353J Contemp Med Sci | Vol. 7, No. 6, November-December 2021: 353–357 Original Pyrimidine Derivatives as Promising Candidates for Potent Antiangiogenic: A silico Study Nadhir N. A. Jafar1*, Ahmed A. Hussein2 1Pharmacy College, Al-Zahraa University for Women, Karbala 65001, Iraq. 2Pharmacy Department, Al-Mustaqbal University College, 51001 Hillah, Babil, Iraq. *Correspondence to: Nadhir N. A. Jafar (E-mail: nather.najim@alzahraa.edu.iq) Abstract Objectives: This study planned to explore the effect of many synthetic compounds derived from (4-chloro-6-methoxy-N,N-dimethyl pyrimidin-2-amine) as antiangiogenic. Methods: Docking study has been done by using Molecular Operating Environment (2019) to examine the energy binding affinity of tested compounds with VEGFR-2 kinase and using Discovery Studio Visualizer v20.1.0.19295 free version to visualize the surface binding cavity. Results: Theoretical calculation of these compounds showed significant results in comparing to the reference drug compounds, compound (1) which is 4-(4-(1,2,3-selenadiazol-4-yl)phenoxy)-6-methoxy-N,N-dimethylpyrimidin-2-amine gives the lowest binding energy equal to (–8.116) Kcal/mol and nearest to the reference drug compound, and also it has excellent RMSD equal to (0.9263). The other compounds 4-(4-(1,2,3-thiadiazol-4-yl)phenoxy)-6-methoxy-N,N-dimethylpyrimidin-2-amine, 4-methoxy-N,N-dimethyl-6-(phenylthio) pyrimidin-2- amine, 4-(benzo[d]thiazol-2-ylthio)-6-methoxy-N,N-dimethylpyrimidin-2-amine have –7.739, –7.211 and –7.841 Kcal/mol binding energy and 2.668, 1.745 and 1.377 RMSD respectively. Conclusion: Compound (1) can be recommended as a powerful antiangiogenic due to its theoretical results for binding energy. Keywords: 1,2,3-seleniadiazole, anti-angiogenesis, anticancer, binding energy, pyrimidine ISSN 2413-0516 Introduction Cancer cells have a very high metabolism process in compar- ison with normal cells and this led to high oxygen demand and more supplying of nutrients, this issue causes hypoxia which is considered the main regulation mechanism for angiogenesis.1,2 Scientists have been researched and concen- trated on how tumors get the oxygen and nutrients needed. In 1989, the vascular endothelial growth factor (VEGF) pro- tein was discovered by a team of scientists due to the belief that it induces angiogenesis3 by binding to their receptors in the endothelial cells of blood vessels and stimulate proliferation.4-6 The induction from the tumor itself causing angiogenesis, vasculogenesis, increasing vessel permeability, and migration to be around the tumor to supply it with oxygen and nutri- ents.7,8 The VEGF receptor inhibitors play an important role in the treatment of tumors by causing tumor starvation by pre- venting the proliferation of endothelial blood vessels that led to decreasing of oxygen and nutrients they need9 and will give tumor growth suppression10 such as Sorafenib (Nexavar)® which has been approved as a potent antiangiogenic drug.11 The first objective of this study is testing in-silico pyrimidine derivative as a new pharmacophore antiangiogenic ligand, it is safer because it is a part unit in nucleic bases of RNA and DNA and this feature gave its derivatives widespread pharmacolog- ical activities.12,13 Pyrimidine derivatives have been used as potent anticancer in cases of breast, stomach, colon, pancre- atic, and other types of cancer,14,15 antimicrobial effects,14,16,17 potent antitubercular agents,18 antimalarial effects especially for resistant species,19 potent anti-inflammatory,20 efficient antiviral activity, antihypertensive activity21 and especially for Varicella-zoster virus.22,23 The second objective of our study is to figure out a new activity of previously synthesized compounds with pyrimidine ring such as [1,2,3-selenadiazole, 1,2,3-thiadiazole, benzo[d]thiazol-2-ylthio] and thiophenyl compounds.24 These compounds have been studied are organosulfur and organoselenium compounds which have significant activity as anti-fungal activity,24 antibacterial effect,25-30 due to the patients with cancer that suffering from microbial infec- tions,31 so the most significant features will be emphasized in this article for pyrimidine with the substitutions that men- tioned using a potent anticancer and antimicrobial activities to produce a single drug with double activities to add a new cost-effective feature. Consequently, merged the pyrimidine with fourth substitutions to discover in silico a new activity and to get more potent binding energy with vascular endothe- lial growth factor receptor protein. Materials and Methods Docking Requirements Docking study has been done by using Molecular Operating Environment (2019)32 to examine the energy binding affinity of tested compounds below with VEGFR-2 kinase and using Discovery Studio Visualizer v20.1.0.19295 free version33 to visualize the surface binding cavity. Preparation of Ligands The compounds that have been used were already synthesized, then, they have been processed by MOE in form of 2D, pre- pared with protonate 3D, partial charge automatically calcu- lated, energy minimization to get the most stable conformation and saved in form 3D form as (moe) file, then all of them have been imported in database and saved as MDB file to be used in docking process.34,35 (Submitted: 09 September 2021 – Revised version received: 22 September 2021 – Accepted: 01 October 2021 – Published online: 26 December 2021) 354 J Contemp Med Sci | Vol. 7, No. 6, November-December 2021: 353–357 Pyrimidine Derivatives as Promising Candidates for Potent Antiangiogenic: A silico Study Original N.N.A. Jafar and A.A. Hussein Fig. 2 Diagram interaction of compound (1) with the crystal structure of the VEGFR2 kinase. Protein Arrangement and Preparation The crystal structure of the VEGFR2 kinase which is complex with PF- 00337210 (N,2-dimethyl-6-(7-(2-morpholinoethoxy) quinoline-4-yloxy)benzofuran-3-carboxamide) that has been downloaded from the Protein Data Bank website (PDB ID code is: 2XIR) with resolution: 1.50 Å.36 Preparation of crystal structure of a protein by adding hydrogen atoms during proto- nation 3D has been done at first, then checking all atom’s con- nection errors have been done by automatic correction, potential fixation of all protein atoms with Amber12: EHT. Finally, Selection of all active sites and the creation of them as dummies by using a site finder (Figure 1).34,35 Results and Discussion The results are given in Table 1, which explains the core com- pound which gives good interaction with low binding energy equal to (–5.911) with RMSD equal to (0.691), whereas the substituted synthesized compounds 1, 2, 3, and 4 gave the lowest binding energy equal to (–8.116, –7.739, –7.211 and –7.84), respectively, and nearest to the reference drug com- pound, and also it has very good RMSD equal to (0.9263), that means substations play an important role in the protein binding process in comparing with the starting pyrimidine derivative compound (5). Docking Study The prepared database of compounds mentioned previously has been tested on the protein VEGA-2 receptor. Generally, the docking was done by loading the protein with dummies atoms that represent active sites in the protein, modifying the default properties in MOE software, set docking site as dummy atoms, ligand as MDB file, rigid receptor method, triangle matcher as method placement, London dG and GBVI/WSA dG as score method and have been selected the best 10 confir- mations out of 200 different conformations for each ligand. Then we chose the best pose that has the lowest energy with good RMSD values from the obtained docking results.35,37,38 The compound (1) has been interacted with protein amino acids [CYS 919 (A) H-acceptor interaction of (N) with (N25) in ligand; ASP 1046 (A) H-acceptor interaction of (N) with (N27) in ligand; LEU 840 (A) pi-H interaction of (CD1) with (5-ring) in ligand; VAL 899 (A) pi-H interaction of (CG1) with (6-ring) in ligand] with distances 3.14 Å, 3.21 Å, 3.82 Å, 4.44 Å and E (kcal/mol) –0.7, –2.4, –0.6, –0.6 respectively as shown in Figures 2 and 3. The compound (2) has interacted with amino acids [ASP 1046 (A) H-acceptor interaction of (N) with (O) in ligand; LEU 840(A) pi-H interaction of (CD2) with (5-ring) in ligand; LYS 868(A) pi-H interaction of (CE) with (6-ring) in ligand] with distances 2.95 Å, 3.95 Å, 4.27 Å and E (kcal/mol) –1.8, –1.2, –1.2 respectively. The compound (3) has interacted with amino acids [ASP 1046 (A) H-acceptor interaction of (N) with (O) in ligand; VAL 848(A) pi-H interaction of (CG1) with (6-ring) Fig. 1 Crystal structure of the VEGFR2 kinase PDB code (2XIR). Table 1. Binding energies of the ligand with protein No. Compound S rmsd_refine E_conf E_ place E_ score1 E_ refine E_ score2 1 Reference –9.822 1.516 11.596 –67.448 –16.645 –45.713 –9.822 2 1 –8.116 0.926 –100.626 –55.464 –9.436 –36.111 –8.116 3 2 –7.739 2.668 –89.229 –56.335 –9.539 –33.926 –7.739 4 3 –7.211 1.745 –118.107 –61.455 –9.759 –31.147 –7.211 5 4 –7.841 1.377 –107.456 –55.826 –9.683 –36.329 –7.841 6 5 –5.911 0.691 –128.838 –56.396 –8.053 –29.731 –5.911 S, The final score; RMSD, Root-mean-square deviation between the pose before refinement and the pose after refinement; E_conf, The energy of the conformer; E_place, Score from the placement stage; E_score1, Score from the rescoring stage(s); E_refine, Score from the refinement stage and No. of conf-number of conformations generated by ligand. 355J Contemp Med Sci | Vol. 7, No. 6, November-December 2021: 353–357 N.N.A. Jafar and A.A. Hussein Original Pyrimidine Derivatives as Promising Candidates for Potent Antiangiogenic: A silico Study in ligand; LYS 868(A) pi-H interaction of (CE) with (6-ring) in ligand] with distances 2.94 Å, 4.42 Å, 4.07 Å and E (kcal/mol) –1.9, –0.7, –1.1 respectively. The compound (4) has interacted with amino acids [ASP 1046 (A) H-acceptor interaction of (N) with (N9) in ligand; VAL 848(A) pi-H interaction of (CG1) with (5-ring) in ligand] with distances 3.26 Å, 4.23 Å and E (kcal/mol) –1.6, –0.9 respectively. Structure-Activity Relationship (SAR) The primary study of SAR has focused on the impact of sub- stituents in replacing chlorine atoms in the pyrimidine core, which is related to H-bond accepter via N or O-atoms or arene amino acid interaction. The compound (5) represents a core compound that has been used to synthesize other four compounds which have been interacted with amino acids [ASP 1046 (A) H-acceptor interaction of (N) with (N2) in ligand; VAL 899(A) pi-H inter- action of (CG1) with (6-ring) in ligand] with distances 3.5 Å, 4.43 Å and E (kcal/mol) –1.2, –0.6 respectively as shown in Figure 4. When replacing chloride in the core compound with four different substituents separately as shown in Scheme 1. Compound 1 has been exhibited –8.116 Kcal/mol binding energy because increasing the hydrogen bonds accepter –4.100 Kcal/mole related with N interacted with ASP 1046 (A) com- pared with the core compound equal to –1.200 Kcal/mol. Fur- thermore, the presence of –1.600 Kcal/mole hydrogen acceptor of N with CYS 919 (A) and changing the interaction of third connect with LYS 868(A) instead of VAL 899 (A) that means the compound has been orientated with the best alignment with protein as in Figures 2, 3. Compound 2 has appeared –7.739 Kcal/mole binding energy from H-acceptor O with ASP 1046 (A) and two Pi-H interactions as in Figure 5, compound 3 and 4 have –7.211 and –7.841 Kcal/mol, respectively, as could be observed in Figures 6 and 7. Fig. 3 Diagram isolated interaction of compound (1) with the crystal structure of the VEGFR2 kinase. Fig. 5 Diagram interaction of compound (2) with the crystal structure of the VEGFR-2. Fig. 6 Diagram interaction of compound (3) with the crystal structure of the VEGFR-2. Scheme 1. Structures of Pyrimidine and four synthesized compounds. Fig. 4 Diagram interaction of compound (5) with the crystal structure of the VEGFR-2. 356 J Contemp Med Sci | Vol. 7, No. 6, November-December 2021: 353–357 Pyrimidine Derivatives as Promising Candidates for Potent Antiangiogenic: A silico Study Original N.N.A. Jafar and A.A. Hussein –7.4 and –8.4, respectively, this issue encourages us to proceed for furthermore studies. Conclusion This research contributes to finding a new core from pyrimi- dine derivatives as promising candidates for powerful antian- giogenic drug in-silico study. Further investigations are recommended for new researchers as driving the possibility for more broad pharmacological examinations. The docking studies and flexible alignment would pro- pose a good affinity of most of the synthesized compounds towards interacting with VEGFR-2 receptor in better binding energy from the data obtained, all compounds exhibited –8.116, –7.739, –7.211 and –7.841 Kcal/mol binding energy, respectively, with compounds 1, 2, 3 and 4 with small RMSD. The results demonstrated that the most dynamic mixes could be helpful as a format for future patterns, advancement, modification, furthermore, assessment to make more extraor- dinary and specific VEGFR‐2 inhibitors with higher anti- cancer analogs.  References 1. Garcia J, Hurwitz HI, Sandler AB, et al. 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This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License which allows users to read, copy, distribute and make derivative works for non-commercial purposes from the material, as long as the author of the original work is cited properly. https://doi.org/10.22317/jcms.v7i6.1087