1
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Pang XF, Dai XY, Zhao LJ, Ye YW, Yang XY, Wang HH, Jiang M, Zhu YQ, Shi B. Short-peptide-based enteral nutrition affects rats MDP translocation and protects against gut-lung injury via the PepT1-NOD2-beclin-1 pathway in vivo. Mol Biol Rep 2024; 51:891. [PMID: 39110355 PMCID: PMC11306270 DOI: 10.1007/s11033-024-09759-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/25/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Peptide transporter 1 (PepT1) transports bacterial oligopeptide products and induces inflammation of the bowel. Nutritional peptides compete for the binding of intestinal bacterial products to PepT1. We investigated the mechanism of short-peptide-based enteral nutrition (SPEN) on the damage to the gut caused by the bacterial oligopeptide product muramyl dipeptide (MDP), which is transported by PepT1. The gut-lung axis is a shared mucosal immune system, and immune responses and disorders can affect the gut-respiratory relationship. METHODS AND RESULTS Sprague-Dawley rats were gavaged with solutions containing MDP, MDP + SPEN, MDP + intact-protein-based enteral nutrition (IPEN), glucose as a control, or glucose with GSK669 (a NOD2 antagonist). Inflammation, mitochondrial damage, autophagy, and apoptosis were explored to determine the role of the PepT1-nucleotide-binding oligomerization domain-containing protein 2 (NOD2)-beclin-1 signaling pathway in the small intestinal mucosa. MDP and proinflammatory factors of lung tissue were explored to determine that MDP can migrate to lung tissue and cause inflammation. Induction of proinflammatory cell accumulation and intestinal damage in MDP gavage rats was associated with increased NOD2 and Beclin-1 mRNA expression. IL-6 and TNF-α expression and apoptosis were increased, and mitochondrial damage was severe, as indicated by increased mtDNA in the MDP group compared with controls. MDP levels and expression of proinflammatory factors in lung tissue increased in the MDP group compared with the control group. SPEN, but not IPEN, eliminated these impacts. CONCLUSIONS Gavage of MDP to rats resulted in damage to the gut-lung axis. SPEN reverses the adverse effects of MDP. The PepT1-NOD2-beclin-1 pathway plays a role in small intestinal inflammation, mitochondrial damage, autophagy, and apoptosis.
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Affiliation(s)
- Xiu-Feng Pang
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Xiao-Yong Dai
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Lu-Jia Zhao
- Department of Geriatrics, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200092, China
| | - You-Wen Ye
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Xiao-Ying Yang
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Huan-Huan Wang
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Meng Jiang
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Yu-Qin Zhu
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China
| | - Bin Shi
- Department of Emergency Intensive Care Unit, Yangpu Hospital, School of Medicine, Tongji University, No. 450, Tengyue Road, Shanghai, 200090, China.
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2
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Pal S, Openy J, Krzyzanowski A, Noisier A, ‘t Hart P. On-Resin Photochemical Decarboxylative Arylation of Peptides. Org Lett 2024; 26:2795-2799. [PMID: 37819674 PMCID: PMC11019635 DOI: 10.1021/acs.orglett.3c03070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Here we describe the application of photochemical decarboxylative arylation as a late-stage functionalization reaction for peptides. The reaction uses redox-active esters of aspartic acid and glutamic acid on the solid phase to provide analogues of aromatic amino acids. By using aryl bromides as arylation reagents, a wide variety of amino acids can be accessed without having to synthesize them individually in solution. The reaction is compatible with proteinogenic amino acids and was used to perform a structure-activity relationship study of a PRMT5 binding peptide.
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Affiliation(s)
- Sunit Pal
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
| | - Joseph Openy
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
| | - Adrian Krzyzanowski
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, 44227 Dortmund, Germany
| | - Anaïs Noisier
- Medicinal
Chemistry, Research and Early Development Cardiovascular, Renal and
Metabolism BioPharmaceutical R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Peter ‘t Hart
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, 44227 Dortmund, Germany
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3
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Ullah A, Ullah S, Halim SA, Waqas M, Ali B, Ataya FS, El-Sabbagh NM, Batiha GES, Avula SK, Csuk R, Khan A, Al-Harrasi A. Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques. Sci Rep 2024; 14:3590. [PMID: 38351259 PMCID: PMC10864406 DOI: 10.1038/s41598-024-53911-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 appeared as a highly contagious disease after its outbreak in December 2019 by the virus, named SARS-CoV-2. The threat, which originated in Wuhan, China, swiftly became an international emergency. Among different genomic products, spike protein of virus plays a crucial role in the initiation of the infection by binding to the human lung cells, therefore, SARS-CoV-2's spike protein is a promising therapeutic target. Using a combination of a structure-based virtual screening and biochemical assay, this study seeks possible therapeutic candidates that specifically target the viral spike protein. A database of ~ 850 naturally derived compounds was screened against SARS-CoV-2 spike protein to find natural inhibitors. Using virtual screening and inhibitory experiments, we identified acetyl 11-keto-boswellic acid (AKBA) as a promising molecule for spike protein, which encouraged us to scan the rest of AKBA derivatives in our in-house database via 2D-similarity searching. Later 19 compounds with > 85% similarity with AKBA were selected and docked with receptor binding domain (RBD) of spike protein. Those hits declared significant interactions at the RBD interface, best possess and excellent drug-likeness and pharmacokinetics properties with high gastrointestinal absorption (GIA) without toxicity and allergenicity. Our in-silico observations were eventually validated by in vitro bioassay, interestingly, 10 compounds (A3, A4, C3, C6A, C6B, C6C, C6E, C6H, C6I, and C6J) displayed significant inhibitory ability with good percent inhibition (range: > 72-90). The compounds C3 (90.00%), C6E (91.00%), C6C (87.20%), and C6D (86.23%) demonstrated excellent anti-SARS CoV-2 spike protein activities. The docking interaction of high percent inhibition of inhibitor compounds C3 and C6E was confirmed by MD Simulation. In the molecular dynamics simulation, we observed the stable dynamics of spike protein inhibitor complexes and the influence of inhibitor binding on the protein's conformational arrangements. The binding free energy ΔGTOTAL of C3 (-38.0 ± 0.08 kcal/mol) and C6E (-41.98 ± 0.08 kcal/mol) respectively indicate a strong binding affinity to Spike protein active pocket. These findings demonstrate that these molecules particularly inhibit the function of spike protein and, therefore have the potential to be evaluated as drug candidates against SARS-CoV-2.
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Affiliation(s)
- Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Pakistan
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Nasser M El-Sabbagh
- Department of Veterinary Pharmacology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Satya Kumar Avula
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Rene Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120, Halle (Saale), Germany
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
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4
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Kim SM, Kim EH, Casel MAB, Kim YI, Sun R, Kwak MJ, Yoo JS, Yu M, Yu KM, Jang SG, Rollon R, Choi JH, Gil J, Eun K, Kim H, Ensser A, Hwang J, Song MS, Kim MH, Jung JU, Choi YK. SARS-CoV-2 variants with NSP12 P323L/G671S mutations display enhanced virus replication in ferret upper airways and higher transmissibility. Cell Rep 2023; 42:113077. [PMID: 37676771 DOI: 10.1016/j.celrep.2023.113077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
With the emergence of multiple predominant SARS-CoV-2 variants, it becomes important to have a comprehensive assessment of their viral fitness and transmissibility. Here, we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmissibility. Specifically, SARS-CoV-2 variants containing the NSP12 mutations P323L or P323L/G671S exhibit enhanced RNA-dependent RNA polymerase (RdRp) activity at 33°C compared with 37°C and high transmissibility. Molecular dynamics simulations and microscale thermophoresis demonstrate that the NSP12 P323L and P323L/G671S mutations stabilize the NSP12-NSP7-NSP8 complex through hydrophobic effects, leading to increased viral RdRp activity. Furthermore, competitive transmissibility assay reveals that reverse genetic (RG)-P323L or RG-P323L/G671S NSP12 outcompetes RG-WT (wild-type) NSP12 for replication in the upper respiratory tract, allowing markedly rapid transmissibility. This suggests that NSP12 P323L or P323L/G671S mutation of SARS-CoV-2 is associated with increased RdRp complex stability and enzymatic activity, promoting efficient transmissibility.
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Affiliation(s)
- Se-Mi Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Eun-Ha Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Young-Il Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Rong Sun
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mi-Jeong Kwak
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ji-Seung Yoo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mina Yu
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Kwang-Min Yu
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seung-Gyu Jang
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Rare Rollon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jeong Ho Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Juryeon Gil
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kiyoung Eun
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hyunggee Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jungwon Hwang
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea; College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea.
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5
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Quagliata M, Stincarelli MA, Papini AM, Giannecchini S, Rovero P. Antiviral Activity against SARS-CoV-2 of Conformationally Constrained Helical Peptides Derived from Angiotensin-Converting Enzyme 2. ACS OMEGA 2023; 8:22665-22672. [PMID: 37387789 PMCID: PMC10275481 DOI: 10.1021/acsomega.3c01436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/16/2023] [Indexed: 07/01/2023]
Abstract
Despite the availability of vaccines, COVID-19 continues to be aggressive, especially in immunocompromised individuals. Therefore, the development of a specific therapeutic agent with antiviral activity against SARS-CoV-2 is necessary. The infection pathway starts when the receptor binding domain of the viral spike protein interacts with the angiotensin converting enzyme 2 (ACE2), which acts as a host receptor for the RBD expressed on the host cell surface. In this scenario, ACE2 analogs binding to the RBD and preventing the cell entry can be promising antiviral agents. Most of the ACE2 residues involved in the interaction belong to the α1 helix, more specifically to the minimal fragment ACE2(24-42). In order to increase the stability of the secondary structure and thus antiviral activity, we designed different triazole-stapled analogs, changing the position and the number of bridges. The peptide called P3, which has the triazole-containing bridge in the positions 36-40, showed promising antiviral activity at micromolar concentrations assessed by plaque reduction assay. On the other hand, the double-stapled peptide P4 lost the activity, showing that excessive rigidity disfavors the interaction with the RBD.
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Affiliation(s)
- Michael Quagliata
- Interdepartmental
Research Unit of Peptide and Protein Chemistry and Biology, Department
of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | | | - Anna Maria Papini
- Interdepartmental
Research Unit of Peptide and Protein Chemistry and Biology, Department
of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Simone Giannecchini
- Department
of Experimental and Clinical Medicine, University
of Florence, 50134 Florence, Italy
| | - Paolo Rovero
- Interdepartmental
Research Unit of Peptide and Protein Chemistry and Biology, Department
of NeuroFarBa, University of Florence, 50019 Sesto Fiorentino, Italy
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6
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Renzi F, Seamann A, Ganguly K, Pandey K, Byrareddy SN, Batra S, Kumar S, Ghersi D. Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:857-867. [PMID: 37325447 PMCID: PMC10262318 DOI: 10.1021/acsptsci.2c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 06/17/2023]
Abstract
Entry inhibitors are an important resource in the response against emerging pathogens like the novel SARS-CoV-2, which enters human cells via interaction between the surface spike glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the spike to ACE2, docking experiments, and molecular dynamics simulations, we identified a stable fragment of ACE2 that binds to the spike, is soluble, and is not predicted to bind to its physiological ligand angiotensin II. From this fragment we computationally designed and experimentally validated a smaller, stable peptide that disrupts ACE2-spike interaction at nanomolar concentrations, suggesting its potential use as a decoy that could interfere with viral binding by competition.
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Affiliation(s)
- Fabiana Renzi
- Department
of Physics, Università di Roma ”La
Sapienza”, 00185 Rome, Italy
| | - Austin Seamann
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Koelina Ganguly
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Kabita Pandey
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Siddappa N. Byrareddy
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Surinder Batra
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Sushil Kumar
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Dario Ghersi
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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7
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Padmanabha Das KM. Editorial: Antiviral drug discovery against pathogens of pandemic concern: Advancements in target site identification and structure-based drug development. Front Mol Biosci 2023; 10:1165208. [PMID: 36968270 PMCID: PMC10034765 DOI: 10.3389/fmolb.2023.1165208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Affiliation(s)
- Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology (BCMP), Harvard Medical School, Boston, MA, United States
- Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- *Correspondence: Krishna M. Padmanabha Das,
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8
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Cipriano M, Ruberti E, Tovani-Palone MR. Combined use of lactoferrin and vitamin D as a preventive and therapeutic supplement for SARS-CoV-2 infection: Current evidence. World J Clin Cases 2022; 10:11665-11670. [PMID: 36405280 PMCID: PMC9669848 DOI: 10.12998/wjcc.v10.i32.11665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/10/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
Lactoferrin is a multifunctional protein that exhibits anti-inflammatory, immune regulating and anti-infective properties. One of its receptor sites is located on severe acute respiratory syndrome coronavirus 2. The binding of lactoferrin with heparin sulfate proteoglycans may prevent the first contact between the virus and host cells, thus preventing subsequent infection. Given that lactoferrin may act as a natural mucosal barrier, an intranasal treatment together with its oral intake can be hypothesized to prevent the spread, infection and inflammation caused by coronavirus disease 2019 (COVID-19). Moreover, the literature reports that vitamin D plays an essential role in promoting immune response. With its anti-inflammatory and immunoregulatory properties, vitamin D is critical for activating the immune system’s defenses, improving immune cell function. Different studies also demonstrate that lactoferrin is a potential activator of the vitamin D receptor. In this sense, the combined use of lactoferrin (through an association of oral intake and a nasal spray formulation) and vitamin D could represent a valuable therapy for COVID-19 treatment and prevention. However, further randomized clinical trials are needed before recommending/prescribing them.
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Affiliation(s)
- Massimiliano Cipriano
- Department of Laparoscopic Surgery, Umberto I General Hospital, Medical School Sapienza University, Rome 161, Italy
| | - Enzo Ruberti
- Department of Human Neuroscience, Sapienza University of Rome, Rome 00185, Italy
| | - Marcos Roberto Tovani-Palone
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai 600 077, India
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9
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de Brevern AG. A Perspective on the (Rise and Fall of) Protein β-Turns. Int J Mol Sci 2022; 23:12314. [PMID: 36293166 PMCID: PMC9604201 DOI: 10.3390/ijms232012314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022] Open
Abstract
The β-turn is the third defined secondary structure after the α-helix and the β-sheet. The β-turns were described more than 50 years ago and account for more than 20% of protein residues. Nonetheless, they are often overlooked or even misunderstood. This poor knowledge of these local protein conformations is due to various factors, causes that I discuss here. For example, confusion still exists about the assignment of these local protein structures, their overlaps with other structures, the potential absence of a stabilizing hydrogen bond, the numerous types of β-turns and the software's difficulty in assigning or visualizing them. I also propose some ideas to potentially/partially remedy this and present why β-turns can still be helpful, even in the AlphaFold 2 era.
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Affiliation(s)
- Alexandre G de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM UMR_S 1134, BIGR, DSIMB Team, F-75014 Paris, France
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10
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Odolczyk N, Klim J, Podsiadła-Białoskórska M, Winiewska-Szajewska M, Szolajska E, Zielenkiewicz U, Poznański J, Zielenkiewicz P. Improvement of native structure-based peptides as efficient inhibitors of protein-protein interactions of SARS-CoV-2 spike protein and human ACE2. Front Mol Biosci 2022; 9:983014. [PMID: 36250011 PMCID: PMC9555309 DOI: 10.3389/fmolb.2022.983014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
New pathogens responsible for novel human disease outbreaks in the last two decades are mainly the respiratory system viruses. Not different was the last pandemic episode, caused by infection of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One of the extensively explored targets, in the recent scientific literature, as a possible way for rapid development of COVID-19 specific drug(s) is the interaction between the receptor-binding domain of the virus’ spike (S) glycoprotein and human receptor angiotensin-converting enzyme 2 (hACE2). This protein-protein recognition process is involved in the early stages of the SARS-CoV-2 life cycle leading to the host cell membrane penetration. Thus, disrupting this interaction may block or significantly reduce the infection caused by the novel pathogen. Previously we have designed (by in silico structure-based analysis) three very short peptides having sequences inspirited by hACE2 native fragments, which effectively bind to the SARS-CoV-2 S protein and block its interaction with the human receptor. In continuation of the above mentioned studies, here we presented an application of molecular modeling approach resulting in improved binding affinity of the previously proposed ligand and its enhanced ability to inhibit meaningful host-virus protein-protein interaction. The new optimized hexapeptide binds to the virus protein with affinity one magnitude higher than the initial ligand and, as a very short peptide, has also great potential for further drug development. The peptide-based strategy is rapid and cost-effective for developing and optimizing efficient protein-protein interactions disruptors and may be successfully applied to discover antiviral candidates against other future emerging human viral infections.
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Affiliation(s)
- Norbert Odolczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- Laboratory of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Joanna Klim
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | | | | | - Ewa Szolajska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Urszula Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- *Correspondence: Jarosław Poznański, ; Piotr Zielenkiewicz,
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
- Laboratory of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- *Correspondence: Jarosław Poznański, ; Piotr Zielenkiewicz,
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11
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Engelhardt PM, Rueda SF, Drexelius M, Neudörfl JM, Lauster D, Hackenberger CPR, Kühne R, Neundorf I, Schmalz HG. Synthetic α-Helical Peptides as Potential Inhibitors of the ACE2 SARS-CoV-2 Interaction. Chembiochem 2022; 23:e202200372. [PMID: 35785462 PMCID: PMC9350387 DOI: 10.1002/cbic.202200372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/04/2022] [Indexed: 11/11/2022]
Abstract
During viral cell entry, the spike protein of SARS‐CoV‐2 binds to the α1‐helix motif of human angiotensin‐converting enzyme 2 (ACE2). Thus, alpha‐helical peptides mimicking this motif may serve as inhibitors of viral cell entry. For this purpose, we employed the rigidified diproline‐derived module ProM‐5 to induce α‐helicity in short peptide sequences inspired by the ACE2 α1‐helix. Starting with Ac‐QAKTFLDKFNHEAEDLFYQ‐NH2 as a relevant section of α1, a series of peptides, N‐capped with either Ac‐βHAsp‐[ProM‐5] or Ac‐βHAsp‐PP, were prepared and their α‐helicities were investigated. While ProM‐5 clearly showed a pronounced effect, an even increased degree of helicity (up to 63 %) was observed in sequences in which non‐binding amino acids were replaced by alanine. The binding affinities of the peptides towards the spike protein, as determined by means of microscale thermophoresis (MST), revealed only a subtle influence of the α‐helical content and, noteworthy, led to the identification of an Ac‐βHAsp‐PP‐capped peptide displaying a very strong binding affinity (KD=62 nM).
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Affiliation(s)
| | - Sebastián Florez Rueda
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, chemical biology, GERMANY
| | - Marco Drexelius
- University of Cologne: Universitat zu Koln, Chemistry, GERMANY
| | | | - Daniel Lauster
- Freie Universitat Berlin Fachbereich Biologie Chemie Pharmazie, biochemistry and chemistry, GERMANY
| | - Christian P R Hackenberger
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, chemical biology, GERMANY
| | - Ronald Kühne
- FMP: Leibniz-Forschungsinstitut fur Molekulare Pharmakologie im Forschungsverbund Berlin eV, drug discovery, GERMANY
| | - Ines Neundorf
- University of Cologne: Universitat zu Koln, chemistry and biochemistry, GERMANY
| | - Hans-Günther Schmalz
- Universitat zu Koln, Department für Chemie, Greinstrasse 4, 50939, Köln, GERMANY
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12
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New Advances in Short Peptides: Looking Forward. Molecules 2022; 27:molecules27113635. [PMID: 35684571 PMCID: PMC9182370 DOI: 10.3390/molecules27113635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
It is beyond doubt that short peptides hold significant promise in bio-medicine, as the most versatile molecules, both structurally and functionally [...]
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13
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Piacentini R, Centi L, Miotto M, Milanetti E, Di Rienzo L, Pitea M, Piazza P, Ruocco G, Boffi A, Parisi G. Lactoferrin Inhibition of the Complex Formation between ACE2 Receptor and SARS CoV-2 Recognition Binding Domain. Int J Mol Sci 2022; 23:ijms23105436. [PMID: 35628247 PMCID: PMC9141661 DOI: 10.3390/ijms23105436] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 02/07/2023] Open
Abstract
The present investigation focuses on the analysis of the interactions among human lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) receptor in order to assess possible mutual interactions that could provide a molecular basis of the reported preventative effect of lactoferrin against CoV-2 infection. In particular, kinetic and thermodynamic parameters for the pairwise interactions among the three proteins were measured via two independent techniques, biolayer interferometry and latex nanoparticle-enhanced turbidimetry. The results obtained clearly indicate that LF is able to bind the ACE2 receptor ectodomain with significantly high affinity, whereas no binding to the RBD was observed up to the maximum “physiological” lactoferrin concentration range. Lactoferrin, above 1 µM concentration, thus appears to directly interfere with RBD–ACE2 binding, bringing about a measurable, up to 300-fold increase of the KD value relative to RBD–ACE2 complex formation.
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Affiliation(s)
- Roberta Piacentini
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
| | - Laura Centi
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
| | - Mattia Miotto
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Edoardo Milanetti
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Di Rienzo
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
| | - Martina Pitea
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- D-Tails s.r.l., Via di Torre Rossa 66, 00165 Rome, Italy
| | - Paolo Piazza
- EDIF Instruments s.r.l., Via Ardeatina 132, 00147 Rome, Italy;
| | - Giancarlo Ruocco
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alberto Boffi
- Department of Biochemistry, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy; (R.P.); (L.C.); (A.B.)
| | - Giacomo Parisi
- Center of Life Nano and Neuro Science, Institute of Italian Technology, Viale Regina Elena 291, 00181 Rome, Italy; (M.M.); (E.M.); (L.D.R.); (M.P.); (G.R.)
- Correspondence:
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14
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Bojarska J. Advances in Research of Short Peptides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082446. [PMID: 35458644 PMCID: PMC9028298 DOI: 10.3390/molecules27082446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/26/2022]
Affiliation(s)
- Joanna Bojarska
- Department of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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15
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Mackin RT, Edwards JV, Atuk EB, Beltrami N, Condon BD, Jayawickramarajah J, French AD. Structure/Function Analysis of Truncated Amino-Terminal ACE2 Peptide Analogs That Bind to SARS-CoV-2 Spike Glycoprotein. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072070. [PMID: 35408469 PMCID: PMC9000588 DOI: 10.3390/molecules27072070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022]
Abstract
The global burden of the SARS-CoV-2 pandemic is thought to result from a high viral transmission rate. Here, we consider mechanisms that influence host cell–virus binding between the SARS-CoV-2 spike glycoprotein (SPG) and the human angiotensin-converting enzyme 2 (ACE2) with a series of peptides designed to mimic key ACE2 hot spots through adopting a helical conformation analogous to the N-terminal α1 helix of ACE2, the region experimentally shown to bind to the SARS-CoV-2 receptor-binding domain (RBD). The approach examines putative structure/function relations by assessing SPG binding affinity with surface plasmon resonance (SPR). A cyclic peptide (c[KFNHEAEDLFEKLM]) was characterized in an α-helical conformation with micromolar affinity (KD = 500 µM) to the SPG. Thus, stabilizing the helical structure of the 14-mer through cyclization improves binding to SPG by an order of magnitude. In addition, end-group peptide analog modifications and residue substitutions mediate SPG binding, with net charge playing an apparent role. Therefore, we surveyed reported viral variants, and a correlation of increased positive charge with increased virulence lends support to the hypothesis that charge is relevant to enhanced viral fusion. Overall, the structure/function relationship informs the importance of conformation and charge for virus-binding analog design.
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Affiliation(s)
- Robert T. Mackin
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
| | - J. Vincent Edwards
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
- Correspondence: ; Tel.: +1-504-286-4360
| | - E. Berk Atuk
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA; (E.B.A.); (N.B.); (J.J.)
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA; (E.B.A.); (N.B.); (J.J.)
| | - Brian D. Condon
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
| | | | - Alfred D. French
- United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center (USDA-ARS-SRRC), New Orleans, LA 70124, USA; (R.T.M.); (B.D.C.); (A.D.F.)
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16
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Rani P, Kapoor B, Gulati M, Atanasov AG, Alzahrani Q, Gupta R. Antimicrobial peptides: A plausible approach for COVID-19 treatment. Expert Opin Drug Discov 2022; 17:473-487. [PMID: 35255763 PMCID: PMC8935455 DOI: 10.1080/17460441.2022.2050693] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), which emerged as a major public health threat, has affected >400 million people globally leading to >5 million mortalities to date. Treatments of COVID-19 are still to be developed as the available therapeutic approaches are not able to combat the virus causing the disease (severe acute respiratory syndrome coronavirus-2; SARS-CoV-2) satisfactorily. However, antiviral peptides (AVPs) have demonstrated prophylactic and therapeutic effects against many coronaviruses (CoVs). AREAS COVERED This review critically discusses various types of AVPs evaluated for the treatment of COVID-19 along with their mechanisms of action. Furthermore, the peptides inhibiting the entry of the virus by targeting its binding to angiotensin-converting enzyme 2 (ACE2) or integrins, fusion mechanism as well as activation of proteolytic enzymes (cathepsin L, transmembrane serine protease 2 (TMPRSS2), or furin) are also discussed. EXPERT OPINION Although extensively investigated, successful treatment of COVID-19 is still a challenge due to emergence of virus mutants. Antiviral peptides are anticipated to be blockbuster drugs for the management of this serious infection because of their formulation and therapeutic advantages. Although they may act on different pathways, AVPs having a multi-targeted approach are considered to have the upper hand in the management of this infection.
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Affiliation(s)
- Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Atanas G Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Magdalenka, Poland.,Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville, Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
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17
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Ershov PV, Mezentsev YV, Ivanov AS. Interfacial Peptides as Affinity Modulating Agents of Protein-Protein Interactions. Biomolecules 2022; 12:106. [PMID: 35053254 PMCID: PMC8773757 DOI: 10.3390/biom12010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/25/2022] Open
Abstract
The identification of disease-related protein-protein interactions (PPIs) creates objective conditions for their pharmacological modulation. The contact area (interfaces) of the vast majority of PPIs has some features, such as geometrical and biochemical complementarities, "hot spots", as well as an extremely low mutation rate that give us key knowledge to influence these PPIs. Exogenous regulation of PPIs is aimed at both inhibiting the assembly and/or destabilization of protein complexes. Often, the design of such modulators is associated with some specific problems in targeted delivery, cell penetration and proteolytic stability, as well as selective binding to cellular targets. Recent progress in interfacial peptide design has been achieved in solving all these difficulties and has provided a good efficiency in preclinical models (in vitro and in vivo). The most promising peptide-containing therapeutic formulations are under investigation in clinical trials. In this review, we update the current state-of-the-art in the field of interfacial peptides as potent modulators of a number of disease-related PPIs. Over the past years, the scientific interest has been focused on following clinically significant heterodimeric PPIs MDM2/p53, PD-1/PD-L1, HIF/HIF, NRF2/KEAP1, RbAp48/MTA1, HSP90/CDC37, BIRC5/CRM1, BIRC5/XIAP, YAP/TAZ-TEAD, TWEAK/FN14, Bcl-2/Bax, YY1/AKT, CD40/CD40L and MINT2/APP.
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Affiliation(s)
- Pavel V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (Y.V.M.); (A.S.I.)
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18
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Tallei TE, Fatimawali, Adam AA, Elseehy MM, El-Shehawi AM, Mahmoud EA, Tania AD, Niode NJ, Kusumawaty D, Rahimah S, Effendi Y, Idroes R, Celik I, Hossain MJ, Emran TB. Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach. Molecules 2022; 27:260. [PMID: 35011492 PMCID: PMC8746556 DOI: 10.3390/molecules27010260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
| | - Fatimawali
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Mona M. Elseehy
- Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria 21545, Egypt;
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta 34511, Egypt;
| | - Adinda Dwi Tania
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Nurdjannah Jane Niode
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Department of Dermatology and Venereology, Faculty of Medicine, University of Sam Ratulangi, RD Kandou Hospital, Manado 95163, Indonesia
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, Indonesia;
| | - Souvia Rahimah
- Food Technology Study Program, Department of Food Industrial Technology, Faculty of Agroindustrial Technology, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta 12110, Indonesia;
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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19
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Nedyalkova M, Vasighi M, Sappati S, Kumar A, Madurga S, Simeonov V. Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach. Pharmaceuticals (Basel) 2021; 14:ph14121328. [PMID: 34959727 PMCID: PMC8704597 DOI: 10.3390/ph14121328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/12/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
The lack of medication to treat COVID-19 is still an obstacle that needs to be addressed by all possible scientific approaches. It is essential to design newer drugs with varied approaches. A receptor-binding domain (RBD) is a key part of SARS-CoV-2 virus, located on its surface, that allows it to dock to ACE2 receptors present on human cells, which is followed by admission of virus into cells, and thus infection is triggered. Specific receptor-binding domains on the spike protein play a pivotal role in binding to the receptor. In this regard, the in silico method plays an important role, as it is more rapid and cost effective than the trial and error methods using experimental studies. A combination of virtual screening, molecular docking, molecular simulations and machine learning techniques are applied on a library of natural compounds to identify ligands that show significant binding affinity at the hydrophobic pocket of the RBD. A list of ligands with high binding affinity was obtained using molecular docking and molecular dynamics (MD) simulations for protein–ligand complexes. Machine learning (ML) classification schemes have been applied to obtain features of ligands and important descriptors, which help in identification of better binding ligands. A plethora of descriptors were used for training the self-organizing map algorithm. The model brings out descriptors important for protein–ligand interactions.
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Affiliation(s)
- Miroslava Nedyalkova
- Inorganic Chemistry Department, Faculty of Chemistry and Pharmacy “St Kliment Ohridski”, University of Sofia, 1164 Sofia, Bulgaria
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
- Correspondence:
| | - Mahdi Vasighi
- Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran;
| | | | - Anmol Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA;
| | - Sergio Madurga
- Department of Material Science and Physical Chemistry & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08007 Barcelona, Spain;
| | - Vasil Simeonov
- Analytical Chemistry Department, Faculty of Chemistry and Pharmacy “St Kliment Ohridski”, University of Sofia, 1164 Sofia, Bulgaria;
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20
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A Collection of Designed Peptides to Target SARS-CoV-2 Spike RBD-ACE2 Interaction. Int J Mol Sci 2021; 22:ijms222111627. [PMID: 34769056 PMCID: PMC8584250 DOI: 10.3390/ijms222111627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023] Open
Abstract
The angiotensin-converting enzyme 2 (ACE2) is the receptor used by SARS-CoV and SARS-CoV-2 coronaviruses to attach to cells via the receptor-binding domain (RBD) of their viral spike protein. Since the start of the COVID-19 pandemic, several structures of protein complexes involving ACE2 and RBD as well as monoclonal antibodies and nanobodies have become available. We have leveraged the structural data to design peptides to target the interaction between the RBD of SARS-CoV-2 and ACE2 and SARS-CoV and ACE2, as contrasting exemplar, as well as the dimerization surface of ACE2 monomers. The peptides were modelled using our original method: PiPreD that uses native elements of the interaction between the targeted protein and cognate partner(s) that are subsequently included in the designed peptides. These peptides recapitulate stretches of residues present in the native interface plus novel and highly diverse conformations surrogating key interactions at the interface. To facilitate the access to this information we have created a freely available and dedicated web-based repository, PepI-Covid19 database, providing convenient access to this wealth of information to the scientific community with the view of maximizing its potential impact in the development of novel therapeutic and diagnostic agents.
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