Structure-Based Development of SARS-CoV-2 Spike Interactors. 2022

Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
Institute of Biostructures and Bioimaging, IBB, CNR, 80131 Napoli, Italy.

Coronaviruses, including SARS-CoV-2 (the etiological agent of the current COVID-19 pandemic), rely on the surface spike glycoprotein to access the host cells, mainly through the interaction of their receptor-binding domain (RBD) with the human angiotensin-converting enzyme 2 (ACE2). Therefore, molecular entities able to interfere with the binding of the SARS-CoV-2 spike protein to ACE2 have great potential to inhibit viral entry. Starting from the available structural data on the interaction between SARS-CoV-2 spike protein and the host ACE2 receptor, we engineered a set of soluble and stable spike interactors, here denoted as S-plugs. Starting from the prototype S-plug, we adopted a computational approach by combining stability prediction, associated to single-point mutations, with molecular dynamics to enhance both S-plug thermostability and binding affinity to the spike protein. The best developed molecule, S-plug3, possesses a highly stable α-helical con-formation (with melting temperature Tm of 54 °C) and can interact with the spike RBD and S1 domains with similar low nanomolar affinities. Importantly, S-plug3 exposes the spike RBD to almost the same interface as the human ACE2 receptor, aimed at the recognition of all ACE2-accessing coronaviruses. Consistently, S-plug3 preserves a low nanomolar dissociation constant with the delta B.1.617.2 variant of SARS-CoV-2 spike protein (KD = 29.2 ± 0.6 nM). Taken together, we provide valid starting data for the development of therapeutical and diagnostic tools against coronaviruses accessing through ACE2.

UI MeSH Term Description Entries
D007703 Peptidyl-Dipeptidase A A peptidyl-dipeptidase that catalyzes the release of a C-terminal dipeptide, oligopeptide-|-Xaa-Yaa, when Xaa is not Pro, and Yaa is neither Asp nor Glu. Thus, conversion of ANGIOTENSIN I to ANGIOTENSIN II, with increase in vasoconstrictor activity, but no action on angiotensin II. It is also able to inactivate BRADYKININ, a potent vasodilator; and has a glycosidase activity which releases GPI-anchored proteins from the membrane by cleaving the mannose linkage in the GPI moiety. (From https://www.uniprot.org April 15, 2020). ACE1 Angiotensin-Converting Enzyme 1,ACE1 Protein,Angiotensin Converting Enzyme,Angiotensin Converting Enzyme 1,Antigens, CD143,CD143 Antigens,Dipeptidyl Carboxypeptidase I,Kininase II,Peptidase P,Angiotensin I-Converting Enzyme,Carboxycathepsin,Dipeptidyl Peptidase A,Kininase A,ACE1 Angiotensin Converting Enzyme 1,Angiotensin I Converting Enzyme,Carboxypeptidase I, Dipeptidyl,Peptidyl Dipeptidase A
D008562 Membrane Glycoproteins Glycoproteins found on the membrane or surface of cells. Cell Surface Glycoproteins,Surface Glycoproteins,Cell Surface Glycoprotein,Membrane Glycoprotein,Surface Glycoprotein,Glycoprotein, Cell Surface,Glycoprotein, Membrane,Glycoprotein, Surface,Glycoproteins, Cell Surface,Glycoproteins, Membrane,Glycoproteins, Surface,Surface Glycoprotein, Cell,Surface Glycoproteins, Cell
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000085962 Angiotensin-Converting Enzyme 2 A transmembrane glycoprotein with an extracellular catalytic domain which functions as a carboxypeptidase. It cleaves a single C-terminal residue from a distinct range of substrates. The catalytic efficiency is 400-fold higher with ANGIOTENSIN II as a substrate than with ANGIOTENSIN I. Angiotensin-converting enzyme 2 is also is a functional receptor for the spike glycoprotein (SPIKE PROTEIN, CORONAVIRUS) of the CORONAVIRUSES SARS-COV, SARS-COV2, and HCOV-NL63. ACE-Related Carboxypeptidase,ACE2 Angiotensin-Converting Enzyme Protein 2,ACE2 Enzyme,ACE2 Protein,Angiotensin Converting Enzyme 2,Angiotensin-Converting Enzyme-Related Carboxypeptidase,ACE Related Carboxypeptidase,ACE2 Angiotensin Converting Enzyme Protein 2,Angiotensin Converting Enzyme Related Carboxypeptidase,Carboxypeptidase, ACE-Related,Carboxypeptidase, Angiotensin-Converting Enzyme-Related
D000086382 COVID-19 A viral disorder generally characterized by high FEVER; COUGH; DYSPNEA; CHILLS; PERSISTENT TREMOR; MUSCLE PAIN; HEADACHE; SORE THROAT; a new loss of taste and/or smell (see AGEUSIA and ANOSMIA) and other symptoms of a VIRAL PNEUMONIA. In severe cases, a myriad of coagulopathy associated symptoms often correlating with COVID-19 severity is seen (e.g., BLOOD COAGULATION; THROMBOSIS; ACUTE RESPIRATORY DISTRESS SYNDROME; SEIZURES; HEART ATTACK; STROKE; multiple CEREBRAL INFARCTIONS; KIDNEY FAILURE; catastrophic ANTIPHOSPHOLIPID ANTIBODY SYNDROME and/or DISSEMINATED INTRAVASCULAR COAGULATION). In younger patients, rare inflammatory syndromes are sometimes associated with COVID-19 (e.g., atypical KAWASAKI SYNDROME; TOXIC SHOCK SYNDROME; pediatric multisystem inflammatory disease; and CYTOKINE STORM SYNDROME). A coronavirus, SARS-CoV-2, in the genus BETACORONAVIRUS is the causative agent. 2019 Novel Coronavirus Disease,2019 Novel Coronavirus Infection,2019-nCoV Disease,2019-nCoV Infection,COVID-19 Pandemic,COVID-19 Pandemics,COVID-19 Virus Disease,COVID-19 Virus Infection,Coronavirus Disease 2019,Coronavirus Disease-19,SARS Coronavirus 2 Infection,SARS-CoV-2 Infection,Severe Acute Respiratory Syndrome Coronavirus 2 Infection,COVID19,2019 nCoV Disease,2019 nCoV Infection,2019-nCoV Diseases,2019-nCoV Infections,COVID 19,COVID 19 Pandemic,COVID 19 Virus Disease,COVID 19 Virus Infection,COVID-19 Virus Diseases,COVID-19 Virus Infections,Coronavirus Disease 19,Disease 2019, Coronavirus,Disease, 2019-nCoV,Disease, COVID-19 Virus,Infection, 2019-nCoV,Infection, COVID-19 Virus,Infection, SARS-CoV-2,Pandemic, COVID-19,SARS CoV 2 Infection,SARS-CoV-2 Infections,Virus Disease, COVID-19,Virus Infection, COVID-19
D000086402 SARS-CoV-2 A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis. 2019 Novel Coronavirus,COVID-19 Virus,COVID19 Virus,Coronavirus Disease 2019 Virus,SARS Coronavirus 2,SARS-CoV-2 Virus,Severe Acute Respiratory Syndrome Coronavirus 2,Wuhan Coronavirus,Wuhan Seafood Market Pneumonia Virus,2019-nCoV,2019 Novel Coronaviruses,COVID 19 Virus,COVID-19 Viruses,COVID19 Viruses,Coronavirus 2, SARS,Coronavirus, 2019 Novel,Coronavirus, Wuhan,Novel Coronavirus, 2019,SARS CoV 2 Virus,SARS-CoV-2 Viruses,Virus, COVID-19,Virus, COVID19,Virus, SARS-CoV-2,Viruses, COVID19
D014759 Viral Envelope Proteins Integral membrane proteins that are incorporated into the VIRAL ENVELOPE. They are glycosylated during VIRAL ASSEMBLY. Envelope Proteins, Viral,Viral Envelope Glycoproteins,Viral Envelope Protein,Virus Envelope Protein,Virus Peplomer Proteins,Bovine Leukemia Virus Glycoprotein gp51,Hepatitis Virus (MHV) Glycoprotein E2,LaCrosse Virus Envelope Glycoprotein G1,Simian Sarcoma Virus Glycoprotein 70,Viral Envelope Glycoprotein gPr90 (Murine Leukemia Virus),Viral Envelope Glycoprotein gp55 (Friend Virus),Viral Envelope Proteins E1,Viral Envelope Proteins E2,Viral Envelope Proteins gp52,Viral Envelope Proteins gp70,Virus Envelope Proteins,Envelope Glycoproteins, Viral,Envelope Protein, Viral,Envelope Protein, Virus,Envelope Proteins, Virus,Glycoproteins, Viral Envelope,Peplomer Proteins, Virus,Protein, Viral Envelope,Protein, Virus Envelope,Proteins, Viral Envelope,Proteins, Virus Envelope,Proteins, Virus Peplomer
D058873 Pandemics Epidemics of infectious disease that have spread to many countries, often more than one continent, and usually affecting a large number of people. Pandemic
D064370 Spike Glycoprotein, Coronavirus A class I viral fusion protein that forms the characteristic spikes, or peplomers, found on the viral surface that mediate virus attachment, fusion, and entry into the host cell. During virus maturation, it is cleaved into two subunits: S1, which binds to receptors in the host cell, and S2, which mediates membrane fusion. Spike Glycoprotein, Bovine Coronavirus,Spike Glycoproteins, Coronavirus,E2 Spike Glycoprotein, Coronavirus,Glycoprotein S, Coronavirus,Spike Glycoprotein S1, Coronavirus,Spike Protein S2, Coronavirus,Spike Protein, Coronavirus,Coronavirus Spike Glycoprotein,Coronavirus Spike Protein

Related Publications

Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
October 2021, Current opinion in virology,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
January 2020, Computational and structural biotechnology journal,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
January 2022, Current topics in medicinal chemistry,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
January 2020, Frontiers in cellular and infection microbiology,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
April 2021, Cellular and molecular bioengineering,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
March 2022, Cell reports,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
December 2022, bioRxiv : the preprint server for biology,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
April 2020, Cell,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
December 2020, Cell,
Flavia Squeglia, and Maria Romano, and Luciana Esposito, and Giovanni Barra, and Pietro Campiglia, and Marina Sala, and Maria Carmina Scala, and Alessia Ruggiero, and Rita Berisio
July 2023, Nature,
Copied contents to your clipboard!