blocks the CD47/SIRPa interaction without disrupting its binding to other receptors [67] [68] [69] . A novel laser scanning cytometry assay (LSC) was established to measure the cell surface binding of these compounds, and the results showed that NCG00138783 has an IC 50 value of 40 lM. Further medicinal chemistry work attempting to optimize the potency and drug-like properties of NCGC00138783 led to the discovery of its derivatives (Fig. 4 , produced by Chem-Draw). The acyl group of NCGC00138783 is linked with a monocyclic substituted amino group and hydroxyl group to obtain a range of compounds displaying great inhibitory activity toward the CD47/SIRPa interaction. Among these small molecule compounds, NCGC00138783, NCG00538430 and NCG00538419 showed antagonistic activity in both the ALPHA screening assay and LSC assay. To facilitate the understanding of NCGC00138783 binding to CD47/SIRPa, we conducted docking experiments of NCGC00138783 docking to CD47 and SIRPa and employed the CD47/SIRPa complex (PDB ID: 2JJT) as a receptor. Consequently, we found that NCGC00138783 is more prone to bind to SIRPa than CD47 with the corresponding highest LibDock Score of 134 and 85. Furthermore, the 3,5-dimethyl-1H-pyrazolyl group, central [1, 2, 4] triazolo [1,5-c] quinazoline group and amide group of NCGC00138783 are predicted to form hydrogen bonds and T-stacking interactions with SIRPa, including Leu 30 , Gly 34 , Pro 35 , Gln 52 , Lys 53 and Lys 93 , which are key residues in the CD47/SIRPa interaction. The central [1, 2, 4] triazolo [1,5-c] quinazoline scaffold is predicted to form pi-pi stacking with Phe 74 and hydrogen bonding with Gly 34 , which makes it insert into the hydrophobic cavity. The amide group of 3,5-dimethyl-1H-pyrazolyl is predicted to form hydrogen bonding with Gln 52 , which lies in the high polarity area (Fig. 5 , produced by Discovery Studio2019). Above all, NCGC00138783 binds to SIRPa and occupies the key binding positions of the CD47/SIRPa interaction which is essential information for future small molecule inhibitor design and helpful for the discovery of novel inhibitors blocking the CD47/SIRPa interaction. In a patent application, inventors from Aurigene Discovery Technologies Limited reported a series of small molecules blocking the CD47/SIRPa interaction [70] . The scaffold of these compounds is oxadiazole which can enhance macrophage-mediated phagocytosis of human lymphoma and myeloma cells, with corresponding normalized phagocytosis rates in the range of 20%-66% and 17%-77% at 10 lM. Among these small molecules, compounds 1 to 14 display comprehensive effects on both luciferase-based and FACS-based phagocytosis assays, and compound 6 has normalized phagocytosis rates of 66% and 74%, respectively (Fig. 6 , produced by ChemDraw). Moreover, compound 6 inhibited tumor growth in a dose-dependent manner with inhibition rates of 53%, 64% and 67% at doses of 3, 10 and 30 mg/kg, respectively, in an A20 mouse model without body weight loss. Further docking analyses of compound 6 to CD47 (PDB ID: 2JJT) by us revealed that the core 1,2,4-oxadiazol and butyramide groups insert into a hydrophobic pocket containing Trp 40 , Thr 107 and Lys 6 of CD47, which is the key residue in the CD47/SIRPa interaction. The carbonyl group of butyramide is predicted to form hydrogen bonds with Thr 7 and Thr 107 , which is near the core CD47/SIRPa interaction area. Two carbonyl groups of carbamoyl proline are predicted to interact with Asn 5 , which is close to Lys 6 of CD47 (Fig. 7 , produced by Discovery Studio2019). Overall, promising compound 6 could inspire the design of follow-up lead compound scaffolds, and the binding model of compound 6 to CD47 may provide information for further discovery of small molecules blocking the CD47/SIRPa interaction. Analysis of our above docking results and the published phagocytosis assays revealed the common structural characteristics of anti-CD47 compounds: (i) hydrogen bond interactions are crucial for anti-CD47 compound activity; (ii) the 2-position side chain of oxadiazol inserted into the pocket consisting of Asn 5 , Thr 7 , Pro 22 , Phe 24 and Thr 107 has a crucial effect on phagocytic activity; (iii) the terminal group of the oxadiazol 2-position side chain, including the amino group, carboxyl group, amide group and guanidine group, which can form hydrogen bonds with Thr 7 and Thr 107 in the pocket, exhibits higher phagocytic activity; and (iv) the oxadiazol 5-position side chain contains a terminal carboxyl group and ureido. Oxadiazol, ureido and carboxyl groups are separated by one carbon atom, which makes two carbonyl groups in suitable positions to form hydrogen bonds with Asn 5 ; (v) the substituted short carbon chain and substituted ring alpha carbon of the terminal carboxyl group in the oxadiazol 5-position side chain can achieve better activity; (vi) central oxadiazole is needed for pilone pair conjugation with Thr 7 . In addition, analysis of anti-SIRPa compounds also indicates several features: (i) hydrophobic interactions are essential for SIRPa binding; (ii) central quinazoline reaches a hydrophobic pocket containing Val 27 , Leu 30 , Ile 36 , Phe 74 and Lys 93 to form two T-stacking interactions with Phe 74 ; and (iii) amide groups forming hydrogen bonds with Gln 52 , benzene, and four-membered ring-or three-membered ring-substituted amide groups show favorable antagonistic activity. Recently, CD47/SIRPa inhibitors have aroused enormous interest among researchers and have been remarkably affective in cancer treatment. This field is progressing rapidly, and some mAbs targeting the CD47/SIRPa pathway have reached clinical phase II and phase III [71] . Notably, despite the excellent clinical perfor-mance shown by CD47/SIRPa antibodies, the limitations of antibody drugs including poor tumor permeability, undesirable oral bioavailability and poor stability, hinder their clinical application [72] [73] [74] [75] . Small-molecule inhibitors can eliminate the problems caused by antibody drugs and thus have attracted the attention of researchers and have become a promising research area. Currently, several crystal structures of CD47/SIRPa and the structures of antibodies together with receptors have been published which provides guidance for the rational design of small molecule inhibitors blocking the CD47/SIRPa interaction. Moreover, there are two published small molecule compound categories: small molecules containing 3,5-dimethyl-1H-pyrazolyl and [1, 2, 4] triazolo [1,5-c] quinazoline scaffolds and small molecules containing oxadiazole scaffolds. Unfortunately, no small molecules blocking the CD47/SIRPa interaction have reached clinical research yet. The shortage of target structure information limits the development of small molecule inhibitors. Excitingly, using CADD to analyze the CD47/SIRPa interaction will provide some crucial information for the design of small molecule inhibitors. First, CADD allows researchers to analyze the interaction between inhibitors and their receptors based on their crystal structures, which improves the understanding of the interaction process and helps to determine key information, including pocket atoms and hot spot residues. Next, CADD helps researchers to explore the interaction between inhibitors and receptors without crystal structure through docking. Here, based on the previous reports and our docking research, we conclude that Glu 104 and Glu 106 are hot spots on CD47, while Gln 52 , Lys 53 and Phe 56 are hot spots on SIRPa. There is a limited number of small molecule inhibitors targeting the CD47/SIRPa pathway, which indicates the early stage of this research, but the favorable clinical results are promising. The CADD technologies will accelerate the discovery of novel inhibitors. These peptides and small molecule inhibitors will be the foundation for the design of new compounds. As it relates to drug design, the interaction area of CD47/SIRPa is broad. Therefore, it is crucial to identify the best binding positions for small molecules, and drug design based on these structural data will lead to the successful development of CD47/SIRPa inhibitors. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. 5495 2. 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