key: cord-0837703-5z8f4z9j authors: Teralı, Kerem; Baddal, Buket; Gülcan, Hayrettin Ozan title: Prioritizing potential ACE2 inhibitors in the COVID-19 pandemic: insights from a molecular mechanics-assisted structure-based virtual screening experiment date: 2020-07-23 journal: J Mol Graph Model DOI: 10.1016/j.jmgm.2020.107697 sha: bf71dd26d727be2f3d0e06109da8c6ea7dea8903 doc_id: 837703 cord_uid: 5z8f4z9j Angiotensin-converting enzyme 2 (ACE2) is a membrane-bound zinc metallopeptidase that generates the vasodilatory peptide angiotensin 1–7 and thus performs a protective role in heart disease. It is considered an important therapeutic target in controlling the COVID-19 outbreak, since SARS-CoV-2 enters permissive cells via an ACE2-mediated mechanism. The present in silico study attempted to repurpose existing drugs for use as prospective viral-entry inhibitors targeting human ACE2. Initially, a clinically approved drug library of 7,173 ligands was screened against the receptor using molecular docking, followed by energy minimization and rescoring of docked ligands. Finally, potential binders were inspected to ensure molecules with different scaffolds were engaged in favorable contacts with both the metal cofactor and the critical residues lining the receptor’s active site. The results of the calculations suggest that lividomycin, burixafor, quisinostat, fluprofylline, pemetrexed, spirofylline, edotecarin, and diniprofylline emerge as promising repositionable drug candidates for stabilizing the closed (substrate/inhibitor-bound) conformation of ACE2, thereby shifting the relative positions of the receptor’s critical exterior residues recognized by SARS-CoV-2. This study is among the rare ones in the relevant scientific literature to search for potential ACE2 inhibitors. In practical terms, the drugs, unmodified as they are, may be introduced into the therapeutic armamentarium of the ongoing fight against COVID-19 now, or their scaffolds may serve as rich skeletons for designing novel ACE2 inhibitors in the near future. A previously unknown coronavirus (CoV) has crossed the species barrier and emerged as the Despite being implicated as a major public health concern, to date, no effective therapeutics 60 have been approved against SARS-CoV-2, with a number of treatment options (remdesivir; 61 lopinavir with ritonavir; lopinavir with ritonavir plus interferon beta-1a; and chloroquine or viral surface [7] , and gives CoVs a crown-like appearance by forming spikes on their surface. 70 S protein binds to a membrane receptor on the host cells, angiotensin-converting enzyme 2 71 (ACE2; EC 3.4.17.23) mediating the viral and cellular membrane fusion, which represents the 72 critical initial stage of the infection. SARS-CoV-2 exploits human ACE2 for host cell entry 73 [8, 9] , although CD147/S protein-mediated route of invasion has also recently been reported 74 [10] . SARS-CoV-2 S protein comprises two functional subunits responsible for binding to the 75 host cell receptor (S1 subunit) and fusion of the viral and cellular membranes (S2 subunit). 76 Viral entry depends on binding of the S1 subunit to ACE2 through the receptor-binding 77 domain (RBD) in the S1 subunit, facilitating viral attachment to the surface of target cells 78 [11]. Additionally, entry requires S protein priming by cellular serine protease TMPRSS2, 79 which entails S protein cleavage at the S1/S2 and the S2ʹ site and allows fusion of viral and 80 cellular membranes, a process driven by the S2 subunit [12] . Strikingly, SARS-CoV-2 has 81 been shown to harbor a furin cleavage site at the S1/S2 boundary which is processed during 82 biosynthesis, and which represents a novel feature setting SARS-CoV-2 S protein apart from 83 SARS-CoV S protein that possesses a monobasic S1/S2 cleavage site processed upon entry 84 into target cells [13] . physiological context, ACE2, as part of the renin-angiotensin system (RAS), catalyzes the 92 cleavage of angiotensin II to angiotensin 1-7, the latter being a potent vasodilator with 93 protective properties for the cardiovascular system [18] . In order to facilitate countermeasure developments, a 3.5-Å-resolution cryo-electron microscopy structure of the SARS-CoV-2 S 95 trimer in prefusion conformation has been recently determined. This analysis revealed that the 96 predominant state of the trimer has one of the three RBDs rotated up in a receptor-accessible 97 conformation, and also provided biophysical and structural evidence that the SARS-CoV-2 S 98 protein ectodomain binds to the PD of ACE2 with an affinity of ~15 nM, which is ~10-to 20-99 fold higher than the affinity with which SARS-CoV S binds to ACE2 [19] . Further studies on 100 the molecular basis of viral recognition using full-length ACE2 revealed that the SARS-CoV-101 2 RBD is recognized by the extracellular PD of ACE2 mainly through polar residues and that 102 two S protein trimers can simultaneously bind to an ACE2 homodimer [20] . The X-ray 103 crystallographic data on the complex structure of the SARS-CoV-2 RBD bound with ACE2 104 fully corroborated other evidence describing the residues in the SARS-CoV-2 RBD that are 105 critical for ACE2 binding, the majority of which are highly conserved or share similar side Glu 402 , and a water molecule to complete the tetrahedral geometry about the metal center. These residues compose the signature motif HEXXH + E (where X is any residue) that is This study was not supported financially by any grants. 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