An Anti-Cancer Drug Candidate OSI-027 and its Analog as Inhibitors of mTOR: Computational Insights Into the Inhibitory Mechanisms

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An Anti-Cancer Drug Candidate OSI-027 and its Analog as Inhibitors of mTOR: Computational Insights Into the Inhibitory Mechanisms

Mohd Rehan *

King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia

ABSTRACT

The mammalian target of rapamycin (mTOR) is a serine-threonine kinase, which regulates cellular metabolism and growth, and is a validated therapeutic target in various cancers. Recently, OSI-027, a selective ATP competitive inhibitor of mTOR, has been developed. The OSI-027 is an orally bioavailable compound whose anti-cancer activities were observed in various cancer cell lines and tumor xenograft models. The current study is thefirst attempt to explore the binding mode and the molecular-interactions of OSI-027 with mTOR using molecular docking and (un) binding simulation approaches. The study identified various interacting residues and their extent of involvement in binding was emphasized using different methods. The (un)binding simulation analyses provided snapshots of various phases in OSI-027 binding and identified residues important for binding but away from the catalytic site. Further, to explore a better binder for mTOR among OSI-027 analogs, the virtual screening led to propose an OSI-027 analog with CID: 73294902 as a better inhibitor than the OSI-027 and the native ligand PI-103. The binding mode of the proposed compound is compared with those of OSI-027 and other native inhibitors. The comparison of (un)binding simulation phases of proposed compound with that of OSI-027 revealed that both, bound to the same catalytic site, follow different (un)binding path. Thus, the current study presents computational insights into the OSI-027 mediated inhibition of mTOR kinase and proposed an OSI-027 analog as better mTOR inhibitor, and thus, a good drug for further research in experimental laboratories. J. Cell. Biochem. 9999: 1–10, 2017. ^©2017 Wiley Periodicals, Inc.

KEY WORDS:

OSI-027; mTOR; DOCKING; MOLECULAR INTERACTIONS; BINDING POSE

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ancer is one of the leading causes of morbidity and mortality in human population accounting worldwide for 14.1 million new cancer cases, 8.2 million cancer deaths, and 32.6 million people living with cancer within 5 years of diagnosis [Stewart and Wild, 2014]. Within the next two decades, it is expected that the number of new cancer cases will rise from 14.1 to 22 million annually and the cancer deaths will rise from 8.2 to 13 million per year [Stewart and Wild, 2014]. Keeping in view the continuous devastation the disease is causing, there is an urgent necessity for the discovery of novel anti-cancer drugs. The upcoming targeted therapies hold a lot of promise, whereby an inhibitor is designed against single or multiple cancer-signaling proteins [Khan et al., 2013; Baig et al., 2016]. An important signaling pathway called PI3K/Akt/mTOR pathway is believed to be the most frequently dysregulated pathway in various cancers [Samuels et al., 2004; Engelman et al., 2006; Liu et al., 2009] and therefore, the key proteins of this pathway is often targeted in multitude of cancer types [Morgensztern and McLeod, 2005; Shuttleworth et al., 2011; Jamal et al., 2014; Polivka and Janku, 2014; Porta et al., 2014; Rehan et al., 2014; Rehan, 2015]. One

of such key proteins of this pathway is mammalian target of rapamycin (mTOR), which is widely exploited as a drug target for anti-cancer therapy [Helena et al., 2012; Kist and Caceres, 2016;

Wang et al., 2016].

The mTOR is a serine-threonine kinase discovered in the 1990s as serendipity while investigating the action mechanism of rapamycin [Tsang et al., 2007]. The mTOR regulates cellular metabolism and growth in response to nutrients and growth factors and, thus, is a suitable therapeutic target in various cancers [Shaw and Cantley, 2006; Zoncu et al., 2011]. The mTOR forms two multi-protein complexes, mTOR Complex-1 (mTORC1) by binding to a regulatory associated protein of mTOR (Raptor) and mTOR Complex-2 (mTORC2) by binding to rapamycin insensitive companion of mTOR (Rictor), respectively [Loewith et al., 2002; Guertin and Sabatin, 2007]. The mTORC1 is a downstream regulator of AKT, which is susceptible to rapamycin inhibition, whereas, the mTORC2 is an upstream regulator of AKT [Fasolo and Sessa, 2008]. The protein encompasses various domains including the most important catalytic domain known as kinase domain (550 residues). The

*Correspondence to: Mohd Rehan, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia. E-mail: [email protected]

Manuscript Received: 14 March 2017; Manuscript Accepted: 4 May 2017

Accepted manuscript online in Wiley Online Library (wileyonlinelibrary.com): 5 May 2017

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Journal of Cellular Biochemistry 9999:1–10 (2017)

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Fig. 1. Two dimensional structures of OSI-027 analogs, OSI-027, and native ligand PI-103. All OSI-027 analogs (Panels A–W with exceptions of P and I). OSI-027 (Panel I). and PI-103 (Panel P) are shown. The nitrogen atoms in blue and oxygen in red colors are shown.

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kinase domain is a typical bilobed fold consisted of N-terminal lobe and a larger C-terminal lobe, and the catalytic site or ATP binding site is found as a cleft between the two lobes [Walker et al., 1999]. The mTOR was discovered as a target of rapamycin in mammalian cells, so theﬁrst known inhibitor of mTOR was rapamycin [Corradetti and Guan, 2006]. The rapamycin binds to FRB domain of mTOR and acts as an allosteric inhibitor [Choi et al., 1996; Choo and Blenis, 2009].

The rapamycin inhibits mTORC1 dependent signaling function alone and does not bind to mTORC2 [Wander et al., 2011]. Therefore, attempts have been increasingly made to develop ATP-competitive mTOR inhibitors which block the kinase function, to inhibit both the mTORC1 and the mTORC2 dependent signaling functions [Brachmann et al., 2009; Engelman, 2009; Tanneeru and Guruprasad, 2011; Zhang et al., 2011; Zaytseva et al., 2012] and, thus, provide higher efﬁcacy over allosteric inhibitors.

The OSI-027 (Fig. 1P) is an orally bioavailable, potent, and a selective ATP-competitive catalytic site inhibitor of mTOR which exhibits 100-fold selectivity for mTOR relative to PI3K isoforms and DNA-PK [Bhagwat et al., 2011]. Being a catalytic site inhibitor, OSI-027 acts on both the mTOR complexes and inhibits phosphorylation of mTORC1 substrates (4E-BP1 and S6K1) and mTORC2 substrate (AKT) in various cancer models in vitro and in vivo [Bhagwat et al., 2011]. The OSI-027 diminishes proliferation and induces apoptosis in various lymphoid cell lines and clinical samples. Further, the drug is well tolerated in vivo and induces remarkable growth inhibition in multiple tumor xenograft models [Bhagwat et al., 2011; Gupta et al., 2012]. The remarkable antileukemic effects of the drug are observed on a variety of cell lines and primary leukemic progenitors from patients and the response is enhanced when used in vitro as combination chemotherapy [Carayol et al., 2010; Altman et al., 2011]. The OSI-027 is currently in Phase I clinical trials in cancer patients for advanced solid tumors including lymphomas (http://www.ClinicalTrials.gov; NCT00698243). In spite of the proven mTOR inhibitory activity and anti-cancer potential of OSI- 027, the binding mode and detailed molecular interactions of the drug

have not been explored yet. The current study is theﬁrst attempt to investigate the inhibitory mechanism of the drug through the structural details of the drug binding to mTOR. The study also explored the inhibitory potential of OSI-027 analogs in search of a better inhibitor.

MATERIALS AND METHODS

COLLECTION OF DATA

The three dimensional coordinate structure of OSI-027 was fetched from PubChem database with CID: 44224160. The crystal structures of human mTOR kinase domain co-complexed with distinct ATP competitive inhibitors were obtained from Protein Data Bank with PDB ID: 4JT6, 4JT5, 4JSX, and 4JSP. Of the four mTOR co-complexed structures, the 4JT6 was arbitrarily selected for OSI-027 docking. The native ligand PI-103 in the mTOR co-complex structure 4JT6 was used as probe for grid generation at the catalytic site.

STRUCTURAL ANALOGS OF OSI-027

Structural analogs of OSI-027 were retrieved from PubChem using search option“Similar Compounds,”based on similarity score (Tanimoto

Fig. 2. Molecular docking of OSI-027 into the catalytic site of human mTOR. The mTOR is shown in surface and OSI-027 in red stick representations. The inset shows the blown-up catalytic site and the labeled interacting residues are shown as surface in various colors.

TABLE I. The Human mTOR Residues Interacting With OSI-027 Are Listed With the Number of Non-Bonding Contacts and Loss in Accessible Surface Area (DASA)

Interacting residues

No. of hydrophobic

contacts DASA (Å²)

Leu-2185 2 26.19

Ile-2237 1 12.27

Trp-2239 13 62.31

Val-2240 2 9.03

Cys-2243 1 17.74

Asp-2244 1 15.89

Thr-2245 5 30.39

Met-2345 6 30.62

JOURNALOFCELLULARBIOCHEMISTRY INSIGHTS INTOOSI-027ANDANALOGSINHIBITINGmTOR

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Fig. 3. (Un)binding simulation analyses of OSI-027 binding to the catalytic site of mTOR. Panels A–K: The (un)binding simulation phases of OSI-027 (Panel A denotes farthest phase from the catalytic site, Panel J the closest to the catalytic site, and Panel K the catalytic site phase, respectively). The hydrogen bonds are shown as green-dashed lines with indicated bond length and the residues involved in hydrophobic interactions are shown as red arcs. The residues which are overlapping to the last phase (K) are encircled.

TABLE II. The Binding Strengths of OSI-027 and its Analogs Are Compared With the Native Ligand PI-103

Serial no. CID No. of interacting residues Dock (grid) score pK_d Binding energy (kcal/mol)

1 73294902 14 53.06 6.69 9.13

2 45376664 11 47.56 6.78 9.25

3 45376800 10 45.40 6.30 8.59

4 73297166 11 44.73 6.14 8.37

5 72698550 9 43.62 5.88 8.02

6 45376928 11 43.41 6.59 8.99

7 45376405 10 43.13 6.33 8.64

8 45376402 8 42.73 6.22 8.48

9 9884685 (PI-103) 11 42.70 6.51 8.88

10 73297164 11 41.97 5.97 8.15

11 89361707 10 41.97 6.44 8.79

12 45376409 14 41.74 6.44 8.78

13 45377062 15 40.79 6.75 9.21

14 45376138 11 40.18 6.16 8.40

15 45376410 11 40.11 6.31 8.61

16 44224160 (OSI-027) 8 39.91 5.83 7.96

17 45377477 8 39.44 6.23 8.50

18 58423416 12 39.17 6.26 8.54

19 73357458 9 38.91 5.87 8.00

20 57748088 12 38.53 5.93 8.09

21 73294748 7 37.08 5.31 7.25

22 88233435 7 36.62 5.74 7.83

23 45376666 8 35.62 6.17 8.41

CID is the Compound Id from PubChem for each compound and the“Kd”denotes the dissociation constant. The number of interacting residues, the binding energy and pKd

orlog(Kd) values are provided for all the compounds. The PI-103 and OSI-027 are marked as bold. The higher absolute values of Dock score and binding energy indicate better docking and binding, respectively.

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coefficient). For computation of similarity score (Tanimoto coefficient) between two compounds, PubChem uses PubChem dictionary-based binaryfingerprint of the compounds. Thefingerprint comprises of a sequence of chemical substructure“keys”and each key has two forms

(binary key) which indicate whether the chemical substructure is present in the compound or not. The“Similar Compounds”search to the query OSI-027 used the default similarity score (Tanimoto coefﬁcient)>90%

and provided 54 compounds initially.

FILTERING OF DRUGLIKE COMPOUNDS

The retrieved 54 similar compounds of OSI-027 were furtherﬁltered for their druglikeness using Lipinski’s Rule-of-Five (Lipinski et al., 2001). The rule says that for a compound to be drug-like or lead-like, it should have following properties:

(1) molecular weight<500 g/mol;

(2) lipophilicity (log P)<5;

(3) H-bond donors<5;

(4) H-bond acceptors (sum of all nitrogen and oxygen atoms)<10;

(5) number of rotatable bonds<10.

Theﬁfth condition is not always included, if included then one of the four rules can be violated.

Onﬁltering using Lipinski’s Rule-of-Five (Lipinski et al., 2001), the initially retrieved 54 compounds shortlisted to 37. The redundant and irrelevant structures were removed leaving with 21 OSI-027 analogs which were used in the current study.

MOLECULAR DOCKING

The molecular docking of OSI-027 and its structural analogs to the catalytic site of mTOR were performed by Dock v.6.5 [Ewing et al., 2001].

Fig. 4. The bar graph for dock scores of all OSI-027 analogs. The serial numbers of OSI-027 analogs (Table 2) are shown as ticks on X-axis. The dock score is indicated by Y-axis and denoted by the length of the bar for each compound. The higher absolute value of the dock score imply better docking. The OSI-027 is shown as cyan bar with serial number 9, whereas, the native ligand PI-103 is shown as green bar with serial number 16. The selected OSI-027 analog CTD-73294902 with highest score is outperforming by greater margin and is shown as magenta bar with serial number 1. The rest of OSI-027 analogs are shown as light blue bars.

Fig. 5. Comparative binding analyses of CID-73294902 (Panel A), OSI-027 (Panel B) with native ATP competitive inhibitors PI-103 (Panel C), PP242 (Panel D), Torin2 (Panel E), and AGS (Panel F). The hydrogen bonds labeled with bond length arc presented as green-dashed lines and the residues forming hydrophobic interactions are labeled with residue number and are presented as red arcs. The encircled residues are the overlapping interacting residues between the two neighboring ligands.

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The docking program was also assessed using self-docking of native ligand PI-103 whereby PI-103 was extracted from the catalytic site of mTOR, randomly transformed (translated and rotated), and again docked into the catalytic site of mTOR. The root mean square deviation (rmsd) of docked PI-103 and the co-complexed PI-103 was performed by Dock v.6.5. The Chimera v.1.6.2 [Pettersen et al., 2004] served as assisting tool for docking and used in protein and ligand structure preparations.

PROTEIN-LIGAND COMPLEX ANALYSIS

The illustrations of protein-ligand complexes were prepared by PyMOL v.1.3 [DeLano, 2002], whereas, the protein-ligand interaction plots were illustrated by Ligplotþv.1.4.5 [Wallace et al., 1995;

Laskowski and Swindells, 2011]. To measure the degree of involvement of a residue in binding, loss in Accessible Surface Area (ASA) after ligand binding was checked. A residue is involved in binding if it loses more than 10 Å²ASA while going from unbound protein to the complex form [Ghosh et al., 2009]. The ASA for both the protein forms, the unbound form and the complex form, was calculated by Naccess v.2.1.1 [Hubbard and Thornton, 1993]. For a residue, the loss in ASA (DASA) is evaluated by subtracting ASA of bound form from that of unbound form.

The Dock v.6.5 provided the Dock score (Grid score), a measurement of binding and in addition to this, the dissociation constants and the binding energies were also calculated using X-Score v.1.2.11 [Wang et al., 2002, 2003].

PROTEIN-LIGAND (UN)BINDING SIMULATION

The MoMa-LigPath [Cortes et al., 2005; Devaurs et al., 2013], a Molecular Motion Algorithms (MoMA) based web server (http://moma.

laas.fr), was used for ligand (un)binding simulation from the catalytic site to the protein’s surface. The MoMa-LigPath involves geometric constraints and takes into account theﬂexibility for the ligand and protein side-chains. The program simulates the ligand (un)binding from the catalytic site to the protein’s surface or from protein’s surface to the catalytic site. In the simulation process, it provides snapshots of transient molecular interactions, which help in initial ligand-binding to the protein surface and then driving it toward the catalytic site.

During the simulation process, the program also identiﬁes the additional important residues which are away from the catalytic site.

RESULTS AND DISCUSSION

SELF-DOCKING ANALYSIS OF NATIVE LIGAND PI-103

It is reported that in self-docking analysis, the structures having docked poses with RMSD<2.0 Åare considered suitable for quality docking and virtual screening [Vinh et al., 2012; Zhang et al., 2014;

Ramezani and Shamsara, 2015]. In this view, the self-docking analysis of native ligand PI-103 revealed the RMSD of docked pose as 0.642 Å2.0 Å, and hence, the docking program and the crystal structure of mTOR, PDB Id: 4JT6 was considered good enough for pose prediction and virtual screening.

MOLECULAR DOCKING AND (UN)BINDING SIMULATION ANALYSES OF OSI-027

The docking studies revealed that OSI-027 ﬁts well into the catalytic site of mTOR kinase domain and packed against the residues Leu-2185, Ile-2237, Trp-2239, Val-2240, Cys-2243, Asp-2244, Thr-2245, and Met-2345 (Fig. 2). These eight residues together exerted 31 hydrophobic interactions stabilizing the drug- protein complex (Table I). Further, the high values of the dock score (39.91), binding energy (7.96 kcal/mol), and dissociation constant (pKd, 5.83) also showed that the drug–protein complex was in its most favorable conformation (Table II). The docking analyses showed that the key residue involved in binding was Trp-2239 as it showed maximum loss in accessible surface area due to binding and was involved in maximum number of hydrophobic interactions (Table I). Further, the visual analysis in PyMOL revealed a possible aromatic stacking interaction between methoxyindole moiety of OSI-027 and indole side chain

TABLE III. The Human mTOR Residues Interacting With Selected Analog CID-73294902 Are Listed With the Number of Non-Bonding Contacts and Loss in Accessible Surface Area (DASA)

Interacting residues

No. of hydrophobic

contacts DASA (Å²)

Ile-2163 1 22.08

Gln-2167 1 14.8

Leu-2185 4 31.15

Lys-2187 3 15.58

Glu-2190 3 18.38

Asp-2195 1 7.56

Tyr-2225 5 7.69

Ile-2237 5 27.58

Gly-2238 1 3.92

Trp-2239 11 39.17

Thr-2245 1 17.18

Met-2345 1 29.75

Ile-2356 6 44.74

Asp-2357 5 34.2

Fig. 6. Binding orientations of OSI-027, PI-103, and CID-73294902 in the catalytic site of mTOR. The compounds’colors are chosen with the option of

“color by elements”in Pymol keeping carbon backbones in different colors (OSI-027, cyan; PI-103, green; and CID-73294902, magenta). Nitrogen atoms in blue and oxygen atoms in red color are shown. The portion of mTOR catalytic site is shown in surface representation in light orange color.

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of Trp-2239. The (un)binding simulation analyses (Fig. 3) showed how OSI-027 was driven from surface of the protein to the catalytic site through varying molecular interactions. The simulation also provided snapshots of appearing and disappearing transient molecular interactions during binding process. The residues that appeared more commonly in simulation phases were more important for binding. This provided another way of

ranking residues’importance for their involvement in binding. In addition, few additional residues (Gln-2161, Ile-2163, Thr2164, Lys-2171, Arg-2251, and Ile-2356) were identiﬁed which despite being away from the catalytic site, still play a role in binding of OSI-027 to the surface of the protein (Fig. 3). Of these additional residues, the Lys-2171 formed hydrogen bonds in various simulation phases. The key residue Trp-2239 as mentioned above

Fig. 7. (Un)binding simulation analyses of CED-73294902 binding to the catalytic site of mTOR. Panels A–O: The (un)binding simulation phases of OSI-027 (Panel A denotes farthest phase from the catalytic site, Panel N the closest to the catalytic site, and Panel O the catalytic site phase, respectively). The hydrogen bonds are shown as green-dashed lines with indicated bond length and the residues involved in hydrophobic interactions are shown as red arcs. The residues which are overlapping to the last phase (O) are encircled.

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was also involved in various (un)binding simulation phases from protein’s surface to the catalytic site and was shared by the most of simulation phases.

VIRTUAL SCREENING OF OSI-027 ANALOGS FOR BETTER mTOR INHIBITOR

Virtual screening of all 21 OSI-027 analogs were performed through molecular docking against mTOR catalytic site (Fig. 1). The docking scores, binding energies, and dissociation constant values for all OSI-027 analogs are provided as Table II. The ligand-protein interaction plots for all analogs are provided as Supplementary File S1. The dock scores for all the analog complexes are illustrated as bar graph for visual analyses (Fig. 4). The OSI-027 analog with highest dock score (53.06), named in the current study as CID-73294902, was outperforming by greater margin to other analogs (Fig. 4).

Therefore, CID-73294902 was proposed as the best inhibitor among OSI-027 analogs, and was selected for further study.

MOLECULAR DOCKING AND (UN)BINDING SIMULATION ANALYSES OF BEST PROPOSED INHIBITOR CID-73294902 AMONG OSI-027 ANALOGS

The CID-73294902 bound to the catalytic site and packed against the residues Ile-2163, Gln-2167, Leu-2185, Lys-2187, Glu-2190, Asp-2195, Tyr-2225, Ile-2237, Gly-2238, Trp-2239, Thr-2245, Met-2345, Ile-2356, and Asp-2357 (Fig. 5A). The 14 residues together exerted 48 hydrophobic interactions stabilizing the drug–protein complex (Table III) as opposed to 31 hydrophobic interactions of eight residues in OSI-027 binding. The binding strength of CID-73294902 is better than that of OSI-027 and native inhibitor PI-103 as depicted by dock score (53.06), binding energy (9.13 kcal/mol), and dissociation constant (pKd, 6.69), all of which have absolute values greater than the respective scores of OSI-027 and PI-103 (Table II). The key residues identiﬁed in binding of the compound CID-73294902 were Trp-2239 and Ile-2356 due to their involvement in maximum number of hydrophobic interactions and maximum loss in accessible surface area after binding (Table III).

Like OSI-027, the visual analysis of this OSI-027 analog also showed that there may exist an aromatic stacking interaction between imidazo-triazine moiety of CID-73294902 and indole side chain of Trp-2239.

Comparative binding modes of CID-73294902, the native inhibitor PI-103, and the OSI-027 in the catalytic site of mTOR are illustrated in Figure 6. The comparison in the binding modes of CID-73294902 and PI-103 (Fig. 5) showed that the CID-73294902 shared 10 interacting residues (Ile-2163, Leu-2185, Glu-2190, Asp-2195, Tyr-2225, Ile-2237, Gly-2238, Trp-2239, Ile-2356, and Asp-2357) with PI-103 as opposed to OSI-027 (Fig. 5), which shared only four interacting residues with PI-103. This suggested that the binding of CID-73294902 to the catalytic site of mTOR is stronger than that of OSI-027, and may inhibit the kinase function strongly as engaging greater number of important residues of mTOR in binding. However, of the 10 shared residues, Asp-2195 and Tyr-2225 were involved in hydrogen bond formation in the bound inhibitor PI-103 but in CID-73294902, the Asp-2195, and Tyr-2225 were involved in hydrophobic interactions.

The (un)binding simulation analysis of CID-73294902 (Fig. 7) provided snapshots of transient molecular interactions appearing and disappearing while moving from the catalytic site to the surface of the protein. As mentioned earlier also, the residues overlapping in multiple phases are playing important role in binding. The residue Gln-2167 found to form hydrogen bond while the compound being close to the surface of the protein. The simulation also identiﬁed additional residues (Ser-2165, Lys-2166, and Ser-2342) which despite being distal from catalytic site, played role in initial binding at the surface of the protein. The simulation provided the whole track of exit path of the bound compound moving away from the catalytic site. The exit path comparison of CID-73294902 and OSI-027 (Fig. 8) showed that both were beginning from the same catalytic site, diverging to different orientation, and thus, follow different (un)binding simulation tracks.

The proposed inhibitor CID-73294902 performed better than OSI-027 and PI-103 as it involved greater number of interacting residues with increased hydrophobic interactions (Table II).

Further, the binding strength scores of CID-73294902 showed better binding than those of OSI-027 and PI-103 (Table II). This indicates that the CID-73294902 may inhibit mTOR better than OSI-027 and PI-103, and therefore, may provide as an alternate drug with better anti-cancer results. However, further laboratory experiments are required to explore the therapeutic potential of the proposed inhibitor CID-73294902.

COMPARISON IN BINDING MODES OF OSI-027 AND CID-73294902 WITH OTHER NATIVE INHIBITORS

The known ATP competitive inhibitors available as mTOR-inhibitor complexes in PDB database are PI-103 (PDB Id: 4JT6), PP242 (PDB Id: 4JT5), Torin2 (PDB Id: 4JSX), and AGS (PDB Id: 4JSP). When binding of OSI-027 was compared with these native inhibitors, the

Fig. 8. Different paths for unbinding of OSI-027 (colored cyan) and C1D- 73294902 (colored magenta) from the catalytic site of mTOR. The path of unbinding is shown by the compound continuously going away from catalytic sites in lines representations and ending at sticks representation.

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number of overlapping interacting residues found were 4, 5, 6, and 6 with PI-103, PP242, Torin2, and AGS, respectively (Fig. 5, Table IV).

Further, the three interacting residues (Ile-2237, Trp-2239, and Val-2240) were found to be consistently overlapping among OSI-027 and all the native inhibitors (Fig. 5, Table IV).

Similarly, on comparison of binding of CID-73294902 with the four native inhibitors, the number of overlapping interacting residues found were 10, 10, 6, and 10 with PI-103, PP242, Torin2, and AGS, respectively (Fig. 5, Table IV). Further, the four interacting residues (Ile-2237, Gly-2238. Trp-2239, and Ile-2356) were found to be consistently overlapping among CID-73294902 and all the native inhibitors (Fig. 5, Table IV).

Theseﬁndings suggested that OSI-027 and CID-73294902 bound to the similar region in the catalytic site as other native inhibitors did and likely resulted in inhibiting the kinase activity of mTOR [Bhagwat et al., 2011] by engaging the common important residues.

CONCLUSIONS

The current study of docking and (un)binding simulation showed that OSI-027 bound to the catalytic site of mTOR and blocked the kinase function by reserving important residues in multiple molecular interactions. The binding mode of OSI-027 in mTOR catalytic site and the interacting residues were identiﬁed and analyzed. The Trp-2239 was proposed as the key residue for showing maximum loss in accessible surface area due to binding, exerting maximum number of hydrophobic interactions, and showing consistent appearance in all (un)binding simulation phases. Further, in pursuit of a better inhibitor, taking OSI-027 as lead compound, OSI-027 analogs were considered in the study. The virtual screening of OSI-027 analogs led to identiﬁcation of CID-73294902, which was proposed to bind mTOR better than the original drug candidate OSI-027 and the bound

inhibitor PI-103. The study explored the binding mode of CID- 73294902 with the mTOR interacting residues and their molecular interactions. The greater number of interacting residues with increased hydrophobic interactions and higher absolute values of dock score, dissociation constant, and binding energy than those of OSI-027 and PI-103 suggested that this may be a better inhibitor of mTOR. Thus, the study provided a novel OSI-027 analog for experimental biologist to explore the potential of the proposed compound CID-73294902, apparently a better anti-cancer compound. Finally, the study will help experimental biologist in understanding the binding mechanism of OSI-027 and in designing better anti-cancer drugs.

ACKNOWLEDGMENTS

I highly acknowledge Prof. M.A. Beg for proof reading of the manuscript and for providing valuable suggestions. The research facilities and necessary support provided by King Fahd Medical Research Center (KFMRC), King Abdulaziz University are acknowl- edged. Thanks are also due to Dr. J. Cortes for providing stand alone version of MoMA-LigPath. I also thank M.S. Gazdar, head of library, KFMRC for easy access of books and journals.

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TABLE IV. The mTOR Interacting Residues of OSI-027 and CID- 73294902 Overlapping With Those of the Known Native Inhibitors PI-103, PP242, Torin2, and AGS Are Tabulated for Comparison

Native inhibitors

Docked compounds PI-103 PP242 Torin2 AGS

OSI-027 Leu-2185 Leu-2185 Leu-2185

Ile-2237 Ile-2237 Ile-2237 Ile-2237 Trp-2239 Trp-2239 Trp-2239 Trp-2239 Val-2240 Val-2240 Val-2240 Val-2240

Cys-2243

Thr-2245 Thr-2245 Met-2345 Met-2345 Met-2345 CID-73294902 Ile-2163

Gln-2167

Leu-2185 Leu-2185 Leu-2185

Lys-2187 Lys-2187

Glu-2190

Asp-2195 Asp-2195

Tyr-2225 Tyr-2225 Tyr-2225

Ile-2237 Ile-2237 Ile-2237 Ile-2237 Gly-2238 Gly-2238 Gly-2238 Gly-2238 Trp-2239 Trp-2239 Trp-2239 Trp-2239 Thr-2245 Thr-2245 Met-2345 Met-2345 Met-2345 Ile-2356 Ile-2356 Ile-2356 Ile-2356 Asp-2357 Asp-2357

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An Anti-Cancer Drug Candidate OSI-027 and its Analog as Inhibitors of mTOR: Computational Insights Into the Inhibitory Mechanisms