Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 35
Filter
1.
Molecules ; 27(7)2022 Mar 31.
Article in English | MEDLINE | ID: covidwho-1785839

ABSTRACT

Respiratory syncytial virus infection (RSVI) is an acute medical and social problem in many countries globally. Infection is most dangerous for infants under one year old and the elderly. Despite its epidemiological relevance, only two drugs are registered for clinical use against RSVI: ribavirin (approved in a limited number of countries due to side effects) and palivizumab (Synagis), which is intended only for the prevention, but not the treatment, of infection. Currently, various research groups are searching for new drugs against RSV, with three main areas of research: small molecules, polymeric drugs (proteins and peptides), and plant extracts. This review is devoted to currently developed protein and peptide anti-RSV drugs.


Subject(s)
Respiratory Syncytial Virus Infections , Respiratory Tract Infections , Aged , Antiviral Agents/therapeutic use , Humans , Infant , Palivizumab/therapeutic use , Peptides/pharmacology , Peptides/therapeutic use , Respiratory Syncytial Virus Infections/drug therapy , Respiratory Tract Infections/drug therapy
2.
Bioengineered ; 13(4): 9435-9454, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1778851

ABSTRACT

Betacoronaviruses (ß-CoVs) have caused major viral outbreaks in the last two decades in the world. The mutation and recombination abilities in ß-CoVs resulted in zoonotic diseases in humans. Proteins responsible for viral attachment and replication are highly conserved in ß-CoVs. These conserved proteins have been extensively studied as targets for preventing infection and the spread of ß-CoVs. Peptides are among the most promising candidates for developing vaccines and therapeutics against viral pathogens. The immunostimulatory and viral inhibitory potential of natural and synthetic peptides has been extensively studied since the SARS-CoV outbreak. Food-derived peptides demonstrating high antiviral activity can be used to develop effective therapeutics against ß-CoVs. Specificity, tolerability, and customizability of peptides can be explored to develop potent drugs against ß-CoVs. However, the proteolytic susceptibility and low bioavailability of peptides pose challenges for the development of therapeutics. This review illustrates the potential role of peptides in eliciting an adaptive immune response and inhibiting different stages of the ß-CoV life cycle. Further, the challenges and future directions associated with developing peptide-based therapeutics and vaccines against existing and future ß-CoV pathogens have been discussed.


Subject(s)
Coronavirus Infections , Vaccines , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Coronavirus Infections/drug therapy , Coronavirus Infections/prevention & control , Humans , Mutation , Peptides/genetics , Peptides/therapeutic use , Vaccines/therapeutic use
3.
Perm J ; 252021 12 14.
Article in English | MEDLINE | ID: covidwho-1766163

ABSTRACT

This case report describes a successful outcome involving a patient with severe COVID-19 viral pneumonia utilizing a novel therapeutic approach with the glycoprotein IIb/IIIa inhibitor, eptifibatide.


Subject(s)
COVID-19 , COVID-19/drug therapy , Eptifibatide , Humans , Peptides/therapeutic use , Platelet Aggregation Inhibitors/therapeutic use , Platelet Glycoprotein GPIIb-IIIa Complex
4.
Curr HIV Res ; 19(6): 465-475, 2021.
Article in English | MEDLINE | ID: covidwho-1688732

ABSTRACT

A number of different viral families have developed convergent methods to infect cells. Class I fusion proteins are commonly used by members of Arenaviridae, Coronaviridae, Filovirdae, Orthomyxoviridae, Paramyxoviridae, and Retroviridae. Class I viral fusion proteins are trimers that are involved in recognizing the cellular receptor, with a region that is responsible for fusing the viral and target cell membranes. During the fusion process, the fusion region folds into a six-helix bundle (6 HB) which approximates the two membranes leading to fusion. For Human Immunodeficiency Virus (HIV), the gp41 subunit is responsible for the formation of this 6 HB. The fusion inhibitor drug enfuvirtide, or T20, is the only US Food and Drug Administration and European Medicines Agency approved drug which targets this crucial step and has been widely used in combination regimens for the treatment of HIV since March 2003. In this review, we describe the current state of peptide-based fusion inhibitors in the treatment of HIV, and review how the field of HIV research is driving advances in the development of similar therapeutics in other viral systems, including the Severe Acute Respiratory Syndrome (SARS) coronaviruses.


Subject(s)
HIV Fusion Inhibitors , HIV Infections , Anti-Retroviral Agents/therapeutic use , HIV Envelope Protein gp41 , HIV Fusion Inhibitors/pharmacology , HIV Fusion Inhibitors/therapeutic use , HIV Infections/drug therapy , HIV Infections/prevention & control , Humans , Peptide Fragments , Peptides/pharmacology , Peptides/therapeutic use
5.
Chem Biol Interact ; 351: 109706, 2022 Jan 05.
Article in English | MEDLINE | ID: covidwho-1464614

ABSTRACT

The challenges and difficulties associated with conventional drug delivery systems have led to the emergence of novel, advanced targeted drug delivery systems. Therapeutic drug delivery of proteins and peptides to the lungs is complicated owing to the large size and polar characteristics of the latter. Nevertheless, the pulmonary route has attracted great interest today among formulation scientists, as it has evolved into one of the important targeted drug delivery platforms for the delivery of peptides, and related compounds effectively to the lungs, primarily for the management and treatment of chronic lung diseases. In this review, we have discussed and summarized the current scenario and recent developments in targeted delivery of proteins and peptide-based drugs to the lungs. Moreover, we have also highlighted the advantages of pulmonary drug delivery over conventional drug delivery approaches for peptide-based drugs, in terms of efficacy, retention time and other important pharmacokinetic parameters. The review also highlights the future perspectives and the impact of targeted drug delivery on peptide-based drugs in the coming decade.


Subject(s)
Drug Carriers/chemistry , Lung/metabolism , Peptides/administration & dosage , Proteins/administration & dosage , Administration, Inhalation , Animals , Drug Carriers/administration & dosage , Humans , Lung/drug effects , Lung Diseases/drug therapy , Nanoparticles/administration & dosage , Nanoparticles/chemistry , Peptides/therapeutic use , Proteins/therapeutic use
6.
J Immunol ; 207(10): 2521-2533, 2021 11 15.
Article in English | MEDLINE | ID: covidwho-1468558

ABSTRACT

Many patients with coronavirus disease 2019 in intensive care units suffer from cytokine storm. Although anti-inflammatory therapies are available to treat the problem, very often, these treatments cause immunosuppression. Because angiotensin-converting enzyme 2 (ACE2) on host cells serves as the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), to delineate a SARS-CoV-2-specific anti-inflammatory molecule, we designed a hexapeptide corresponding to the spike S1-interacting domain of ACE2 receptor (SPIDAR) that inhibited the expression of proinflammatory molecules in human A549 lung cells induced by pseudotyped SARS-CoV-2, but not vesicular stomatitis virus. Accordingly, wild-type (wt), but not mutated (m), SPIDAR inhibited SARS-CoV-2 spike S1-induced activation of NF-κB and expression of IL-6 and IL-1ß in human lung cells. However, wtSPIDAR remained unable to reduce activation of NF-κB and expression of proinflammatory molecules in lungs cells induced by TNF-α, HIV-1 Tat, and viral dsRNA mimic polyinosinic-polycytidylic acid, indicating the specificity of the effect. The wtSPIDAR, but not mutated SPIDAR, also hindered the association between ACE2 and spike S1 of SARS-CoV-2 and inhibited the entry of pseudotyped SARS-CoV-2, but not vesicular stomatitis virus, into human ACE2-expressing human embryonic kidney 293 cells. Moreover, intranasal treatment with wtSPIDAR, but not mutated SPIDAR, inhibited lung activation of NF-κB, protected lungs, reduced fever, improved heart function, and enhanced locomotor activities in SARS-CoV-2 spike S1-intoxicated mice. Therefore, selective targeting of SARS-CoV-2 spike S1-to-ACE2 interaction by wtSPIDAR may be beneficial for coronavirus disease 2019.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Anti-Inflammatory Agents/therapeutic use , COVID-19/therapy , Lung/immunology , Peptides/metabolism , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/metabolism , A549 Cells , Angiotensin-Converting Enzyme 2/genetics , Animals , COVID-19/immunology , Cytokines/metabolism , Female , HEK293 Cells , Humans , Inflammation Mediators/metabolism , Locomotion , Male , Mice , Molecular Targeted Therapy , NF-kappa B/metabolism , Peptides/genetics , Peptides/therapeutic use , Signal Transduction , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
7.
ACS Appl Mater Interfaces ; 13(41): 48469-48477, 2021 Oct 20.
Article in English | MEDLINE | ID: covidwho-1461961

ABSTRACT

The COVID-19 pandemic highlighted the importance of developing surfaces and coatings with antiviral activity. Here, we present, for the first time, peptide-based assemblies that can kill viruses. The minimal inhibitory concentration (MIC) of the assemblies is in the range tens of micrograms per milliliter. This value is 2 orders of magnitude smaller than the MIC of metal nanoparticles. When applied on a surface, by drop casting, the peptide spherical assemblies adhere to the surface and form an antiviral coating against both RNA- and DNA-based viruses including coronavirus. Our results show that the coating reduced the number of T4 bacteriophages (DNA-based virus) by 3 log, compared with an untreated surface and 6 log, when compared with a stock solution. Importantly, we showed that this coating completely inactivated canine coronavirus (RNA-based virus). This peptide-based coating can be useful wherever sterile surfaces are needed to reduce the risk of viral transmission.


Subject(s)
Antiviral Agents/chemistry , Peptides/chemistry , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Bacteriophages/drug effects , COVID-19/drug therapy , COVID-19/virology , Coronavirus/drug effects , Coronavirus/isolation & purification , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Dihydroxyphenylalanine/chemistry , Dog Diseases/drug therapy , Dog Diseases/virology , Dogs , Humans , Metal Nanoparticles/chemistry , Peptides/pharmacology , Peptides/therapeutic use , SARS-CoV-2/isolation & purification , Virus Inactivation/drug effects
8.
Brief Bioinform ; 23(1)2022 01 17.
Article in English | MEDLINE | ID: covidwho-1447578

ABSTRACT

Coronavirus disease 2019 (COVID-19) has impacted public health as well as societal and economic well-being. In the last two decades, various prediction algorithms and tools have been developed for predicting antiviral peptides (AVPs). The current COVID-19 pandemic has underscored the need to develop more efficient and accurate machine learning (ML)-based prediction algorithms for the rapid identification of therapeutic peptides against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Several peptide-based ML approaches, including anti-coronavirus peptides (ACVPs), IL-6 inducing epitopes and other epitopes targeting SARS-CoV-2, have been implemented in COVID-19 therapeutics. Owing to the growing interest in the COVID-19 field, it is crucial to systematically compare the existing ML algorithms based on their performances. Accordingly, we comprehensively evaluated the state-of-the-art IL-6 and AVP predictors against coronaviruses in terms of core algorithms, feature encoding schemes, performance evaluation metrics and software usability. A comprehensive performance assessment was then conducted to evaluate the robustness and scalability of the existing predictors using well-constructed independent validation datasets. Additionally, we discussed the advantages and disadvantages of the existing methods, providing useful insights into the development of novel computational tools for characterizing and identifying epitopes or ACVPs. The insights gained from this review are anticipated to provide critical guidance to the scientific community in the rapid design and development of accurate and efficient next-generation in silico tools against SARS-CoV-2.


Subject(s)
Antiviral Agents/chemistry , COVID-19 , Machine Learning , Pandemics/prevention & control , Peptides/chemistry , SARS-CoV-2/metabolism , Software , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/epidemiology , Humans , Peptides/therapeutic use
9.
Front Immunol ; 12: 714177, 2021.
Article in English | MEDLINE | ID: covidwho-1444042

ABSTRACT

Sepsis continues to be a major cause of morbidity, mortality, and post-recovery disability in patients with a wide range of non-infectious and infectious inflammatory disorders, including COVID-19. The clinical onset of sepsis is often marked by the explosive release into the extracellular fluids of a multiplicity of host-derived cytokines and other pro-inflammatory hormone-like messengers from endogenous sources ("cytokine storm"). In patients with sepsis, therapies to counter the pro-inflammatory torrent, even when administered early, typically fall short. The major focus of our proposed essay is to promote pre-clinical studies with hCG (human chorionic gonadotropin) as a potential anti-inflammatory therapy for sepsis.


Subject(s)
Anti-Inflammatory Agents/therapeutic use , Chorionic Gonadotropin/therapeutic use , Peptides/therapeutic use , Sepsis/drug therapy , Animals , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/metabolism , Bacteria/metabolism , Chorionic Gonadotropin/chemistry , Chorionic Gonadotropin/metabolism , Cytokine Release Syndrome/drug therapy , Glycoproteins/chemistry , Glycoproteins/metabolism , Humans , Inflammation , Peptides/chemistry , Peptides/metabolism
10.
Protein J ; 40(6): 799-841, 2021 12.
Article in English | MEDLINE | ID: covidwho-1401053

ABSTRACT

As expected, several new variants of Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) emerged and have been detected around the world throughout this Coronavirus Disease of 2019 (COVID-19) pandemic. Currently, there is no specific developed drug against COVID-19 and the challenge of developing effective antiviral strategies based on natural agents with different mechanisms of action becomes an urgent need and requires identification of genetic differences among variants. Such data is used to improve therapeutics to combat SARS-CoV-2 variants. Nature is known to offer many biotherapeutics from animal venoms, algae and plant that have been historically used in traditional medicine. Among these bioresources, snake venom displays many bioactivities of interest such as antiviral, antiplatelet, antithrombotic, anti-inflammatory, antimicrobial and antitumoral. COVID-19 is a viral respiratory sickness due to SARS-CoV-2 which induces thrombotic disorders due to cytokine storm, platelet hyperactivation and endothelial dysfunction. This review aims to: (1) present an overview on the infection, the developed thrombo-inflammatory responses and mechanisms of induced thrombosis of COVID-19 compared to other similar pathogenesis; (2) underline the role of natural compounds such as anticoagulant, antiplatelet and thrombolytic agents; (3) investigate the management of coagulopathy related to COVID-19 and provide insight on therapeutic such as venom compounds. We also summarize the updated advances on antiviral proteins and peptides derived from snake venoms that could weaken coagulopathy characterizing COVID-19.


Subject(s)
COVID-19/drug therapy , Peptides/therapeutic use , SARS-CoV-2/drug effects , Snake Venoms/therapeutic use , Anticoagulants/therapeutic use , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , COVID-19/pathology , COVID-19/virology , Humans , Pandemics , Peptides/chemistry , SARS-CoV-2/pathogenicity , Snake Venoms/chemistry
11.
Molecules ; 26(2)2021 Jan 15.
Article in English | MEDLINE | ID: covidwho-1389464

ABSTRACT

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.


Subject(s)
Anti-Infective Agents/pharmacology , Antiviral Agents/pharmacology , Peptides/chemistry , Peptides/pharmacology , Peptides/therapeutic use , Amino Acids/chemistry , Anti-Infective Agents/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Computer Simulation , Cosmeceuticals/chemistry , Cosmeceuticals/therapeutic use , Dietary Supplements , Gene Transfer Techniques , Humans , Lactoferrin/chemistry , Lipid Bilayers , Nanostructures/administration & dosage , Nanostructures/chemistry , Peptides/administration & dosage , Stem Cells , Vaccines, Subunit/chemistry , Vaccines, Subunit/pharmacology
12.
Int J Mol Sci ; 22(17)2021 Aug 30.
Article in English | MEDLINE | ID: covidwho-1379977

ABSTRACT

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19). The virus enzyme, called 3CLpro or main protease (Mpro), is essential for viral replication, making it a most promising target for antiviral drug development. Recently, we adopted the drug repurposing as appropriate strategy to give fast response to global COVID-19 epidemic, by demonstrating that the zonulin octapeptide inhibitor AT1001 (Larazotide acetate) binds Mpro catalytic domain. Thus, in the present study we tried to investigate the antiviral activity of AT1001, along with five derivatives, by cell-based assays. Our results provide with the identification of AT1001 peptide molecular framework for lead optimization step to develop new generations of antiviral agents of SARS-CoV-2 with an improved biological activity, expanding the chance for success in clinical trials.


Subject(s)
Antiviral Agents/pharmacology , Molecular Docking Simulation , Oligopeptides/chemistry , Peptides/metabolism , SARS-CoV-2/drug effects , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/therapeutic use , Binding Sites , COVID-19/drug therapy , COVID-19/virology , Catalytic Domain , Cell Line , Cytomegalovirus/drug effects , Drug Repositioning , Herpesvirus 3, Human/drug effects , Humans , Molecular Dynamics Simulation , Peptides/chemical synthesis , Peptides/pharmacology , Peptides/therapeutic use , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Viral Matrix Proteins/chemistry , Viral Matrix Proteins/metabolism
13.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1367012

ABSTRACT

Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR.


Subject(s)
COVID-19/drug therapy , Epitopes/immunology , Peptides/immunology , Receptors, Antigen, T-Cell/immunology , SARS-CoV-2/immunology , Amino Acid Sequence/genetics , COVID-19/genetics , COVID-19/immunology , COVID-19/virology , Computer Simulation , Deep Learning , Epitopes/genetics , Humans , Peptides/genetics , Peptides/therapeutic use , Protein Binding/genetics , Receptors, Antigen, T-Cell/genetics , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Software
14.
Molecules ; 26(15)2021 Aug 03.
Article in English | MEDLINE | ID: covidwho-1346518

ABSTRACT

The market of biomolecules with therapeutic scopes, including peptides, is continuously expanding. The interest towards this class of pharmaceuticals is stimulated by the broad range of bioactivities that peptides can trigger in the human body. The main production methods to obtain peptides are enzymatic hydrolysis, microbial fermentation, recombinant approach and, especially, chemical synthesis. None of these methods, however, produce exclusively the target product. Other species represent impurities that, for safety and pharmaceutical quality reasons, must be removed. The remarkable production volumes of peptide mixtures have generated a strong interest towards the purification procedures, particularly due to their relevant impact on the manufacturing costs. The purification method of choice is mainly preparative liquid chromatography, because of its flexibility, which allows one to choose case-by-case the experimental conditions that most suitably fit that particular purification problem. Different modes of chromatography that can cover almost every separation case are reviewed in this article. Additionally, an outlook to a very recent continuous chromatographic process (namely Multicolumn Countercurrent Solvent Gradient Purification, MCSGP) and future perspectives regarding purification strategies will be considered at the end of this review.


Subject(s)
Peptides/chemistry , Peptides/chemical synthesis , Peptides/isolation & purification , Chromatography, Liquid , Humans , Peptides/therapeutic use
15.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1321558

ABSTRACT

Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the development of an accurate in silico method for the prediction of peptide antiviral activities is important. This study leverages advances in deep learning and cheminformatics to produce a novel sequence-based deep neural network classifier for the prediction of antiviral peptide activity. The method outperforms the existent best-in-class, with an external test accuracy of 93.9%, Matthews correlation coefficient of 0.87 and an Area Under the Curve of 0.93 on the dataset of experimentally validated peptide activities. This cutting-edge classifier is available as an online web server at https://research.timmons.eu/ennavia, facilitating in silico screening and design of peptide antiviral drugs by the wider research community.


Subject(s)
Antiviral Agents/chemistry , COVID-19/drug therapy , Peptides/chemistry , SARS-CoV-2/chemistry , Algorithms , Amino Acid Sequence/genetics , Antiviral Agents/therapeutic use , COVID-19/genetics , COVID-19/virology , Computer Simulation , Humans , Machine Learning , Neural Networks, Computer , Peptides/therapeutic use , SARS-CoV-2/drug effects , SARS-CoV-2/pathogenicity , Software
16.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1316804

ABSTRACT

Antiviral peptide (AVP) is a kind of antimicrobial peptide (AMP) that has the potential ability to fight against virus infection. Machine learning-based prediction with a computational biology approach can facilitate the development of the novel therapeutic agents. In this study, we proposed a double-stage classification scheme, named AVPIden, for predicting the AVPs and their functional activities against different viruses. The first stage is to distinguish the AVP from a broad-spectrum peptide collection, including not only the regular peptides (non-AMP) but also the AMPs without antiviral functions (non-AVP). The second stage is responsible for characterizing one or more virus families or species that the AVP targets. Imbalanced learning is utilized to improve the performance of prediction. The AVPIden uses multiple descriptors to precisely demonstrate the peptide properties and adopts explainable machine learning strategies based on Shapley value to exploit how the descriptors impact the antiviral activities. Finally, the evaluation performance of the proposed model suggests its ability to predict the antivirus activities and their potential functions against six virus families (Coronaviridae, Retroviridae, Herpesviridae, Paramyxoviridae, Orthomyxoviridae, Flaviviridae) and eight kinds of virus (FIV, HCV, HIV, HPIV3, HSV1, INFVA, RSV, SARS-CoV). The AVPIden gives an option for reinforcing the development of AVPs with the computer-aided method and has been deployed at http://awi.cuhk.edu.cn/AVPIden/.


Subject(s)
Antiviral Agents/chemistry , COVID-19/drug therapy , Peptides/chemistry , SARS-CoV-2/chemistry , Algorithms , Amino Acid Sequence/genetics , Antiviral Agents/therapeutic use , COVID-19/genetics , COVID-19/virology , Computational Biology , Humans , Machine Learning , Peptides/therapeutic use , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Software
17.
Molecules ; 25(19)2020 Sep 24.
Article in English | MEDLINE | ID: covidwho-1302391

ABSTRACT

There is a vast practice of using antimalarial drugs, RAS inhibitors, serine protease inhibitors, inhibitors of the RNA-dependent RNA polymerase of the virus and immunosuppressants for the treatment of the severe form of COVID-19, which often occurs in patients with chronic diseases and older persons. Currently, the clinical efficacy of these drugs for COVID-19 has not been proven yet. Side effects of antimalarial drugs can worsen the condition of patients and increase the likelihood of death. Peptides, given their physiological mechanism of action, have virtually no side effects. Many of them are geroprotectors and can be used in patients with chronic diseases. Peptides may be able to prevent the development of the pathological process during COVID-19 by inhibiting SARS-CoV-2 virus proteins, thereby having immuno- and bronchoprotective effects on lung cells, and normalizing the state of the hemostasis system. Immunomodulators (RKDVY, EW, KE, AEDG), possessing a physiological mechanism of action at low concentrations, appear to be the most promising group among the peptides. They normalize the cytokines' synthesis and have an anti-inflammatory effect, thereby preventing the development of disseminated intravascular coagulation, acute respiratory distress syndrome and multiple organ failure.


Subject(s)
Anti-Inflammatory Agents/therapeutic use , Antiviral Agents/therapeutic use , Coronavirus Infections/drug therapy , Immunologic Factors/therapeutic use , Peptides/therapeutic use , Pneumonia, Viral/drug therapy , Respiratory System Agents/therapeutic use , Acute Disease , Anti-Inflammatory Agents/chemical synthesis , Antiviral Agents/chemical synthesis , Betacoronavirus/drug effects , Betacoronavirus/growth & development , COVID-19 , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Cytokine Release Syndrome/complications , Cytokine Release Syndrome/diagnosis , Cytokine Release Syndrome/drug therapy , Cytokine Release Syndrome/virology , Disseminated Intravascular Coagulation/complications , Disseminated Intravascular Coagulation/diagnosis , Disseminated Intravascular Coagulation/drug therapy , Disseminated Intravascular Coagulation/virology , Host-Pathogen Interactions/drug effects , Humans , Immunologic Factors/chemical synthesis , Lung/blood supply , Lung/drug effects , Lung/pathology , Lung/virology , Pandemics , Peptides/chemical synthesis , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Respiratory Insufficiency/complications , Respiratory Insufficiency/diagnosis , Respiratory Insufficiency/prevention & control , Respiratory Insufficiency/virology , Respiratory System Agents/chemical synthesis , SARS-CoV-2 , Structure-Activity Relationship
18.
Brief Bioinform ; 22(6)2021 11 05.
Article in English | MEDLINE | ID: covidwho-1284855

ABSTRACT

Targeting the interaction between severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2)-receptor-binding domain (RBD) and angiotensin-converting enzyme 2 (ACE2) is believed to be an effective strategy for drug design to inhibit the infection of SARS-CoV-2. Herein, several ultrashort peptidase inhibitors against the RBD-ACE2 interaction were obtained by a computer-aided approach based on the RBD-binding residues on the protease domain (PD) of ACE2. The designed peptides were tested on a model coronavirus GX_P2V, which has 92.2 and 86% amino acid identity to the SARS-CoV-2 spike protein and RBD, respectively. Molecular dynamics simulations and binding free energy analysis predicted a potential binding pocket on the RBD of the spike protein, and this was confirmed by the specifically designed peptides SI5α and SI5α-b. They have only seven residues, showing potent antiviral activity and low cytotoxicity. Enzyme-linked immunosorbent assay result also confirmed their inhibitory ability against the RBD-ACE2 interaction. The ultrashort peptides are promising precursor molecules for the drug development of Corona Virus Disease 2019, and the novel binding pocket on the RBD may be helpful for the design of RBD inhibitors or antibodies against SARS-CoV-2.


Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , COVID-19/drug therapy , Peptides/chemistry , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/genetics , Antiviral Agents/chemistry , Binding Sites/drug effects , COVID-19/genetics , COVID-19/virology , Drug Design , Humans , Molecular Dynamics Simulation , Peptides/genetics , Peptides/therapeutic use , Protein Binding/drug effects , Protein Domains/drug effects , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
19.
Mol Cells ; 44(6): 408-421, 2021 Jun 30.
Article in English | MEDLINE | ID: covidwho-1249737

ABSTRACT

The outbreak of coronavirus disease 2019 (COVID-19) has not only affected human health but also diverted the focus of research and derailed the world economy over the past year. Recently, vaccination against COVID-19 has begun, but further studies on effective therapeutic agents are still needed. The severity of COVID-19 is attributable to several factors such as the dysfunctional host immune response manifested by uncontrolled viral replication, type I interferon suppression, and release of impaired cytokines by the infected resident and recruited cells. Due to the evolving pathophysiology and direct involvement of the host immune system in COVID-19, the use of immune-modulating drugs is still challenging. For the use of immune-modulating drugs in severe COVID-19, it is important to balance the fight between the aggravated immune system and suppression of immune defense against the virus that causes secondary infection. In addition, the interplaying events that occur during virus-host interactions, such as activation of the host immune system, immune evasion mechanism of the virus, and manifestation of different stages of COVID-19, are disjunctive and require thorough streamlining. This review provides an update on the immunotherapeutic interventions implemented to combat COVID-19 along with the understanding of molecular aspects of the immune evasion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may provide opportunities to develop more effective and promising therapeutics.


Subject(s)
Antibodies, Monoclonal, Humanized/therapeutic use , Antiviral Agents/therapeutic use , COVID-19/therapy , Immune Evasion/drug effects , Immunologic Factors/therapeutic use , Virus Replication/drug effects , COVID-19/immunology , COVID-19/pathology , COVID-19/prevention & control , COVID-19 Vaccines/administration & dosage , Clinical Trials as Topic , Cytokines/antagonists & inhibitors , Cytokines/biosynthesis , Dexamethasone/therapeutic use , Drug Combinations , Humans , Immunity, Innate/drug effects , Immunization, Passive/methods , Interleukin 1 Receptor Antagonist Protein/therapeutic use , Peptides/therapeutic use , SARS-CoV-2/drug effects , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Virus Replication/immunology
20.
Molecules ; 26(8)2021 Apr 09.
Article in English | MEDLINE | ID: covidwho-1178365

ABSTRACT

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe respiratory syndrome in humans, which is now referred to as coronavirus disease 2019 (COVID-19). Since December 2019, the new pathogen has rapidly spread globally, with over 65 million cases reported to the beginning of December 2020, including over 1.5 million deaths. Unfortunately, currently, there is no specific and effective treatment for COVID-19. As SARS-CoV-2 relies on its spike proteins (S) to bind to a host cell-surface receptor angiotensin-converting enzyme-2(ACE2), and this interaction is proved to be responsible for entering a virus into host cells, it makes an ideal target for antiviral drug development. In this work, we design three very short peptides based on the ACE2 sequence/structure fragments, which may effectively bind to the receptor-binding domain (RBD) of S protein and may, in turn, disrupt the important virus-host protein-protein interactions, blocking early steps of SARS-CoV-2 infection. Two of our peptides bind to virus protein with affinity in nanomolar range, and as very short peptides have great potential for drug development.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Angiotensin-Converting Enzyme 2/chemistry , Binding Sites , COVID-19/drug therapy , COVID-19/pathology , COVID-19/virology , Drug Design , Humans , Molecular Dynamics Simulation , Peptides/chemistry , Peptides/metabolism , Peptides/therapeutic use , Protein Binding , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/chemistry
SELECTION OF CITATIONS
SEARCH DETAIL