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1.
Proteins ; 90(4): 982-992, 2022 04.
Article in English | MEDLINE | ID: covidwho-1557819

ABSTRACT

Recently, multifunctional fish peptides (FWPs) have gained a lot of attention because of their different biological activities. In the present study, three angiotensin-I converting enzyme (ACE-I) inhibitory peptides [Ala-Pro-Asp-Gly (APDG), Pro-Thr-Arg (PTR), and Ala-Asp (AD)] were isolated and characterized from ribbonfish protein hydrolysate (RFPH) and described their mechanism of action on ACE activity. As per the results, peptide PTR showed ≈ 2 and 2.5-fold higher enzyme inhibitory activity (IC50 = 0.643 ± 0.0011 µM) than APDG (IC50 = 1.061 ± 0.0127 µM) and AD (IC50 = 2.046 ± 0.0130 µM). Based on experimental evidence, peptides were used for in silico analysis to check the inhibitory activity of the main protease (PDB: 7BQY) of SARS-CoV-2. The results of the study reveal that PTR (-46.16 kcal/mol) showed higher binding affinity than APDG (-36.80 kcal/mol) and AD (-30.24 kcal/mol) compared with remdesivir (-30.64 kcal/mol). Additionally, physicochemical characteristics of all the isolated peptides exhibited appropriate pharmacological properties and were found to be nontoxic. Besides, 20 ns molecular dynamic simulation study confirms the rigid nature, fewer confirmation variations, and binding stiffness of the peptide PTR with the main protease of SARS-CoV-2. Therefore, the present study strongly suggested that PTR is the perfect substrate for inhibiting the main protease of SARS-CoV-2 through the in silico study, and this potential drug candidate may promote the researcher for future wet lab experiments.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/chemistry , COVID-19/drug therapy , Fish Proteins/chemistry , Peptides/chemistry , SARS-CoV-2/drug effects , Viral Protease Inhibitors/chemistry , Amino Acid Sequence , Binding Sites , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Hydrolysates/chemistry , Thermodynamics , Viral Protease Inhibitors/pharmacology
2.
Int J Mol Sci ; 22(21)2021 Oct 28.
Article in English | MEDLINE | ID: covidwho-1488613

ABSTRACT

The renin-angiotensin system (RAS) is a key regulator of blood pressure and hypertension. Angiotensin-converting enzyme 2 (ACE2) and angiotensin-converting enzyme I (ACE) are two main components of the RAS that play a major role in blood pressure homeostasis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses ACE2 as a receptor to enter cells. Despite some controversies, numerous studies have reported a significant association between the use of ACE inhibitors and reduced risk of COVID-19. In our previous studies, we produced and identified peptide sequences present in whey hydrolysates exhibiting high ACE inhibitory activity. Therefore, the aim of this work is to obtain an improved understanding of the function of these natural peptides as RAS inhibitors and investigate their potential therapeutic role in the COVID-19 pandemic. The molecular interactions between peptides IPP, LIVTQ, IIAE, LVYPFP, and human ACE2 were assessed by employing a molecular docking approach. The results show that natural whey-derived peptides have a dual inhibitory action against both ACE and ACE2. This dual activity distinguishes these ACE inhibitory peptides from synthetic drugs, such as Captopril and Lisinopril which were not shown to inhibit ACE2 activity, and may represent a potential strategy in the treatment of COVID-19.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19 , Peptides/chemistry , Peptides/pharmacology , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme Inhibitors/chemistry , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Humans , Molecular Docking Simulation , Peptides/metabolism , Peptidyl-Dipeptidase A/chemistry , Renin-Angiotensin System/drug effects , Whey Proteins/chemistry
3.
J Mol Model ; 27(7): 206, 2021 Jun 24.
Article in English | MEDLINE | ID: covidwho-1384472

ABSTRACT

The interaction between SARS-CoV-2 Spike protein and angiotensin-converting enzyme 2 (ACE2) is essential to viral attachment and the subsequent fusion process. Interfering with this event represents an attractive avenue for the development of therapeutics and vaccine development. Here, a hybrid approach of ligand- and structure-based virtual screening techniques were employed to disclose similar analogues of a reported antiviral phytochemical, glycyrrhizin, targeting the blockade of ACE2 interaction with the SARS-CoV-2 Spike. A ligand-based similarity search using a stringent cut-off revealed 40 FDA-approved compounds in DrugBank. These filtered hits were screened against ACE2 using a blind docking approach to determine the natural binding tendency of the compounds with ACE2. Three compounds, deslanoside, digitoxin, and digoxin, were reported to show strong binding with ACE2. These compounds bind at the H1-H2 binding pocket, in a manner similar to that of glycyrrhizin which was used as a control. To achieve consistency in the docking results, docking calculations were performed via two sets of docking software that predicted binding energy as ACE2-Deslanoside (AutoDock, -10.3 kcal/mol and DockThor, -9.53 kcal/mol), ACE2-Digitoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.84 kcal/mol), and ACE2-Digoxin (AutoDock, -10.6 kcal/mol and DockThor, -8.81 kcal/mol). The docking results were validated by running molecular simulations in aqueous solution that demonstrated the stability of ACE2 with no major conformational changes in the ligand original binding mode (~ 2 Å average RMSD). Binding interactions remained quite stable with an increased potential for getting stronger as the simulation proceeded. MMGB/PBSA binding free energies were also estimated and these supported the high stability of the complexes compared to the control (~ -50 kcal/mol net MMGB/PBSA binding energy versus ~ -30 kcal/mol). Collectively, the data demonstrated that the compounds shortlisted in this study might be subjected to experimental evaluation to uncover their real blockade capacity of SARS-CoV-2 host ACE2 receptor.


Subject(s)
Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antiviral Agents/pharmacology , COVID-19/drug therapy , Glycyrrhizic Acid/pharmacology , Receptors, Virus/antagonists & inhibitors , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/metabolism , Virus Internalization/drug effects , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme Inhibitors/chemistry , Animals , Antiviral Agents/chemistry , Binding Sites , COVID-19/enzymology , COVID-19/virology , Drug Discovery , Drug Repositioning , Glycyrrhizic Acid/analogs & derivatives , Glycyrrhizic Acid/chemistry , Host-Pathogen Interactions , Humans , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Conformation , Receptors, Virus/chemistry , Receptors, Virus/metabolism , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Structure-Activity Relationship
4.
Bioorg Chem ; 116: 105272, 2021 11.
Article in English | MEDLINE | ID: covidwho-1370451

ABSTRACT

Hypertension has been recognized as one of the most frequent comorbidities and risk factors for the seriousness and adverse consequences in COVID-19 patients. 3,4-dihydropyrimidin-2(1H) ones have attracted researchers to be synthesized via Beginilli reaction and evaluate their antihypertensive activities as bioisosteres of nifedipine a well-known calcium channel blocker. In this study, we report synthesis of some bioisosteres of pyrimidines as novel CCBs with potential ACE2 inhibitory effect as antihypertensive agents with protective effect against COVID-19 infection by suppression of ACE2 binding to SARS-CoV-2 Spike RBD. All compounds were evaluated for their antihypertensive and calcium channel blocking activities using nifedipine as a reference standard. Furthermore, they were screened for their ACE2 inhibition potential in addition to their anti-inflammatory effects on LPS-stimulated THP-1 cells. Most of the tested compounds exhibited significant antihypertensive activity, where compounds 7a, 8a and 9a exhibited the highest activity compared to nifedipine. Moreover, compounds 4a,b, 5a,b, 7a,b, 8a,c and 9a showed promising ACE2:SARS-CoV-2 Spike RBD inhibitory effect. Finally, compounds 5a, 7b and 9a exerted a promising anti-inflammatory effect by inhibition of CRP and IL-6 production. Ultimately, compound 9a may be a promising antihypertensive candidate with anti-inflammatory and potential efficacy against COVID-19 via ACE2 receptor inhibition.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/pharmacology , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Antihypertensive Agents/pharmacology , Antiviral Agents/pharmacology , COVID-19/drug therapy , Calcium Channel Blockers/pharmacology , Angiotensin-Converting Enzyme Inhibitors/chemical synthesis , Angiotensin-Converting Enzyme Inhibitors/chemistry , Anti-Inflammatory Agents, Non-Steroidal/chemical synthesis , Anti-Inflammatory Agents, Non-Steroidal/chemistry , Antihypertensive Agents/chemical synthesis , Antihypertensive Agents/chemistry , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Calcium Channel Blockers/chemical synthesis , Calcium Channel Blockers/chemistry , Humans , SARS-CoV-2/drug effects
5.
J Food Biochem ; 44(12): e13494, 2020 12.
Article in English | MEDLINE | ID: covidwho-1066710

ABSTRACT

Bioactive peptides produced from natural sources are considered as strategic target for drug discovery. Hyperglycemia caused protein glycation alters the structure of many tissues that impairs their functions and lead complications diseases in human body. This study investigated the bioactive peptides produced from red and brown Lens culinaris that might inhibit protein glycation to prevent diabetic complications. In this study, red and brown Lens culinaris protein hydrolysates were prepared by tryptic digestion, using an enzyme/substrate ratio of 1:20 (g/g), at 37°C, 12 hr then peptide fractions <3 kDa were filtered by using ultrafiltration membranes. Protective ability against protein glycation, DPPH radical scavenging, and anti-proliferative activities (on HepG2, MCF-7, and PC3 cell lines) of peptide fractions were assayed in vitro. Results showed that glycation was inhibited by peptides from 28.1% to 68.3% in different test model. PC3 cell line was more sensitive to the peptides which showed strong anticancer activity with lower IC50 (0.96 mg/ml). Peptide fractions were sequenced by HPLC-MS-MS. Twenty eight novel peptides sequences was identified. In silico study, two peptides could be developed as a potential bioactive peptides exhibited antiglycation, antioxidant, and antiproliferative activities. PRACTICAL APPLICATIONS: Peptides are becoming an emerging source of medications with the development of new technologies. We have selected Lens Culinaris as one of the rich sources of proteins to explore novel bioactive peptides encapsulated in its seeds. Peptides fractions demonstrated protective ability against protein glycation, strong antioxidant potential, and promising antiproliferative activity. We have identified 28 novel peptides and molecular docking study revealed that some peptides showed strong binding potential to insulin receptor and ACE. Thus, these peptides might be used to manage diabetes complication as well as COVID-19 disease due to their interaction with ACE. However, those peptides needs to be further studied as a potential new drug.


Subject(s)
Antioxidants/chemistry , Lens Plant/chemistry , Peptides/chemistry , Plant Proteins/chemistry , Angiotensin-Converting Enzyme Inhibitors/chemistry , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antioxidants/pharmacology , Cell Line , Cell Proliferation/drug effects , Chromatography, High Pressure Liquid , Glycosylation/drug effects , Humans , Mass Spectrometry , Molecular Docking Simulation , Peptides/pharmacology , Plant Proteins/pharmacology , Protein Hydrolysates/chemistry , Protein Hydrolysates/pharmacology , Seeds/chemistry
6.
Phys Chem Chem Phys ; 22(48): 28434-28439, 2020 Dec 23.
Article in English | MEDLINE | ID: covidwho-970867

ABSTRACT

The sudden arrival of novel coronavirus disease 2019 (COVID-19) has stunned the world with its rapidly spreading virus. Remdesivir, a broad spectrum anti-viral drug, is now under in vitro and in vivo investigation as a potential agent against SARS-CoV-2. However, the results of this therapy were recently equivocal due to no significant benefit in the clinical trial. Herein, combination molecular docking with dissipative particle dynamics (DPD) simulations is used to theoretically design angiotensin-converting enzyme inhibitor (ACEI)-containing remdesivir-loaded PLGA nanoparticles (NPs) for anti-SARS-CoV-2 therapy. Based on the therapeutic and lung protective effect of ACEI, the classical lisinopril molecule covalently grafted onto PLGA (L-PLGA) has been used to encapsulate remdesivir. A binding model is used to confirm the interactions between lisinopril and ACE on the surface of cells, as well as remdesivir and its intracellular targeting protein (RNA-dependent RNA polymerase (RdRp)). Furthermore, DPD simulations are applied to study the nano-aggregation of drug-free L-PLGA, and remdesivir loaded in L-PLGA. The lisinopril molecules were directly demonstrated to be on the surface of L-PLGA NPs. Molecular docking proved that hydrogen bonding was decisive for the encapsulation of remdesivir. With an increase in concentration, remdesivir loaded L-PLGA formed spherical NPs, and then underwent precipitation. Similar to the above conditions, high remdesivir loading was also observed to cause precipitation formation. Thus, the optimized remdesivir NPs in our study give insights into a rational platform for formulation design against this global pandemic.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Angiotensin-Converting Enzyme Inhibitors/metabolism , Antiviral Agents/metabolism , Drug Carriers/chemistry , Lisinopril/metabolism , Nanoparticles/chemistry , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Alanine/chemistry , Alanine/metabolism , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Drug Synergism , Humans , Lisinopril/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Polylactic Acid-Polyglycolic Acid Copolymer/chemistry , Protein Binding , SARS-CoV-2/drug effects
7.
Molecules ; 25(23)2020 Nov 28.
Article in English | MEDLINE | ID: covidwho-948909

ABSTRACT

AIMS: Angiotensin-converting enzyme 2 (ACE2) plays an important role in the entry of coronaviruses into host cells. The current paper described how carnosine, a naturally occurring supplement, can be an effective drug candidate for coronavirus disease (COVID-19) on the basis of molecular docking and modeling to host ACE2 cocrystallized with nCoV spike protein. METHODS: First, the starting point was ACE2 inhibitors and their structure-activity relationship (SAR). Next, chemical similarity (or diversity) and PubMed searches made it possible to repurpose and assess approved or experimental drugs for COVID-19. Parallel, at all stages, the authors performed bioactivity scoring to assess potential repurposed inhibitors at ACE2. Finally, investigators performed molecular docking and modeling of the identified drug candidate to host ACE2 with nCoV spike protein. RESULTS: Carnosine emerged as the best-known drug candidate to match ACE2 inhibitor structure. Preliminary docking was more optimal to ACE2 than the known typical angiotensin-converting enzyme 1 (ACE1) inhibitor (enalapril) and quite comparable to known or presumed ACE2 inhibitors. Viral spike protein elements binding to ACE2 were retained in the best carnosine pose in SwissDock at 1.75 Angstroms. Out of the three main areas of attachment expected to the protein-protein structure, carnosine bound with higher affinity to two compared to the known ACE2 active site. LibDock score was 92.40 for site 3, 90.88 for site 1, and inside the active site 85.49. CONCLUSION: Carnosine has promising inhibitory interactions with host ACE2 and nCoV spike protein and hence could offer a potential mitigating effect against the current COVID-19 pandemic.


Subject(s)
Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/pharmacology , Biological Availability , COVID-19/drug therapy , Carnosine/chemistry , Carnosine/metabolism , Carnosine/pharmacology , Catalytic Domain , Crystallization , Humans , Molecular Docking Simulation , Protein Interaction Domains and Motifs/drug effects , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Structure-Activity Relationship
8.
Int J Mol Sci ; 21(21)2020 Nov 07.
Article in English | MEDLINE | ID: covidwho-937518

ABSTRACT

Growing interest in hypertension-one of the main factors characterizing the cardiometabolic syndrome (CMS)-and anti-hypertensive drugs raised from the emergence of a new coronavirus, SARS-CoV-2, responsible for the COVID19 pandemic. The virus SARS-CoV-2 employs the Angiotensin-converting enzyme 2 (ACE2), a component of the RAAS (Renin-Angiotensin-Aldosterone System) system, as a receptor for entry into the cells. Several classes of synthetic drugs are available for hypertension, rarely associated with severe or mild adverse effects. New natural compounds, such as peptides, might be useful to treat some hypertensive patients. The main feature of ACE inhibitory peptides is the location of the hydrophobic residue, usually Proline, at the C-terminus. Some already known bioactive peptides derived from marine resources have potential ACE inhibitory activity and can be considered therapeutic agents to treat hypertension. Peptides isolated from marine vertebrates, invertebrates, seaweeds, or sea microorganisms displayed important biological activities to treat hypertensive patients. Here, we reviewed the anti-hypertensive activities of bioactive molecules isolated/extracted from marine organisms and discussed the associated molecular mechanisms involved. We also examined ACE2 modulation in sight of SARS2-Cov infection prevention.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antihypertensive Agents/pharmacology , Antiviral Agents/chemistry , Hypertension/drug therapy , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme Inhibitors/chemistry , Angiotensin-Converting Enzyme Inhibitors/therapeutic use , Animals , Antihypertensive Agents/therapeutic use , Antiviral Agents/pharmacology , COVID-19/prevention & control , Fishes/metabolism , Halobacteriales/chemistry , Humans , Molecular Docking Simulation , Oncorhynchus keta/metabolism , Peptides/chemistry , Peptides/pharmacology , SARS-CoV-2/drug effects , Sea Cucumbers/chemistry , Undaria/chemistry
9.
J Agric Food Chem ; 68(47): 13982-13989, 2020 Nov 25.
Article in English | MEDLINE | ID: covidwho-920571

ABSTRACT

Angiotensin-converting enzyme 2 (ACE2) is a host receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Inhibiting the interaction between the envelope spike glycoproteins (S-proteins) of SARS-CoV-2 and ACE2 is a potential antiviral therapeutic approach, but little is known about how dietary compounds interact with ACE2. The objective of this study was to determine if flavonoids and other polyphenols with B-ring 3',4'-hydroxylation inhibit recombinant human (rh)ACE2 activity. rhACE2 activity was assessed with the fluorogenic substrate Mca-APK(Dnp). Polyphenols reduced rhACE2 activity by 15-66% at 10 µM. Rutin, quercetin-3-O-glucoside, tamarixetin, and 3,4-dihydroxyphenylacetic acid inhibited rhACE2 activity by 42-48%. Quercetin was the most potent rhACE2 inhibitor among the polyphenols tested, with an IC50 of 4.48 µM. Thus, quercetin, its metabolites, and polyphenols with 3',4'-hydroxylation inhibited rhACE2 activity at physiologically relevant concentrations in vitro.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/chemistry , Peptidyl-Dipeptidase A/chemistry , Polyphenols/chemistry , Quercetin/chemistry , Angiotensin-Converting Enzyme 2 , Enzyme Assays , Humans , Kinetics , Recombinant Proteins/chemistry , Temperature
10.
Molecules ; 25(17)2020 Sep 01.
Article in English | MEDLINE | ID: covidwho-742825

ABSTRACT

Over the years, coronaviruses (CoV) have posed a severe public health threat, causing an increase in mortality and morbidity rates throughout the world. The recent outbreak of a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the current Coronavirus Disease 2019 (COVID-19) pandemic that affected more than 215 countries with over 23 million cases and 800,000 deaths as of today. The situation is critical, especially with the absence of specific medicines or vaccines; hence, efforts toward the development of anti-COVID-19 medicines are being intensively undertaken. One of the potential therapeutic targets of anti-COVID-19 drugs is the angiotensin-converting enzyme 2 (ACE2). ACE2 was identified as a key functional receptor for CoV associated with COVID-19. ACE2, which is located on the surface of the host cells, binds effectively to the spike protein of CoV, thus enabling the virus to infect the epithelial cells of the host. Previous studies showed that certain flavonoids exhibit angiotensin-converting enzyme inhibition activity, which plays a crucial role in the regulation of arterial blood pressure. Thus, it is being postulated that these flavonoids might also interact with ACE2. This postulation might be of interest because these compounds also show antiviral activity in vitro. This article summarizes the natural flavonoids with potential efficacy against COVID-19 through ACE2 receptor inhibition.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Betacoronavirus/physiology , Biological Products/pharmacology , Coronavirus Infections/virology , Flavonoids/pharmacology , Pneumonia, Viral/virology , Angiotensin-Converting Enzyme 2 , Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/chemistry , Biological Products/chemistry , COVID-19 , Coronavirus Infections/drug therapy , Coronavirus Infections/epidemiology , Disease Susceptibility , Flavonoids/chemistry , Humans , Life Cycle Stages , Models, Molecular , Pandemics , Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology , Population Surveillance , SARS-CoV-2 , Structure-Activity Relationship
11.
Endocr Metab Immune Disord Drug Targets ; 20(6): 807-811, 2020.
Article in English | MEDLINE | ID: covidwho-689779
12.
J Mol Graph Model ; 100: 107697, 2020 11.
Article in English | MEDLINE | ID: covidwho-665694

ABSTRACT

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.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/chemistry , Betacoronavirus/chemistry , Peptidyl-Dipeptidase A/chemistry , Small Molecule Libraries/chemistry , Amino Acid Motifs , Angiotensin-Converting Enzyme 2 , Betacoronavirus/enzymology , COVID-19 , Carbazoles/chemistry , Catalytic Domain , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Drug Repositioning , Dyphylline/analogs & derivatives , Dyphylline/chemistry , Host-Pathogen Interactions , Humans , Hydroxamic Acids/chemistry , Ligands , Molecular Docking Simulation , Pandemics , Paromomycin/analogs & derivatives , Paromomycin/chemistry , Pemetrexed/chemistry , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , SARS-CoV-2 , Structure-Activity Relationship , Thermodynamics
13.
ChemMedChem ; 15(18): 1682-1690, 2020 09 16.
Article in English | MEDLINE | ID: covidwho-641524

ABSTRACT

Angiotensin converting enzyme 2 (ACE2) is the human receptor that interacts with the spike protein of coronaviruses, including the one that produced the 2020 coronavirus pandemic (COVID-19). Thus, ACE2 is a potential target for drugs that disrupt the interaction of human cells with SARS-CoV-2 to abolish infection. There is also interest in drugs that inhibit or activate ACE2, that is, for cardiovascular disorders or colitis. Compounds binding at alternative sites could allosterically affect the interaction with the spike protein. Herein, we review biochemical, chemical biology, and structural information on ACE2, including the recent cryoEM structures of full-length ACE2. We conclude that ACE2 is very dynamic and that allosteric drugs could be developed to target ACE2. At the time of the 2020 pandemic, we suggest that available ACE2 inhibitors or activators in advanced development should be tested for their ability to allosterically displace the interaction between ACE2 and the spike protein.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/metabolism , Betacoronavirus/chemistry , Peptidyl-Dipeptidase A/metabolism , Receptors, Virus/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Allosteric Regulation , Angiotensin-Converting Enzyme 2 , Angiotensin-Converting Enzyme Inhibitors/chemistry , Catalytic Domain , Humans , Peptidyl-Dipeptidase A/chemistry , Protein Binding , Protein Domains , Receptors, Virus/antagonists & inhibitors , Receptors, Virus/chemistry , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry
14.
Bioinformatics ; 36(14): 4227-4230, 2020 08 15.
Article in English | MEDLINE | ID: covidwho-260277

ABSTRACT

SUMMARY: iBioProVis is an interactive tool for visual analysis of the compound bioactivity space in the context of target proteins, drugs and drug candidate compounds. iBioProVis tool takes target protein identifiers and, optionally, compound SMILES as input, and uses the state-of-the-art non-linear dimensionality reduction method t-Distributed Stochastic Neighbor Embedding (t-SNE) to plot the distribution of compounds embedded in a 2D map, based on the similarity of structural properties of compounds and in the context of compounds' cognate targets. Similar compounds, which are embedded to proximate points on the 2D map, may bind the same or similar target proteins. Thus, iBioProVis can be used to easily observe the structural distribution of one or two target proteins' known ligands on the 2D compound space, and to infer new binders to the same protein, or to infer new potential target(s) for a compound of interest, based on this distribution. Principal component analysis (PCA) projection of the input compounds is also provided, Hence the user can interactively observe the same compound or a group of selected compounds which is projected by both PCA and embedded by t-SNE. iBioProVis also provides detailed information about drugs and drug candidate compounds through cross-references to widely used and well-known databases, in the form of linked table views. Two use-case studies were demonstrated, one being on angiotensin-converting enzyme 2 (ACE2) protein which is Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike protein receptor. ACE2 binding compounds and seven antiviral drugs were closely embedded in which two of them have been under clinical trial for Coronavirus disease 19 (COVID-19). AVAILABILITY AND IMPLEMENTATION: iBioProVis and its carefully filtered dataset are available at https://ibpv.kansil.org/ for public use. CONTACT: vatalay@metu.edu.tr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Models, Molecular , Peptidyl-Dipeptidase A/chemistry , Software , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2 , Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/chemistry , Betacoronavirus , COVID-19 , Coronavirus Infections , Humans , Internet , Pandemics , Pneumonia, Viral , Principal Component Analysis , Receptors, Adrenergic, beta-2/chemistry , Receptors, Adrenergic, beta-3/chemistry , SARS-CoV-2 , User-Computer Interface
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