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Simon JP, Dong S. In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature. Int J Biol Macromol 2024; 275:133710. [PMID: 38977046 DOI: 10.1016/j.ijbiomac.2024.133710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.
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Affiliation(s)
- Jerine Peter Simon
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Shouliang Dong
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China,; Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China.
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Kong X, Wang W, Zhong Y, Wang N, Bai K, Wu Y, Qi Q, Zhang Y, Liu X, Xie J. Recent advances in the exploration and discovery of SARS-CoV-2 inhibitory peptides from edible animal proteins. Front Nutr 2024; 11:1346510. [PMID: 38389797 PMCID: PMC10883054 DOI: 10.3389/fnut.2024.1346510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), is spreading worldwide. Although the COVID-19 epidemic has passed its peak of transmission, the harm it has caused deserves our attention. Scientists are striving to develop medications that can effectively treat COVID-19 symptoms without causing any adverse reactions. SARS-CoV-2 inhibitory peptides derived from animal proteins have a wide range of functional activities in addition to safety. Identifying animal protein sources is crucial to obtaining SARS-CoV-2 inhibitory peptides from animal sources. This review aims to reveal the mechanisms of action of these peptides on SARS-CoV-2 and the possibility of animal proteins as a material source of SARS-CoV-2 inhibitory peptides. Also, it introduces the utilization of computer-aided design methods, phage display, and drug delivery strategies in the research on SARS-CoV-2 inhibitor peptides from animal proteins. In order to identify new antiviral peptides and boost their efficiency, we recommend investigating the interaction between SARS-CoV-2 inhibitory peptides from animal protein sources and non-structural proteins (Nsps) using a variety of technologies, including computer-aided drug approaches, phage display techniques, and drug delivery techniques. This article provides useful information for the development of novel anti-COVID-19 drugs.
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Affiliation(s)
- Xiaoyue Kong
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Wei Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yizhi Zhong
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nan Wang
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Kaiwen Bai
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yi Wu
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Qianhui Qi
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Yu Zhang
- Institute of Quality and Standard for Agriculture Products, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Xingquan Liu
- College of Food and Health, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Junran Xie
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Wei Z, Chen M, Lu X, Liu Y, Peng G, Yang J, Tang C, Yu P. A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques. Curr Top Med Chem 2024; 24:667-685. [PMID: 38549525 DOI: 10.2174/0115680266281358240206112605] [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: 10/08/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 05/31/2024]
Abstract
Peptides acquire target affinity based on the combination of residues in their sequences and the conformation formed by their flexible folding, an ability that makes them very attractive biomaterials in therapeutic, diagnostic, and assay fields. With the development of computer technology, computer-aided design and screening of affinity peptides has become a more efficient and faster method. This review summarizes successful cases of computer-aided design and screening of affinity peptide ligands in recent years and lists the computer programs and online servers used in the process. In particular, the characteristics of different design and screening methods are summarized and categorized to help researchers choose between different methods. In addition, experimentally validated sequences are listed, and their applications are described, providing directions for the future development and application of computational peptide screening and design.
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Affiliation(s)
- Zheng Wei
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Meilun Chen
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Xiaoling Lu
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Yijie Liu
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Guangnan Peng
- School of Life Science, Central South University, Changsha, Hunan, 410013, China
| | - Jie Yang
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Chunhua Tang
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
| | - Peng Yu
- Xiangya School of Pharmacy, Central South University, Changsha, Hunan, 410013, China
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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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Shukla SP, Cho KB, Rustagi V, Gao X, Fu X, Zhang SX, Guo B, Udugamasooriya DG. "Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Int J Mol Sci 2021; 22:ijms22168963. [PMID: 34445669 PMCID: PMC8396575 DOI: 10.3390/ijms22168963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. More importantly, these compounds do not decrease ACE2 expression nor its enzyme activity (which is important in normal blood pressure regulation), suggesting safe applicability in humans
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Affiliation(s)
- Satya Prakash Shukla
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Kwang Bog Cho
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Vineeta Rustagi
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xiang Gao
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xinping Fu
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Shaun Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Bin Guo
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- Correspondence: (B.G.); (D.G.U.)
| | - D. Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- MD Anderson Cancer Center, Department of Cancer Systems Imaging, 1881 East Road, Houston, TX 77030-4009, USA
- Correspondence: (B.G.); (D.G.U.)
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