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Xu Z, Zhang R, Chen H, Zhang L, Yan X, Qin Z, Cong S, Tan Z, Li T, Du M. Characterization and preparation of food-derived peptides on improving osteoporosis: A review. Food Chem X 2024; 23:101530. [PMID: 38933991 PMCID: PMC11200288 DOI: 10.1016/j.fochx.2024.101530] [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: 03/24/2024] [Revised: 05/18/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
Osteoporosis is a systemic bone disease characterized by reduced bone mass and deterioration of the microstructure of bone tissue, leading to an increased risk of fragility fractures and affecting human health worldwide. Food-derived peptides are widely used in functional foods due to their low toxicity, ease of digestion and absorption, and potential to improve osteoporosis. This review summarized and discussed methods of diagnosing osteoporosis, treatment approaches, specific peptides as alternatives to conventional drugs, and the laboratory preparation and identification methods of peptides. It was found that peptides interacting with RGD (arginine-glycine-aspartic acid)-binding active sites in integrin could alleviate osteoporosis, analyzed the interaction sites between these osteogenic peptides and integrin, and further discussed their effects on improving osteoporosis. These may provide new insights for rapid screening of osteogenic peptides, and provide a theoretical basis for their application in bone materials and functional foods.
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Affiliation(s)
- Zhe Xu
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
- Institute of Bast Fiber Crops & Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Rui Zhang
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
| | - Hongrui Chen
- School of Food and Bioengineering, Food Microbiology Key Laboratory of Sichuan Province, Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Xihua University, Chengdu, Sichuan 611130, China
| | - Lijuan Zhang
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Xu Yan
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Zijin Qin
- Department of Food Science and Technology, University of Georgia, Clarke, Athens, GA 30602, USA
| | - Shuang Cong
- College of Life Sciences, Yantai University, Yantai, Shandong 264005, China
| | - Zhijian Tan
- Institute of Bast Fiber Crops & Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Tingting Li
- College of Life Sciences, Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Ministry of Education, Dalian 116600, China
| | - Ming Du
- School of Food Science and Technology, State Key Laboratory of Marine Food Processing and Safety Control, Dalian Polytechnic University, Dalian 116034, China
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2
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Cancelarich NL, Arrulo M, Gugliotti ST, Barbosa EA, Moreira DC, Basso NG, Pérez LO, Teixeira C, Gomes P, de la Torre BG, Albericio F, Eaton P, Leite JRSA, Marani MM. First Bioprospecting Study of Skin Host-Defense Peptides in Odontophrynus americanus. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38900961 DOI: 10.1021/acs.jnatprod.4c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The adaptation of amphibians to diverse environments is closely related to the characteristics of their skin. The complex glandular system of frog skin plays a pivotal role in enabling these animals to thrive in both aquatic and terrestrial habitats and consists of crucial functions such as respiration and water balance as well as serving as a defensive barrier due to the secretion of bioactive compounds. We herein report the first investigation on the skin secretion of Odontophrynus americanus, as a potential source of bioactive peptides and also as an indicator of its evolutionary adaptations to changing environments. Americanin-1 was isolated and identified as a neutral peptide exhibiting moderate antibacterial activity against E. coli. Its amphipathic sequence including 19 amino acids and showing a propensity for α-helix structure is discussed. Comparisons of the histomorphology of the skin of O. americanus with other previously documented species within the same genus revealed distinctive features in the Patagonian specimen, differing from conspecifics from other Argentine provinces. The presence of the Eberth-Katschenko layer, a prevalence of iridophores, and the existence of glycoconjugates in its serous glands suggest that the integument is adapted to retain skin moisture. This adaptation is consistent with the prevailing aridity of its native habitat.
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Affiliation(s)
- Natalia L Cancelarich
- Instituto Patagónico para el Estudio de Ecosistemas Continentales (IPEEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bvd. Brown 2915, Puerto Madryn, Argentina U9120ACD
| | - Miriam Arrulo
- School of Medicine and Population Health, The University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Eder A Barbosa
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília, 70910-900, Brazil
- Laboratorio de Síntese e Análise de Biomoléculas, LSAB, Instituto de Química-UnB, Brasília 70910-900, Brazil
| | - Daniel C Moreira
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília, 70910-900, Brazil
| | - Néstor G Basso
- Instituto de Diversidad y Evolución Austral (IDEAus), CONICET, Bvd. Brown 2915, Puerto Madryn, Argentina U9120ACD
| | - Luis Orlando Pérez
- Instituto Patagónico de Ciencias Sociales y Humanas (IPCSH), CONICET, Bvd. Brown 2915, Puerto Madryn, Argentina U9120ACD
| | - Cátia Teixeira
- Laboratório Associado para a Química Verde-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
- Gyros Protein Technologies, Inc., Tucson, Arizona 85714, United States
| | - Paula Gomes
- Laboratório Associado para a Química Verde-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Beatriz G de la Torre
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Fernando Albericio
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- Networking Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Peter Eaton
- Bridge, School of Chemistry, University of Lincoln, Lincoln LN6 7EL, United Kingdom
| | - José R S A Leite
- Núcleo de Pesquisa em Morfologia e Imunologia Aplicada, NuPMIA, Faculdade de Medicina, Universidade de Brasília, UnB, Brasília, 70910-900, Brazil
| | - Mariela M Marani
- Instituto Patagónico para el Estudio de Ecosistemas Continentales (IPEEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bvd. Brown 2915, Puerto Madryn, Argentina U9120ACD
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3
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Mustapha T, B S, Zubair T, Patil RB, Bhongade BA, Sangshetti JN, Mali A, Babalola BJ, Moin AT, Islam T. In vitro and in silico investigation of effects of antimicrobial peptides from Solanaceae plants against rice sheath blight pathogen Rhizoctinia solani. PLoS One 2024; 19:e0302440. [PMID: 38870165 PMCID: PMC11175423 DOI: 10.1371/journal.pone.0302440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 04/01/2024] [Indexed: 06/15/2024] Open
Abstract
Rhizoctonia solani, the causative agent of sheath blight disease in rice, poses a significant threat to agricultural productivity. Traditional management approaches involving chemical fungicides have been effective but come with detrimental consequences for the ecosystem. This study aimed to investigate sustainable alternatives in the form of antifungal peptides derived from Solanaceous plant species as potential agents against R. solani. Peptide extracts were obtained using an optimized antimicrobial peptide (AMP) extraction method and desalted using the solid-phase extraction technique. The antifungal potential of peptide-rich extracts from Solanum tuberosum and Capsicum annum was assessed through in vitro tests employing the agar well diffusion method. Furthermore, peptide-protein docking analysis was performed on HPEPDOCK and HDOCK server; and molecular dynamics simulations (MDS) of 100 ns period were performed using the Gromacs 2020.4. The results demonstrated significant inhibition zones for both extracts at concentrations of 100 mg/mL. Additionally, the extracts of Solanum tuberosum and Capsicum annum had minimum inhibitory concentrations of 50 mg/mL and 25 mg/mL, respectively with minimum fungicidal concentrations of 25 mg/mL. Insights into the potential mechanisms of key peptides inhibiting R. solani targets were gleaned from in-silico studies. Notably, certain AMPs exhibited favorable free energy of binding against pathogenicity-related targets, including histone demethylase, sortin nexin, and squalene synthase, in protein-peptide docking simulations. Extended molecular dynamics simulations lasting 100 ns and MM-PBSA calculations were performed on select protein-peptide complexes. AMP10 displayed the most favorable binding free energy against all target proteins, with AMP3, AMP12b, AMP6, and AMP15 also exhibiting promising results against specific targets of R. solani. These findings underscore the potential of peptide extracts from S. tuberosum and C. annum as effective antifungal agents against rice sheath blight caused by R. solani.
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Affiliation(s)
- Tijjani Mustapha
- Department of Biological Sciences, Federal University, Dutse, Nigeria
| | - Shefin B
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Trivandrum, India
| | | | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Vadgaon (Bk), Pune, Maharashtra, India
| | - Bhoomendra A. Bhongade
- Department of Pharmaceutical Chemistry, RAK College of Pharmacy, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Jaiprakash N. Sangshetti
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, (MS), India
| | - Aniket Mali
- Cancer Research Lab, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | | | - Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
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4
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Seixas Feio JA, de Oliveira ECL, de Sales CDS, da Costa KS, e Lima AHL. Investigating molecular descriptors in cell-penetrating peptides prediction with deep learning: Employing N, O, and hydrophobicity according to the Eisenberg scale. PLoS One 2024; 19:e0305253. [PMID: 38870192 PMCID: PMC11175476 DOI: 10.1371/journal.pone.0305253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/27/2024] [Indexed: 06/15/2024] Open
Abstract
Cell-penetrating peptides comprise a group of molecules that can naturally cross the lipid bilayer membrane that protects cells, sharing physicochemical and structural properties, and having several pharmaceutical applications, particularly in drug delivery. Investigations of molecular descriptors have provided not only an improvement in the performance of classifiers but also less computational complexity and an enhanced understanding of membrane permeability. Furthermore, the employment of new technologies, such as the construction of deep learning models using overfitting treatment, promotes advantages in tackling this problem. In this study, the descriptors nitrogen, oxygen, and hydrophobicity on the Eisenberg scale were investigated, using the proposed ConvBoost-CPP composed of an improved convolutional neural network with overfitting treatment and an XGBoost model with adjusted hyperparameters. The results revealed favorable to the use of ConvBoost-CPP, having as input nitrogen, oxygen, and hydrophobicity together with ten other descriptors previously investigated in this research line, showing an increase in accuracy from 88% to 91.2% in cross-validation and 82.6% to 91.3% in independent test.
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Affiliation(s)
- Juliana Auzier Seixas Feio
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
| | - Ewerton Cristhian Lima de Oliveira
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - Claudomiro de Souza de Sales
- Laboratório de Inteligência Computacional e Pesquisa Operacional, Campus Belém, Instituto de Tecnologia, Universidade Federal do Pará, Pará, Brazil
| | - Kauê Santana da Costa
- Laboratório de Simulação Computacional, Campus Marechal Rondom, Instituto de Biodiversidade, Universidade Federal do Oeste do Pará, Santarém, Pará, Brazil
| | - Anderson Henrique Lima e Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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5
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Sahoo PK, Hanovice N, Ward P, Agrawal M, Smith TP, SiMa H, Dulin JN, Vaughn LS, Tuszynski M, Welshhans K, Benowitz L, English A, Houle JD, Twiss JL. Disruption of Core Stress Granule Protein Aggregates Promotes CNS Axon Regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597743. [PMID: 38895344 PMCID: PMC11185597 DOI: 10.1101/2024.06.07.597743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Depletion or inhibition of core stress granule proteins, G3BP1 in mammals and TIAR-2 in C. elegans , increases axon regeneration in injured neurons that show spontaneous regeneration. Inhibition of G3BP1 by expression of its acidic or 'B-domain' accelerates axon regeneration after nerve injury bringing a potential therapeutic intervention to promote neural repair in the peripheral nervous system. Here, we asked if G3BP1 inhibition is a viable strategy to promote regeneration in the injured mammalian central nervous system where axons do not regenerate spontaneously. G3BP1 B-domain expression was found to promote axon regeneration in both the mammalian spinal cord and optic nerve. Moreover, a cell permeable peptide to a subregion of G3BP1's B-domain (rodent G3BP1 amino acids 190-208) accelerated axon regeneration after peripheral nerve injury and promoted the regrowth of reticulospinal axons into the distal transected spinal cord through a bridging peripheral nerve graft. The rodent and human G3BP1 peptides promoted axon growth from rodent and human neurons cultured on permissive substrates, and this function required alternating Glu/Asp-Pro repeats that impart a unique predicted tertiary structure. These studies point to G3BP1 granules as a critical impediment to CNS axon regeneration and indicate that G3BP1 granule disassembly represents a novel therapeutic strategy for promoting neural repair after CNS injury.
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6
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Duarte Filho LAMDS, Yanaguibashi Leal CE, Bodet PE, Beserra de Alencar Filho E, Almeida JRGDS, Porta Zapata M, Achour O, Groult H, Gouveia Veloso CA, Viegas Júnior C, Bourgougnon N, Picot L. The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy. Mar Drugs 2024; 22:244. [PMID: 38921555 PMCID: PMC11205194 DOI: 10.3390/md22060244] [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: 01/16/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Brown seaweeds of the Fucus genus represent a rich source of natural antiviral products. In this study, a Fucus ceranoides hydroalcoholic extract (FCHE) was found to inhibit 74.2 ± 1.3% of the proteolytic activity of the free SARS-CoV-2 3CL protease (3CLpro), an enzyme that plays a pivotal role in polyprotein processing during coronavirus replication and has been identified as a relevant drug discovery target for SARS- and MERS-CoVs infections. To purify and identify 3CLpro ligands with potential inhibitory activity using a one-step approach, we immobilized the enzyme onto magnetic microbeads (3CLpro-MPs), checked that the enzymatic activity was maintained after grafting, and used this bait for a ligand-fishing strategy followed by a high-resolution mass spectrometry analysis of the fished-out molecules. Proof of concept for the ligand-fishing capacity of the 3CLpro-MPs was demonstrated by doping the FCHE extract with the substrate peptide TSAVLQ-pNA, resulting in the preferential capture of this high-affinity peptide within the macroalgal complex matrix. Ligand fishing in the FCHE alone led to the purification and identification via high-resolution mass spectrometry (HRMS) of seven hepta-, octa-, and decapeptides in an eluate mix that significantly inhibited the free 3CLpro more than the starting FCHE (82.7 ± 2.2% inhibition). Molecular docking simulations of the interaction between each of the seven peptides and the 3CLpro demonstrated a high affinity for the enzyme's proteolytic active site surpassing that of the most affine peptide ligand identified so far (a co-crystallographic peptide). Testing of the corresponding synthetic peptides demonstrated that four out of seven significantly inhibited the free 3CLpro (from 46.9 ± 6.4 to 76.8 ± 3.6% inhibition at 10 µM). This study is the first report identifying peptides from Fucus ceranoides with high inhibitory activity against the SARS-CoV-2 3CLprotease which bind with high affinity to the protease's active site. It also confirms the effectiveness of the ligand-fishing strategy for the single-step purification of enzyme inhibitors from complex seaweed matrices.
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Affiliation(s)
| | - Cintia Emi Yanaguibashi Leal
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Université de Picardie Jules Verne, 80039 Amiens, France;
| | - Pierre-Edouard Bodet
- Plateforme D’analyse Haute Résolution des Biomolécules, UMR CNRS 7266 LIENSs, La Rochelle Université, 17042 La Rochelle, France;
| | | | | | - Manon Porta Zapata
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Oussama Achour
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Hugo Groult
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Carlos Arthur Gouveia Veloso
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Claudio Viegas Júnior
- Institute of Chemistry, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil;
| | - Nathalie Bourgougnon
- Laboratoire de Biotechnologie et Chimie Marines, LBCM, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56000 Vannes, France;
| | - Laurent Picot
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
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7
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Kröner L, Lötters S, Hopp MT. Insights into caudate amphibian skin secretions with a focus on the chemistry and bioactivity of derived peptides. Biol Chem 2024; 0:hsz-2024-0035. [PMID: 38766708 DOI: 10.1515/hsz-2024-0035] [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: 02/28/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Amphibians are well-known for their ability to produce and secrete a mixture of bioactive substances in specialized skin glands for the purpose of antibiotic self-protection and defense against predators. Some of these secretions contain various small molecules, such as the highly toxic batrachotoxin, tetrodotoxin, and samandarine. For some time, the presence of peptides in amphibian skin secretions has attracted researchers, consisting of a diverse collection of - to the current state of knowledge - three to 104 amino acid long sequences. From these more than 2000 peptides many are known to exert antimicrobial effects. In addition, there are some reports on amphibian skin peptides that can promote wound healing, regulate immunoreactions, and may serve as antiparasitic and antioxidative substances. So far, the focus has mainly been on skin peptides from frogs and toads (Anura), eclipsing the research on skin peptides of the ca. 700 salamanders and newts (Caudata). Just recently, several novel observations dealing with caudate peptides and their structure-function relationships were reported. This review focuses on the chemistry and bioactivity of caudate amphibian skin peptides and their potential as novel agents for clinical applications.
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Affiliation(s)
- Lorena Kröner
- Department of Chemistry, Institute for Integrated Natural Sciences, 38899 University of Koblenz , D-56070 Koblenz, Germany
| | - Stefan Lötters
- Department of Biogeography, University of Trier, D-54286 Trier, Germany
| | - Marie-T Hopp
- Department of Chemistry, Institute for Integrated Natural Sciences, 38899 University of Koblenz , D-56070 Koblenz, Germany
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8
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Calcagnile M, Damiano F, Lobreglio G, Siculella L, Bozzetti MP, Forgez P, Malgoyre A, Libert N, Bucci C, Alifano M, Alifano P. In silico evidence that substitution of glycine for valine (p.G8V) in a common variant of TMPRSS2 isoform 1 increases accessibility to an endocytic signal: Implication for SARS-cov-2 entry into host cells and susceptibility to COVID-19. Biochimie 2024; 225:89-98. [PMID: 38754620 DOI: 10.1016/j.biochi.2024.05.004] [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: 02/16/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The TMPRSS2 protease plays a key role in the entry of the SARS-CoV-2 into cells. The TMPRSS2 gene is highly polymorphic in humans, and some polymorphisms may affect the susceptibility to COVID-19 or disease severity. rs75603675 (c.23G > T) is a missense variant that causes the replacement of glycine with valine at position 8 (p.G8V) in the TMPRSS2 isoform 1. According to GnomAD v4.0.0 database, the allele frequency of the rs75603675 on a global scale is 38.10 %, and range from 0.92 % in East Asian to 40.77 % in non-Finnish European (NFE) population. We analyzed the occurrence of the rs75603675 in two cohorts of patients, the first with severe/critical COVID-19 enrolled in a French hospital (42 patients), and the second with predominantly asymptomatic/pauci-symptomatic/mild COVID-19 enrolled in an Italian hospital (69 patients). We found that the TMPRSS2-c.23T minor allele frequency was similar in the two cohorts, 46.43 % and 46.38 %, respectively, and higher than the frequency in the NFE population (40.77 %). Chi-square test provided significant results (p < 0.05) when the genotype data (TMPRSS2-c.23T/c.23T homozygotes + TMPRSS2-c.23G/c.23T heterozygotes vs. TMPRSS2-c.23G/c.23G homozygotes) of the two patient groups were pooled and compared to the expected data for the NFE population, suggesting a possible pathogenetic mechanism of the p.G8V substitution. We explored the possible effects of the p.G8V substitution and found that the N-terminal region of the TMPRSS2 isoform 1 contains a signal for clathrin/AP-2-dependent endocytosis. In silico analysis predicted that the p.G8V substitution may increase the accessibility to the endocytic signal, which could help SARS-CoV-2 enter cells.
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Affiliation(s)
- Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Giambattista Lobreglio
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100, Lecce, Italy
| | - Luisa Siculella
- Department of Experimental Medicine, University of Salento, Lecce, Italy
| | - Maria Pia Bozzetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Patricia Forgez
- INSERM UMR-S 1124 T3S, Eq 5 CELLULAR HOMEOSTASIS, CANCER and THERAPY, University of Paris, Campus Saint Germain, Paris, France
| | - Alexandra Malgoyre
- Institut de Recherche Biomedicale des Armées, French Armed Forces Health Services, Brétigny sur Orge, France; Ecole Du Val de Grâce, French Armed Forces Health Service, France; Laboratoire de Biologie de L'Exercice pour La Performance et La Santé, Université Evry-Paris-Saclay, Evry, France
| | - Nicolas Libert
- Ecole Du Val de Grâce, French Armed Forces Health Service, France; Hopital D'Instruction des Armées, French Armed Forces Health Services, Clamart, France
| | - Cecilia Bucci
- Department of Experimental Medicine, University of Salento, Lecce, Italy
| | - Marco Alifano
- Thoracic Surgery Department, Cochin Hospital, APHP Centre, University of Paris, France; INSERM U1138 Team «Cancer, Immune Control, and Escape», Cordeliers Research Center, University of Paris, France.
| | - Pietro Alifano
- Department of Experimental Medicine, University of Salento, Lecce, Italy.
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9
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Shanthappa PM, Suravajhala R, Kumar G, Melethadathil N. Computational exploration of novel antimicrobial modalities targeting fucose-binding lectins and ribosomes in Mycobacterium smegmatis using tRNA-encoded peptides. J Biomol Struct Dyn 2024:1-13. [PMID: 38676533 DOI: 10.1080/07391102.2024.2335555] [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: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role of tRNAs in biology and has expanded our understanding of the genetic code. This presents an immense, unexplored potential in the realm of tRNA-peptide interactions, paving the way for groundbreaking discoveries and innovative applications in various biological functions. This study explores the antimicrobial potential of tREPs against protein targets by employing a computational method that uses verified data sources and highly recognized predictive algorithms to provide a sorted list of likely antimicrobial peptides, which were then filtered for toxicity, cell permeability, allergenicity and half-life. These peptides were then docked with screened protein targets and computationally validated using molecular dynamics (MD) simulations for 150 ns and the binding free energy was estimated. The peptides Pep2 (VVLWRKPRVRKTG) and Pep6 (HRLRLRRRKPWW) exhibited good binding affinities of -110.5 +/- 2.5 and -129.0 +/- 3.9, respectively, with RMSD values of 0.4 and 0.25 nm against the fucose-binding lectin (7NEF) and the 30S ribosome of Mycobacterium smegmatis (5O5J) protein targets. The 7NEF-Pep2 and 5O5J-Pep6 complexes indicated higher negative binding free energies of -52.55 kcal/mol and -55.52 kcal/mol respectively, as calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). Thus, the tREPs derived peptides designed as a part of this study, provide novel approaches for potential anti-bacterial therapeutic modalities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pallavi M Shanthappa
- Department of Computer Science, School of Computing, Amrita Vishwa Vidyapeetham, Mysuru, India
| | | | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, India
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10
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Zhang X, Malle MG, Thomsen RP, Sørensen RS, Sørensen EW, Hatzakis NS, Kjems J. Deconvoluting the Effect of Cell-Penetrating Peptides for Enhanced and Controlled Insertion of Large-Scale DNA Nanopores. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18422-18433. [PMID: 38573069 DOI: 10.1021/acsami.3c18636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA nanopores have emerged as powerful tools for molecular sensing, but the efficient insertion of large DNA nanopores into lipid membranes remains challenging. In this study, we investigate the potential of cell-penetrating peptides (CPPs), specifically SynB1 and GALA, to enhance the insertion efficiency of large DNA nanopores. We constructed SynB1- or GALA-functionalized DNA nanopores with an 11 nm inner diameter and visualized and quantified their membrane insertion using a TIRF microscopy-based single-liposome assay. The results demonstrated that incorporating an increasing number of SynB1 or GALA peptides into the DNA nanopore significantly enhanced the membrane perforation. Kinetic analysis revealed that the DNA nanopore scaffold played a role in prearranging the CPPs, which facilitated membrane interaction and pore formation. Notably, the use of pH-responsive GALA peptides allowed highly efficient and pH-controlled insertion of large DNA pores. Furthermore, single-channel recording elucidated that the insertion process of single GALA-modified nanopores into planar lipid bilayers was dynamic, likely forming transient large toroidal pores. Overall, our study highlights the potential of CPPs as insertion enhancers for DNA nanopores, which opens avenues for improved molecule sensing and the controlled release of cargo molecules.
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Affiliation(s)
- Xialin Zhang
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | - Rasmus P Thomsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
| | | | | | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
- Novonordisk Center for Protein Research, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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11
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Pradhan S, Mirdha L, Sengupta T, Chakraborty H. Phosphatidylglycerol Acts as a Switch for Cholesterol-Dependent Membrane Binding of ApoE Signal Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8126-8132. [PMID: 38568020 DOI: 10.1021/acs.langmuir.4c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The apolipoprotein E (ApoE) signal peptide is a short stretch of N-terminal amino acids that direct the ApoE protein to the endoplasmic reticulum after synthesis. Previous studies have shown that this peptide can bind to lipid membranes in a cholesterol-dependent manner; however, the mechanism of this interaction is yet to be clarified. In this study, we aimed to investigate how the composition of neighboring lipids affects the membrane-binding of the ApoE signal peptide. We found that a negatively charged lipid, such as phosphatidylglycerol, can act as a switch that reduces the binding efficiency of the peptide to cholesterol-rich membranes. Interestingly, phosphatidylethanolamine does not activate the cholesterol-dependent binding of the ApoE signal peptide yet acts synergistically to enhance the cholesterol sensitivity in phosphatidylglycerol-containing membranes. To the best of our knowledge, this is the first report of modulation of the affinity of a peptide for a membrane by a neighboring lipid rather than by the lipid-binding domain of the peptide. Our findings revealed a novel role of lipid diversity in modulating the membrane binding of the ApoE signal peptide and its potential implications in the unidirectional trafficking of a newly synthesized protein from the ribosomes to the endoplasmic reticulum.
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Affiliation(s)
- Sasmita Pradhan
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Lipika Mirdha
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Tanusree Sengupta
- Department of Chemistry, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
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12
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Rizarullah, Aditama R, Giri-Rachman EA, Hertadi R. Designing a Novel Multiepitope Vaccine from the Human Papilloma Virus E1 and E2 Proteins for Indonesia with Immunoinformatics and Molecular Dynamics Approaches. ACS OMEGA 2024; 9:16547-16562. [PMID: 38617694 PMCID: PMC11007845 DOI: 10.1021/acsomega.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
One of the deadliest malignant cancer in women globally is cervical cancer. Specifically, cervical cancer is the second most common type of cancer in Indonesia. The main infectious agent of cervical cancer is the human papilloma virus (HPV). Although licensed prophylactic vaccines are available, cervical cancer cases are on the rise. Therapy using multiepitope-based vaccines is a very promising therapy for cervical cancer. This study aimed to develop a multiepitope vaccine based on the E1 and E2 proteins of HPV 16, 18, 45, and 52 using in silico. In this study, we develop a novel multiepitope vaccine candidate using an immunoinformatic approach. We predicted the epitopes of the cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) and evaluated their immunogenic properties. Population coverage analysis of qualified epitopes was conducted to determine the successful use of the vaccine worldwide. The epitopes were constructed into a multiepitope vaccine by using AAY linkers between the CTL epitopes and GPGPG linkers between the HTL epitopes. The tertiary structure of the multiepitope vaccine was modeled with AlphaFold and was evaluated by Prosa-web. The results of vaccine construction were analyzed for B-cell epitope prediction, molecular docking with Toll like receptor-4 (TLR4), and molecular dynamics simulation. The results of epitope prediction obtained 4 CTL epitopes and 7 HTL epitopes that are eligible for construction of multiepitope vaccines. Prediction of the physicochemical properties of multiepitope vaccines obtained good results for recombinant protein production. The interaction showed that the interaction of the multiepitope vaccine-TLR4 complex is stable based on the binding free energy value -106.5 kcal/mol. The results of the immune response simulation show that multiepitope vaccine candidates could activate the adaptive and humoral immune systems and generate long-term B-cell memory. According to these results, the development of a multiepitope vaccine with a reverse vaccinology approach is a breakthrough to develop potential cervical cancer therapeutic vaccines.
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Affiliation(s)
- Rizarullah
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
- Department
of Biochemistry, Faculty of Medicine, Abulyatama
University, Jl. Blangbintang Lama, Aceh Besar 23372, Indonesia
| | - Reza Aditama
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Genetics
and Molecular Biotechnology Research Division, School of Life Sciences
and Technology, Bandung Institute of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Rukman Hertadi
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
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13
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Daniel G, Hilan G, Ploeg L, Sabatino D. Self-assembly of amphiphilic helical-coiled peptide nanofibers and inhibition of fibril formation with curcumin. Bioorg Med Chem Lett 2024; 102:129682. [PMID: 38432287 DOI: 10.1016/j.bmcl.2024.129682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Amphiphilic peptide sequences are conducive to secondary structures that self-assemble into higher-ordered peptide nanostructures. A select set of amphiphilic polycationic peptides displayed stable helical-coiled structures that self-assembled into peptide nanofibers. The progression of peptide fibril formation revealed short protofibrils that extended into thin filaments and into an entangled network of nanofibers over an extended (5 days) incubation period. Ligand binding with 8-anilinonaphthalene-1-sulfonic acid (ANS) and Congo Red (CR) confirmed the amphiphilic helical-coiled peptide structure assembly into nanofibers, whereas curcumin treatment led to inhibition of fibril formation. Considering the vast repertoire of fibrous biomaterials and peptide or protein (mis)folding contingent on fibril formation, this work relates the molecular interplay in between sequence composition, structural folding and the ligand binding events impacting peptide self-assembly into nanofibers.
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Affiliation(s)
- Grace Daniel
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada; Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - George Hilan
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Lisa Ploeg
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - David Sabatino
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada; Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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14
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Mustieles-Del-Ser P, Ruano-Gallego D, Parro V. Immunoanalytical Detection of Conserved Peptides: Refining the Universe of Biomarker Targets in Planetary Exploration. Anal Chem 2024; 96:4764-4773. [PMID: 38484023 DOI: 10.1021/acs.analchem.3c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Ancient peptides are remnants of early biochemistry that continue to play pivotal roles in current proteins. They are simple molecules yet complex enough to exhibit independent functions, being products of an evolved biochemistry at the interface of life and nonlife. Their adsorption to minerals may contribute to their stabilization and preservation over time. To investigate the feasibility of conserved peptide sequences and structures as target biomarkers for the search for life on Mars or other planetary bodies, we conducted a bioinformatics selection of well-conserved ancient peptides and produced polyclonal antibodies for their detection using fluorescence microarray immunoassays. Additionally, we explored how adsorbing peptides to Mars-representative minerals to form organomineral complexes could affect their immunological detection. The results demonstrated that the selected peptides exhibited autonomous folding, with some of them regaining their structure, even after denaturation. Furthermore, their cognate antibodies detected their conformational features regardless of amino acid sequences, thereby broadening the spectrum of target peptide sequences. While certain antibodies displayed unspecific binding to bare minerals, we validated that peptide-mineral complexes can be detected using sandwich immunoassays, as confirmed through desorption and competitive assays. Consequently, we conclude that the diversity of peptide sequences and structures suitable for use as target biomarkers in astrobiology can be constrained to a few well conserved sets, and they can be detected even if they are adsorbed in organomineral complexes.
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Affiliation(s)
- Pedro Mustieles-Del-Ser
- Centro de Astrobiología (CAB) INTA-CSIC, Torrejón de Ardoz 28850, Spain
- Departments of Physics and Mathematics, and Automatics, Universidad de Alcalá (UAH), Alcalá de Henares 28805, Spain
| | | | - Víctor Parro
- Centro de Astrobiología (CAB) INTA-CSIC, Torrejón de Ardoz 28850, Spain
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15
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Shams MH, Sohrabi SM, Jafari R, Sheikhian A, Motedayyen H, Baharvand PA, Hasanvand A, Fouladvand A, Assarehzadegan MA. Designing a T-cell epitope-based vaccine using in silico approaches against the Sal k 1 allergen of Salsola kali plant. Sci Rep 2024; 14:5040. [PMID: 38424208 PMCID: PMC10904830 DOI: 10.1038/s41598-024-55788-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Allergens originated from Salsola kali (Russian thistle) pollen grains are one of the most important sources of aeroallergens causing pollinosis in desert and semi-desert regions. T-cell epitope-based vaccines (TEV) are more effective among different therapeutic approaches developed to alleviate allergic diseases. The physicochemical properties, and B as well as T cell epitopes of Sal k 1 (a major allergen of S. kali) were predicted using immunoinformatic tools. A TEV was constructed using the linkers EAAAK, GPGPG and the most suitable CD4+ T cell epitopes. RS04 adjuvant was added as a TLR4 agonist to the amino (N) and carboxyl (C) terminus of the TEV protein. The secondary and tertiary structures, solubility, allergenicity, toxicity, stability, physicochemical properties, docking with immune receptors, BLASTp against the human and microbiota proteomes, and in silico cloning of the designed TEV were assessed using immunoinformatic analyses. Two CD4+ T cell epitopes of Sal k1 that had high affinity with different alleles of MHC-II were selected and used in the TEV. The molecular docking of the TEV with HLADRB1, and TLR4 showed TEV strong interactions and stable binding pose to these receptors. Moreover, the codon optimized TEV sequence was cloned between NcoI and XhoI restriction sites of pET-28a(+) expression plasmid. The designed TEV can be used as a promising candidate in allergen-specific immunotherapy against S. kali. Nonetheless, effectiveness of this vaccine should be validated through immunological bioassays.
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Affiliation(s)
- Mohammad Hossein Shams
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetic, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Box 6814993165, Ahvaz, Iran
| | - Reza Jafari
- School of Allied Medical Sciences, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Ali Sheikhian
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hossein Motedayyen
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Peyman Amanolahi Baharvand
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Amin Hasanvand
- Department of Physiology and Pharmacology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Ali Fouladvand
- Hepatitis Research Center and Department of Medical Immunology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohammad-Ali Assarehzadegan
- Immunology Research Center, Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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16
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Moreau C, Lukačević T, Pallier A, Sobilo J, Aci-Sèche S, Garnier N, Même S, Tóth É, Lacerda S. Peptide-Conjugated MRI Probe Targeted to Netrin-1, a Novel Metastatic Breast Cancer Biomarker. Bioconjug Chem 2024; 35:265-275. [PMID: 38340041 DOI: 10.1021/acs.bioconjchem.3c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Despite significant progress in cancer imaging and treatment over the years, early diagnosis and metastasis detection remain a challenge. Molecular magnetic resonance imaging (MRI), with its high resolution, can be well adapted to fulfill this need, requiring the design of contrast agents which target specific tumor biomarkers. Netrin-1 is an extracellular protein overexpressed in metastatic breast cancer and implicated in tumor progression and the appearance of metastasis. This study focuses on the design and preclinical evaluation of a novel Netrin-1-specific peptide-based MRI probe, GdDOTA-KKTHDAVR (Gd-K), to visualize metastatic breast cancer. The targeting peptide sequence was identified based on the X-ray structure of the complex between Netrin-1 and its transmembrane receptor DCC. Molecular docking simulations support the probe design. In vitro studies evidenced submicromolar affinity of Gd-K for Netrin-1 (KD = 0.29 μM) and good MRI efficacy (proton relaxivity, r1 = 4.75 mM-1 s-1 at 9.4 T, 37 °C). In vivo MRI studies in a murine model of triple-negative metastatic breast cancer revealed successful tumor visualization at earlier stages of tumor development (smaller tumor volume). Excellent signal enhancement, 120% at 2 min and 70% up to 35 min post injection, was achieved (0.2 mmol/kg injected dose), representing a reasonable imaging time window and a superior contrast enhancement in the tumor as compared to Dotarem injection.
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Affiliation(s)
- Clémentine Moreau
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Tea Lukačević
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Agnès Pallier
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Julien Sobilo
- TAAM-In vivo Imaging Centre, MO2VING, CNRS UAR44, F-45071 Orléans 2, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique, UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067 Orléans Cedex 2, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Sandra Même
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Éva Tóth
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
| | - Sara Lacerda
- Centre de Biophysique Moléculaire, CNRS UPR4301, Université d'Orléans, Rue Charles Sadron, 45071 Orléans Cedex 2, France
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17
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Sodhi H, Panitch A. A Tunable Glycosaminoglycan-Peptide Nanoparticle Platform for the Protection of Therapeutic Peptides. Pharmaceutics 2024; 16:173. [PMID: 38399234 PMCID: PMC10892384 DOI: 10.3390/pharmaceutics16020173] [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: 12/29/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The popularity of Glycosaminoglycans (GAGs) in drug delivery systems has grown as their innate ability to sequester and release charged molecules makes them adept in the controlled release of therapeutics. However, peptide therapeutics have been relegated to synthetic, polymeric systems, despite their high specificity and efficacy as therapeutics because they are rapidly degraded in vivo when not encapsulated. We present a GAG-based nanoparticle system for the easy encapsulation of cationic peptides, which offers control over particle diameter, peptide release behavior, and swelling behavior, as well as protection from proteolytic degradation, using a singular, organic polymer and no covalent linkages. These nanoparticles can encapsulate cargo with a particle diameter range spanning 130-220 nm and can be tuned to release cargo over a pH range of 4.5 to neutral through the modulation of the degree of sulfation and the molecular weight of the GAG. This particle system also confers better in vitro performance than the unencapsulated peptide via protection from enzymatic degradation. This method provides a facile way to protect therapeutic peptides via the inclusion of the presented binding sequence and can likely be expanded to larger, more diverse cargo as well, abrogating the complexity of previously demonstrated systems while offering broader tunability.
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Affiliation(s)
- Harkanwalpreet Sodhi
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA;
| | - Alyssa Panitch
- Department of Biomedical Engineering, University of California, Davis, CA 95616, USA;
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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18
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Chen YC, Wu HY, Lin LC, Chang CW, Liao PC. Characterizing the D-Amino Acid Position in Peptide Epimers by Using Higher-Energy Collisional Dissociation Tandem Mass Spectrometry: A Case Study of Liraglutide. Int J Mol Sci 2024; 25:1379. [PMID: 38338662 PMCID: PMC10855602 DOI: 10.3390/ijms25031379] [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: 12/08/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
D-amino acid-containing peptides (DAACPs) occur in biological and artificial environments. Since the importance of DAACPs has been recognized, various mass spectrometry-based analytical approaches have been developed. However, the capability of higher-energy collisional dissociation (HCD) fragmentation to characterize DAACP sites has not been evaluated. In this study, we compared the normalized spectra intensity under different conditions of HCD and used liraglutide along with its DAACPs as examples. Our results indicated that the difference in the intensity of y ions between DAACPs and all-L liraglutide could not only distinguish them but also localize the sites of D-amino acids in the DAACPs. Our data demonstrate the potential of using HCD for the site characterization of DAACPs, which may have great impact in biological studies and peptide drug development.
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Affiliation(s)
- Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei 106, Taiwan
| | | | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
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19
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Badaczewska-Dawid A, Wróblewski K, Kurcinski M, Kmiecik S. Structure prediction of linear and cyclic peptides using CABS-flex. Brief Bioinform 2024; 25:bbae003. [PMID: 38305457 PMCID: PMC10836054 DOI: 10.1093/bib/bbae003] [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: 06/30/2023] [Revised: 12/08/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.
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Affiliation(s)
| | - Karol Wróblewski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Mateusz Kurcinski
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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20
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Dolley A, Goswami HB, Dowerah D, Dey U, Kumar A, Hmuaka V, Mukhopadhyay R, Kundu D, Varghese GM, Doley R, Chandra Deka R, Namsa ND. Reverse vaccinology and immunoinformatics approach to design a chimeric epitope vaccine against Orientia tsutsugamushi. Heliyon 2024; 10:e23616. [PMID: 38187223 PMCID: PMC10767154 DOI: 10.1016/j.heliyon.2023.e23616] [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: 03/30/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi and it is reportedly associated with up to 20 % of hospitalized cases of febrile illnesses. The major challenge of vaccine development is the lack of identified antigens that can induce both heterotypic and homotypic immunity including the production of antibodies, cytotoxic T lymphocyte, and helper T lymphocytes. We employed a comprehensive immunoinformatic prediction algorithm to identify immunogenic epitopes of the 56-kDa type-specific cell membrane surface antigen and surface cell antigen A of O. tsutsugamushi to select potential candidates for developing vaccines and diagnostic assays. We identified 35 linear and 29 continuous immunogenic B-cell epitopes and 51 and 27 strong-binding T-cell epitopes of major histocompatibility complex class I and class II molecules, respectively, in the conserved and variable regions of the 56-kDa type-specific surface antigen. The predicted B- and T-cell epitopes were used to develop immunogenic multi-epitope candidate vaccines and showed to elicit a broad-range of immune protection. A stable interactions between the multi-epitope vaccines and the host fibronectin protein were observed using docking and simulation methods. Molecular dynamics simulation studies demonstrated that the multi-epitope vaccine constructs and fibronectin docked models were stable during simulation time. Furthermore, the multi-epitope vaccine exhibited properties such as antigenicity, non-allergenicity and ability to induce interferon gamma production and had strong associations with their respective human leukocyte antigen alleles of world-wide population coverage. A correlation of immune simulations and the in-silico predicted immunogenic potential of multi-epitope vaccines implicate for further investigations to accelerate designing of epitope-based vaccine candidates and chimeric antigens for development of serological diagnostic assays for scrub typhus.
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Affiliation(s)
- Anutee Dolley
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Himanshu Ballav Goswami
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Dikshita Dowerah
- Department of Chemical Sciences, Tezpur University, Napaam, 784028, Assam, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Vanlal Hmuaka
- Entomology and Biothreat Management Division, Defence Research Laboratory, Tezpur, 784001, Assam, India
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Debasree Kundu
- Department of Infectious Diseases, Christian Medical College, Vellore, 632002, Tamil Nadu, India
| | - George M. Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, 632002, Tamil Nadu, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Napaam, 784028, Assam, India
| | - Nima D. Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
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Li W, Yang S, An J, Wang M, Li H, Liu X. Statistical Characterization of Food-Derived α-Amylase Inhibitory Peptides: Computer Simulation and Partial Least Squares Regression Analysis. Molecules 2024; 29:395. [PMID: 38257308 PMCID: PMC10819330 DOI: 10.3390/molecules29020395] [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: 12/07/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
α-Amylase inhibitory peptides are used to treat diabetes, but few studies have statistically characterized their interaction with α-amylase. This study performed the molecular docking of α-amylase with inhibitory peptides from published papers. The key sites, side chain chargeability, and hydrogen bond distribution characteristics were analyzed. Molecular dynamics simulated the role of key sites in complex stability. Moreover, partial least squares regression (PLSR) was used to analyze the contribution of different amino acids in the peptides to inhibition. The results showed that, for the α-amylase molecule, His201 and Gln63, with the highest interaction numbers (INs, 15, 15) and hydrogen bond values (HBVs, 11.50, 10.33), are the key sites on α-amylase, and amino acids with positively charged side chains were important for inhibitory activity. For the inhibitory peptides, Asp and Arg had the highest HBVs, and amino acids with charged side chains were more likely to form hydrogen bonds and exert inhibitory activity. In molecular dynamics simulations, peptides involving key binding sites formed more stable complexes with α-amylase than α-amylase alone, suggesting enhanced inhibitory effects. Further, PLSR results showed that amino acids close to the N-terminus of the inhibitory peptide, located in the third and fifth positions, were significantly correlated with its inhibitory activity. In conclusion, this study provides a new approach to developing and screening α-amylase inhibitors.
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Affiliation(s)
- Wenhui Li
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Shangci Yang
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiulong An
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Min Wang
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - He Li
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
| | - Xinqi Liu
- China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
- National Soybean Processing Industry Technology Innovation Center, Beijing Technology and Business University (BTBU), Beijing 100048, China
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22
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Khrustalev VV, Stojarov AN, Akunevich AA, Baranov OE, Popinako AV, Samoilovich EO, Yermalovich MA, Semeiko GV, Sapon EG, Cheprasova VI, Shalygo NV, Poboinev VV, Khrustaleva TA, Khrustaleva OV. Structural Shifts of the Parvovirus B19 Capsid Receptor-binding Domain: A Peptide Study. Protein Pept Lett 2024; 31:128-140. [PMID: 38053353 DOI: 10.2174/0109298665272845231121064717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/25/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Binding appropriate cellular receptors is a crucial step of a lifecycle for any virus. Structure of receptor-binding domain for a viral surface protein has to be determined before the start of future drug design projects. OBJECTIVES Investigation of pH-induced changes in the secondary structure for a capsid peptide with loss of function mutation can shed some light on the mechanism of entrance. METHODS Spectroscopic methods were accompanied by electrophoresis, ultrafiltration, and computational biochemistry. RESULTS In this study, we showed that a peptide from the receptor-binding domain of Parvovirus B19 VP1 capsid (residues 13-31) is beta-structural at pH=7.4 in 0.01 M phosphate buffer, but alpha- helical at pH=5.0, according to the circular dichroism (CD) spectroscopy results. Results of infra- red (IR) spectroscopy showed that the same peptide exists in both alpha-helical and beta-structural conformations in partial dehydration conditions both at pH=7.4 and pH=5.0. In contrast, the peptide with Y20W mutation, which is known to block the internalization of the virus, forms mostly alpha-helical conformation in partial dehydration conditions at pH=7.4. According to our hypothesis, an intermolecular antiparallel beta structure formed by the wild-type peptide in its tetramers at pH=7.4 is the prototype of the similar intermolecular antiparallel beta structure formed by the corresponding part of Parvovirus B19 receptor-binding domain with its cellular receptor (AXL). CONCLUSION Loss of function Y20W substitution in VP1 capsid protein prevents the shift into the beta-structural state by the way of alpha helix stabilization and the decrease of its ability to turn into the disordered state.
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Affiliation(s)
| | | | | | - Oleg Evgenyevich Baranov
- Bach Institute of Biochemistry, Shared-Access Equipment Centre "Industrial Biotechnology" of Russian Academy of Science, Leninskiy prospect, 33/2, Moscow, 119071, Russian Federation
| | - Anna Vladimirovna Popinako
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy prospect, 33/2, Moscow, 119071, Russian Federation
| | - Elena Olegovna Samoilovich
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Marina Anatolyevna Yermalovich
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Galina Valeryevna Semeiko
- Laboratory of Vaccine-controlled Infections, Republican Research and Practical Center for Epidemiology and Microbiology, Filimonova 23, Minsk, 220114, Belarus
| | - Egor Gennadyevich Sapon
- Laboratory of infra-red spectroscopy and infra-red microscopy, Belarusian State Technological University, Sverdlova 13a, Minsk, 220006, Belarus
| | - Victoria Igorevna Cheprasova
- Laboratory of infra-red spectroscopy and infra-red microscopy, Belarusian State Technological University, Sverdlova 13a, Minsk, 220006, Belarus
| | | | - Victor Vitoldovich Poboinev
- Department of General Chemistry, Belarusian State Medical University, Dzerzhinskogo 83, Minsk, 220045, Belarus
| | - Tatyana Aleksandrovna Khrustaleva
- Laboratory of Biomedical Technologies and Medical Rehabilitation, Institute of Physiology of the National Academy of Sciences of Belarus, Academicheskaya 28, Minsk, 220072; Belarus
| | - Olga Victorovna Khrustaleva
- Department of General Chemistry, Belarusian State Medical University, Dzerzhinskogo 83, Minsk, 220045, Belarus
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23
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Röwer C, Olaleye OO, Bischoff R, Glocker MO. Mass Spectrometric ITEM-ONE and ITEM-TWO Analyses Confirm and Refine an Assembled Epitope of an Anti-Pertuzumab Affimer. Biomolecules 2023; 14:24. [PMID: 38254624 PMCID: PMC10813730 DOI: 10.3390/biom14010024] [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: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Intact Transition Epitope Mapping-One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab's heavy chain and together form a surface area of 1381.46 Å2. Despite not being part of Pertuzumab's CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (KD m0g#) of 3.07 × 10-12. The experimentally determined apparent enthalpy (ΔHm0g#) and apparent free energy (ΔGm0g#) of the complex dissociation reaction indicate that the opposite reaction-complex formation-is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab's unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids.
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
| | - Oladapo O. Olaleye
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
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24
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Aldulaijan S. In-silico selection of peptides for the recognition of imidacloprid. PLoS One 2023; 18:e0295619. [PMID: 38085733 PMCID: PMC10715655 DOI: 10.1371/journal.pone.0295619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
The sensitive detection of pesticides using low-cost receptors designed from peptides can widen their uses in the environmental surveillance for emerging pollutants. In-silico selection of peptides can help accelerate the design of receptor sequence banks for a given target of interest. In this work, we started from Lymnaea stagnalis acetylcholine-binding protein Q55R mutant receptor-imidacloprid complex, available in the PDB databank, to select three primary short peptides (YSP09, DMR12, WQW13 respectively having 9, 12 and 13 amino acids (AA) in length) from the pesticide interacting zones with the A, B and C chains of the nicotinic receptor. Using molecular docking and molecular dynamics (MD) simulations, we showed that the three peptides can form complexes with the target imidacloprid, having energies close to that obtained from a reference RNR12 peptide. Combination of these peptides allowed preparing a new set of longer peptides (YSM21, PSM22, PSW31 and WQA34) that have higher stability and affinity as shown by the MM-PBSA calculations. In particular, the WQA34 peptide displayed an average binding free energy of -6.44±0.27 kcal/mol, which is three times higher than that of the reference RNR12 peptide (-2.29±0.25 kcal/mol) and formed a stable complex with imidacloprid. Furthermore, the dissociation constants (Kd), calculated from the binding free energy, showed that WQA32 (40 μM) has three orders of magnitude lower Kd than the reference RNR12 peptide (3.4 × 104 μM). Docking and RMSD scores showed that the WQA34 peptide is potentially selective to the target imidacloprid with respect to acetamiprid and clothianidin. Therefore, this peptide can be used in wet-lab experiments to prepare a biosensor to selectively detect imidacloprid.
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Affiliation(s)
- Sarah Aldulaijan
- Chemistry Department, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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25
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Kumari S, Kessel A, Singhal D, Kaur G, Bern D, Lemay-St-Denis C, Singh J, Jain S. Computational identification of a multi-peptide vaccine candidate in E2 glycoprotein against diverse Hepatitis C virus genotypes. J Biomol Struct Dyn 2023; 41:11044-11061. [PMID: 37194293 DOI: 10.1080/07391102.2023.2212777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/11/2022] [Indexed: 05/18/2023]
Abstract
Hepatitis C Virus (HCV) is estimated to affect nearly 180 million people worldwide, culminating in ∼0.7 million yearly casualties. However, a safe vaccine against HCV is not yet available. This study endeavored to identify a multi-genotypic, multi-epitopic, safe, and globally competent HCV vaccine candidate. We employed a consensus epitope prediction strategy to identify multi-epitopic peptides in all known envelope glycoprotein (E2) sequences, belonging to diverse HCV genotypes. The obtained peptides were screened for toxicity, allergenicity, autoimmunity and antigenicity, resulting in two favorable peptides viz., P2 (VYCFTPSPVVVG) and P3 (YRLWHYPCTV). Evolutionary conservation analysis indicated that P2 and P3 are highly conserved, supporting their use as part of a designed multi-genotypic vaccine. Population coverage analysis revealed that P2 and P3 are likely to be presented by >89% Human Leukocyte Antigen (HLA) molecules from six geographical regions. Indeed, molecular docking predicted the physical binding of P2 and P3 to various representative HLAs. We designed a vaccine construct using these peptides and assessed its binding to toll-like receptor 4 (TLR-4) by molecular docking and simulation. Subsequent analysis by energy-based and machine learning tools predicted high binding affinity and pinpointed the key binding residues (i.e. hotspots) in P2 and P3. Also, a favorable immunogenic profile of the construct was predicted by immune simulations. We encourage the scientific community to validate our vaccine construct in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shweta Kumari
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Divya Singhal
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - David Bern
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | - Jasdeep Singh
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Sahil Jain
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
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26
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Lima JCB, Barbosa JARG. Interaction models between peptide substrate and Alphavirus Protease nsP2 of Chikungunya and Mayaro and implications to the mechanism of action. J Biomol Struct Dyn 2023; 41:10851-10858. [PMID: 36562200 DOI: 10.1080/07391102.2022.2158941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The Arbovirus (Arthropod-borne virus) is a group which comprises viruses whose transmission is carried out by arthropod vectors infecting vertebrates. Some arboviruses related to human diseases have been given considerable relevance as Chikungunya and Mayaro of the family Togaviridae, genus Alphavirus. The lack of proper specific treatment has prompted the requirement for deeper structural studies that could unveil leads to new drugs. Among possible targets, viral proteases are recognized as proteins with big potential. These proteins, termed nsP2 in Alphavirus, have the function of cleaving certain regions of the viral polyprotein, being vital to the viral cycle. In this research, we used docking and molecular dynamics to analyze the contact between the protease nsP2 of Alphavirus Chikungunya and Mayaro and substrates formed by peptides with ten amino acid residues. A model of the Mayaro nsP2 was constructed based on homologous proteases. Our study suggests that the glycine specificity motif, a region where a highly conserved glycine residue in position P2 of the protease substrate is positioned, facilitates the nucleophilic attack by assisting in placing the P1 carbonyl group carbon. Stabilization of different substrate regions maybe explained by relevant contacts with the enzyme. Besides that, the phi and psi angles in the outlier region of the Ramachandran plot found for the P2 glycine of the Chikungunya substrate seems to indicate the necessity of this residue that can accommodate angles not allowed to other residues.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jônatas Cunha Barbosa Lima
- Laboratório de Biofísica Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasilia, DF, Brazil
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27
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Lenin KLD, Antony SP. In silico molecular and functional characterization of a dual function antimicrobial peptide, hepcidin (GIFT-Hep), isolated from genetically improved farmed tilapia (GIFT, Oreochromis niloticus). J Genet Eng Biotechnol 2023; 21:130. [PMID: 37987875 PMCID: PMC10663414 DOI: 10.1186/s43141-023-00579-6] [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: 09/28/2022] [Accepted: 10/26/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Antimicrobial peptides (AMPs), innate immune response molecules in organisms, are also known for their dual functionality, exemplified by hepcidin-an immunomodulator and iron regulator. Identifying and studying various AMPs from fish species can provide valuable insights into the immune profiles of aquaculturally significant fish, which can be made use of in its culture. RESULTS Hepcidin, a dual-function antimicrobial peptide, was isolated from the gill tissue of Genetically Improved Farmed Tilapia (GIFT-Hep). GIFT-Hep consists of a 90 amino acid pre-propeptide with a 24-mer signal, a 40-mer propeptide, and a 26-mer mature peptide region. The mature peptide had a molecular weight of 3015.61 Da, a theoretical pI of 8.78, a net charge of +4.25, and a protein-binding potential of 2.06 kcal/mol. Four disulfide bonds were formed by eight cysteine residues in the mature region. The presence of positively charged arginine residues renders the peptide 50% hydrophobic. Molecular analysis of GIFT-Hep revealed the presence of a furin propeptide convertase motif, RX(K/R)R, which facilitates trimming of the peptide to yield the mature GIFT-Hep. The hypothetical iron regulatory sequence, QSHLSL, was also identified in the mature peptide. In silico predictions about the characteristics of GIFT-Hep, such as charge, hydrophobicity, high surface accessibility, transmembrane helical regions, hydrophobic faces, hot spots, and cell-penetrating properties, suggest that the peptide functions as an iron regulatory antimicrobial agent. CONCLUSIONS This study reports a hepcidin antimicrobial peptide with both HAMP1 and HAMP2 properties isolated from genetically improved farmed tilapia, and further evaluation of the properties will prove the feasibility of GIFT-Hep being used as a therapeutant in aquaculture.
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Affiliation(s)
- K L Dhanya Lenin
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India
| | - Swapna P Antony
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala, 682016, India.
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28
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Muhammad AM, Salum GM, Meguid MAE, Fotouh BE, Dawood RM. Bioinformatics analysis of multi-epitope peptide vaccines against Hepatitis C virus: a molecular docking study. J Genet Eng Biotechnol 2023; 21:117. [PMID: 37962693 PMCID: PMC10646107 DOI: 10.1186/s43141-023-00583-w] [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: 01/16/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Hepatitis C Virus (HCV) infection is one of the causal agents of liver disease burden. Six multiple antigenic peptides were synthesized including (P315, P412, and P517) plus (P1771, P2121, and P2941) to induce humoral and cellular responses, respectively against HCV infection. AIM This paper aimed to employ computational tools to evaluate the efficacy of each peptide individually and to determine the most effective one for better vaccine development and/or immunotherapy. METHODS VaxiJen web and AllerTOP servers were used for antigenicity and allergenicity prediction, respectively. The ToxinPred web server was used to investigate the peptide toxicity. Each peptide was docked with its corresponding receptors. RESULTS No peptides were expected to be toxic. P315 and P2941 are predicted to have robust antigenic properties, lowest allergenicity, and minimal sOPEP energies. In turn, P315 (derived from gpE1) formed the highest hydrophobic bonds with the BCR and CD81 receptors that will elicit B cell function. P2941 (derived from NS5B) was shown to strongly bind to both CD4 and CD8 receptors that will elicit T cell function. CONCLUSION P315 successfully bound to B cell (BCR and CD81) receptors. Also, P2941 is strongly bound to T cell (CD4 and CD8) receptors.
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Affiliation(s)
- Ashraf M Muhammad
- Applied Biotechnology Program, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Ghada M Salum
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt.
| | - Mai Abd El Meguid
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Basma E Fotouh
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
| | - Reham M Dawood
- Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, Dokki, P.O. 12622, Giza, Egypt
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29
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Muhammad SA, Guo J, Noor K, Mustafa A, Amjad A, Bai B. Pangenomic and immunoinformatics based analysis of Nipah virus revealed CD4 + and CD8 + T-Cell epitopes as potential vaccine candidates. Front Pharmacol 2023; 14:1290436. [PMID: 38035008 PMCID: PMC10682379 DOI: 10.3389/fphar.2023.1290436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction: Nipah (NiV) is the zoonotic deadly bat-borne virus that causes neurological and respiratory infections which ultimately lead to death. There are 706 infected cases reported up till now especially in Asia, out of which 409 patients died. There is no vaccine and effective treatment available for NiV infections and we have to timely design such strategies as world could not bear another pandemic situation. Methods: In this study, we screened viral proteins of NiV strains based on pangenomics analysis, antigenicity, molecular weight, and sub-cellular localization. The immunoproteomics based approach was used to predict T-cell epitopes of MHC class-I and II as potential vaccine candidates. These epitopes are capable to activate CD4+, CD8+, and T-cell dependent B-lymphocytes. Results: The two surface proteins including fusion glycoprotein (F) and attachment glycoprotein (G) are antigenic with molecular weights of 60 kDa and 67 kDa respectively. Three epitopes of F protein (VNYNSEGIA, PNFILVRNT, and IKMIPNVSN) were ranked and selected based on the binding affinity with MHC class-I, and 3 epitopes (VILNKRYYS, ILVRNTLIS, and VKLQETAEK) with MHC-II molecules. Similarly, for G protein, 3 epitopes each for MHC-I (GKYDKVMPY, ILKPKLISY, and KNKIWCISL) and MHC-II (LRNIEKGKY, FLIDRINWI, and FLLKNKIWC) with substantial binding energies were predicted. Based on the physicochemical properties, all these epitopes are non-toxic, hydrophilic, and stable. Conclusion: Our vaccinomics and system-level investigation could help to trigger the host immune system to prevent NiV infection.
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Affiliation(s)
- Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Jinlei Guo
- School of Intelligent Medical Engineering, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Komal Noor
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Aymen Mustafa
- University of Health Sciences Lahore, Lahore, Pakistan
| | - Anam Amjad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Baogang Bai
- School of Information and Technology, Wenzhou Business College, Wenzhou, China
- Zhejiang Province Engineering Research Center of Intelligent Medicine, Wenzhou, China
- The 1st School of Medical, School of Information and Engineering, The 1st Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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30
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Greschner AA, Brahiti N, Auger M, Hu L, Soleymani Abyaneh H, Barbeau X, Parent V, Gaillet B, Guay D, Soultan AH, Gauthier MA. PEGylation of a Peptide-Based Amphiphilic Delivery Agent and Influence on Protein Delivery to Cells. Biomacromolecules 2023; 24:4890-4900. [PMID: 37862236 DOI: 10.1021/acs.biomac.3c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The cell membrane is a restrictive biological barrier, especially for large, charged molecules, such as proteins. The use of cell-penetrating peptides (CPPs) can facilitate the delivery of proteins, protein complexes, and peptides across the membrane by a variety of mechanisms that are all limited by endosomal sequestration. To improve CPP-mediated delivery, we previously reported the rapid and effective cytosolic delivery of proteins in vitro and in vivo by their coadministration with the peptide S10, which combines a CPP and an endosomal leakage domain. Amphiphilic peptides with hydrophobic properties, such as S10, can interact with lipids to destabilize the cell membrane, thus promoting cargo internalization or escape from endosomal entrapment. However, acute membrane destabilization can result in a dose-limiting cytotoxicity. In this context, the partial or transient deactivation of S10 by modification with methoxy poly(ethylene glycol) (mPEG; i.e., PEGylation) may provide the means to alter membrane destabilization kinetics, thereby attenuating the impact of acute permeabilization on cell viability. This study investigates the influence of PEGylation parameters (molecular weight, architecture, and conjugation chemistry) on the delivery efficiency of a green fluorescent protein tagged with a nuclear localization signal (GFP-NLS) and cytotoxicity on cells in vitro. Results suggest that PEGylation mostly interferes with adsorption and secondary structure formation of S10 at the cell membrane, and this effect is exacerbated by the mPEG molecular weight. This effect can be compensated for by increasing the concentration of conjugates prepared with lower molecular weight mPEG (5 to ∼20 kDa) but not for conjugates prepared with higher molecular weight mPEG (40 kDa). For conjugates prepared with moderate-to-high molecular weight mPEG (10 to 20 kDa), partial compensation of inactivation could be achieved by the inclusion of a reducible disulfide bond, which provides a mechanism to liberate the S10 from the polymer. Grafting multiple copies of S10 to a high-molecular-weight multiarmed PEG (40 kDa) improved GFP-NLS delivery efficiency. However, these constructs were more cytotoxic than the native peptide. Considering that PEGylation could be harnessed for altering the pharmacokinetics and biodistribution profiles of peptide-based delivery agents in vivo, the trends observed herein provide new perspectives on how to manipulate the membrane permeabilization process, which is an important variable for achieving delivery.
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Affiliation(s)
- Andrea A Greschner
- Institut National de la Recherche Scientifique (INRS),EMT Research Center, 1650 boulevard Lionel-Boulet, Varennes, QC J3X 1P7, Canada
| | - Nadine Brahiti
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
| | - Maud Auger
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
- Département de génie chimique Université Laval, Room #3570, 1065 avenue de la Médecine, Pavillon Adrien-Pouliot, Québec QC G1V 0A6, Canada
| | - Lei Hu
- Institut National de la Recherche Scientifique (INRS),EMT Research Center, 1650 boulevard Lionel-Boulet, Varennes, QC J3X 1P7, Canada
| | - Hoda Soleymani Abyaneh
- Institut National de la Recherche Scientifique (INRS),EMT Research Center, 1650 boulevard Lionel-Boulet, Varennes, QC J3X 1P7, Canada
| | - Xavier Barbeau
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
| | - Victor Parent
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
| | - Bruno Gaillet
- Département de génie chimique Université Laval, Room #3570, 1065 avenue de la Médecine, Pavillon Adrien-Pouliot, Québec QC G1V 0A6, Canada
| | - David Guay
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
- Département de génie chimique Université Laval, Room #3570, 1065 avenue de la Médecine, Pavillon Adrien-Pouliot, Québec QC G1V 0A6, Canada
| | - Al-Halifa Soultan
- Feldan Therapeutics, 2666 boulevard du Parc Technologique Suite 290, Québec QC G1P 4S6, Canada
| | - Marc A Gauthier
- Institut National de la Recherche Scientifique (INRS),EMT Research Center, 1650 boulevard Lionel-Boulet, Varennes, QC J3X 1P7, Canada
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31
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Klaiss-Luna MC, Giraldo-Lorza JM, Jemioła-Rzemińska M, Strzałka K, Manrique-Moreno M. Biophysical Insights into the Antitumoral Activity of Crotalicidin against Breast Cancer Model Membranes. Int J Mol Sci 2023; 24:16226. [PMID: 38003414 PMCID: PMC10671781 DOI: 10.3390/ijms242216226] [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: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Bioactive peptides have emerged as promising therapeutic agents with antimicrobial, antifungal, antiparasitic, and, recently, antitumoral properties with a mechanism of action based on membrane destabilization and cell death, often involving a conformational change in the peptide. This biophysical study aims to provide preliminary insights into the membrane-level antitumoral mode of action of crotalicidin, a cationic host defense peptide from rattlesnake venom, toward breast cancer cell lines. The lipid composition of breast cancer cell lines was obtained after lipid extraction and quantification to prepare representative cell membrane models. Membrane-peptide interaction studies were performed using differential scanning calorimetry and Fourier-transform infrared spectroscopy. The outcome evidences the potential antitumoral activity and selectivity of crotalicidin toward breast cancer cell lines and suggests a mechanism initiated by the electrostatic interaction of the peptide with the lipid bilayer surface and posterior conformation change with membrane intercalation between the acyl chains in negatively charged lipid systems. This research provides valuable information that clears up the antitumoral mode of action of crotalicidin.
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Affiliation(s)
- Maria C. Klaiss-Luna
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A 1226, Medellin 050010, Colombia
| | - Juan M. Giraldo-Lorza
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A 1226, Medellin 050010, Colombia
| | - Małgorzata Jemioła-Rzemińska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Kazimierz Strzałka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Marcela Manrique-Moreno
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A 1226, Medellin 050010, Colombia
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32
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Völkle Nee Evgrafov E, Schulz F, Kanold JM, Michaelis M, Wissel K, Brümmer F, Schenk AS, Ludwigs S, Bill J, Rothenstein D. Functional mimicry of sea urchin biomineralization proteins with CaCO 3-binding peptides selected by phage display. J Mater Chem B 2023; 11:10174-10188. [PMID: 37850271 DOI: 10.1039/d3tb01584j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The intricate process of biomineralization, e.g. in sea urchins, involves the precise interplay of highly regulated mineralization proteins and the spatiotemporal coordination achieved through compartmentalization. However, the investigation of biomineralization effector molecules, e.g. proteins, is challenging, due to their very low abundance. Therefore, we investigate the functional mimicry in the bioinspired precipitation of calcium carbonate (CaCO3) with artificial peptides selected from a peptide library by phage display based on peptide-binding to calcite and aragonite, respectively. The structure-directing effects of the identified peptides were compared to those of natural protein mixes isolated from skeletal (test) structures of two sea urchin species (Arbacia lixula and Paracentrotus lividus). The calcium carbonate samples deposited in the absence or presence of peptides were analyzed with a set of complementary techniques with regard to morphology, polymorph, and nanostructural motifs. Remarkably, some of the CaCO3-binding peptides induced morphological features in calcite that appeared similar to those obtained in the presence of the natural protein mixes. Many of the peptides identified as most effective in exerting a structure-directing effect on calcium carbonate crystallization were rich in basic amino acid residues. Hence, our in vitro mineralization study further highlights the important, but often neglected, role of positively charged soluble organic matrices associated with biological and bioinspired CaCO3 deposition.
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Affiliation(s)
- Elke Völkle Nee Evgrafov
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Fabian Schulz
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Julia Maxi Kanold
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Monika Michaelis
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Kerstin Wissel
- Dept. Chemical Materials Synthesis, Institute for Materials Science, University of Stuttgart, Heisenbergstraβe 3, 70569 Stuttgart, Germany
| | - Franz Brümmer
- Institute for Biomaterials and Biomolecular Systems & Scientific Diving Group (WiTUS), University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Anna S Schenk
- Physical Chemistry IV, Department of Chemistry, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Sabine Ludwigs
- IPOC - Functional Polymers, Institute of Polymer Chemistry (IPOC), University of Stuttgart, Stuttgart 70569, Germany
| | - Joachim Bill
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
| | - Dirk Rothenstein
- Dept. Bioinspired Materials, Institute for Materials Science, University of Stuttgart, Heisenbergstraße 3, 70569 Stuttgart, Germany.
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33
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Murugesan J, Mubarak SJ, Vedagiri H. Design of novel anti-quorum sensing peptides targeting LuxO to combat Vibrio cholerae pathogenesis. In Silico Pharmacol 2023; 11:30. [PMID: 37899970 PMCID: PMC10611667 DOI: 10.1007/s40203-023-00172-2] [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: 08/01/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Vibrio cholerae, the Gram-negative bacterium abruptly colonizes the human intestine causing diarrhea, employing quorum sensing (QS) system as the major survival technique for mediating biofilm formation, virulence, competence, etc. Two distinct QS systems coordinated by the auto-inducer molecules, cholera-specific CqsA/S system and universal LuxS/PQ system, operate in parallel converging into a common phosphorelay pathway involving LuxU and LuxO. The master regulatory proteins of the QS system, AphA and HapR regulate the biofilm formation based on cell density, whose expression is controlled by the global response regulator LuxO. At low cell density, activated LuxO indirectly represses HapR, favoring the virulence cascade expression. Rather at high cell densities, LuxO represses AphA expression subsequently blocking the expression of virulence factors. Hence, targeting LuxO would be a promising strategy to downregulate the virulence pathway and modulate the QS system. With this insight, the present study has been designed to intrude the interaction between LuxU and LuxO through in silico design of novel peptides and validation of these peptides through molecular simulations. QS peptides were designed using QSPred server by altering the template sequence representing the LuxU-LuxO interaction, among which PEP8 exhibited better interaction and stability with the target protein LuxO. These in silico designed novel peptides would serve as potential target-specific molecules that would inhibit the LuxU-LuxO interaction and modulate the QS system to restrict Vibrio cholerae pathogenesis. However, further in vitro validations would substantiate the efficacy of these novel QS peptides. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00172-2.
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Affiliation(s)
- Janaranjani Murugesan
- Medical Genomics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
| | - Shoufia Jabeen Mubarak
- Medical Genomics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
| | - Hemamalini Vedagiri
- Medical Genomics Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, 641046 India
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34
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Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model 2023; 63:6436-6450. [PMID: 37827517 PMCID: PMC10599322 DOI: 10.1021/acs.jcim.3c00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 10/14/2023]
Abstract
Peptides have recently regained interest as therapeutic candidates, but their development remains confronted with several limitations including low bioavailability. Backbone head-to-tail cyclization, i.e., setting a covalent peptide bond linking the last amino acid with the first one, is one effective strategy of peptide-based drug design to stabilize the conformation of bioactive peptides while preserving peptide properties in terms of low toxicity, binding affinity, target selectivity, and preventing enzymatic degradation. Starting from an active peptide, it usually requires the design of a linker of a few amino acids to make it possible to cyclize the peptide, possibly preserving the conformation of the initial peptide and not affecting its activity. However, very little is known about the sequence-structure relationship requirements of designing linkers for peptide cyclization in a rational manner. Recently, we have shown that large-scale data-mining of available protein structures can lead to the precise identification of protein loop conformations, even from remote structural classes. Here, we transpose this approach to linkers, allowing head-to-tail peptide cyclization. First we show that given a linker sequence and the conformation of the linear peptide, it is possible to accurately predict the cyclized peptide conformation. Second, and more importantly, we show that it seems possible to elaborate on the information inferred from protein structures to propose effective candidate linker sequences constrained by length and amino acid composition, providing the first framework for the rational design of head-to-tail cyclization linkers. Finally, we illustrate this for two peptides using a limited set of amino-acids likely not to interfere with peptide function. For a linear peptide derived from Nrf2, the peptide cyclized starting from the experimental structure showed a 26-fold increase in the binding affinity. For urotensin II, a peptide already cyclized by a disulfide bond that exerts a broad array of biological activities, we were able, starting from models of the structure, to design a head-to-tail cyclized peptide, the first synthesized bicyclic 14-residue long urotensin II analogue, showing a retention of in vitro activity. Although preliminary, our results strongly suggest that such an approach has strong potential for cyclic peptide-based drug design.
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Affiliation(s)
- Yasaman Karami
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Samuel Murail
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Julien Giribaldi
- Institut
des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier-CNRS, 34293 Montpellier, France
| | - Benjamin Lefranc
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Florian Defontaine
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Université
de Rouen Normandie, UR CBSA, Research Unit
Bacterial Communication and Anti-infectious Strategies, 27000 Evreux, France
| | - Jérôme Leprince
- Université
de Rouen Normandie, INSERM U1239 NorDiC, Neuroendocrine, Endocrine and Germinal Differentiation and Communication,
INSERM US51 HeRacLeS, F-76000 Rouen, France
| | - Sjoerd de Vries
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
| | - Pierre Tufféry
- Université
Paris Cité, CNRS UMR 8251,
INSERM ERL U1133, 75013 Paris, France
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35
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Cárdenas-Martínez K, Barragán-Cárdenas AC, de la Rosa-Arbeláez M, Parra-Giraldo CM, Ochoa-Zarzosa A, Lopez-Meza JE, Rivera-Monroy ZJ, Fierro-Medina R, García-Castañeda JE. Evaluating the In Vitro Activity and Safety of Modified LfcinB Peptides as Potential Colon Anticancer Agents: Cell Line Studies and Insect-Based Toxicity Assessments. ACS OMEGA 2023; 8:37948-37957. [PMID: 37867694 PMCID: PMC10586019 DOI: 10.1021/acsomega.3c03455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 10/24/2023]
Abstract
Anticancer peptides are increasingly being considered as alternative treatments for cancer due to their potency, selectivity, and low toxicity. Previously, the peptide LfcinB (21-25)Pal showed in vitro anticancer effects against the Caco-2 colon cancer cell line (half-maximal inhibitory concentration (IC50): 86 μM). In this study, we developed modifications to the peptide sequence to increase its anticancer activity. Sequence modifications were made such as the inclusion of amino hexanoic acid (Ahx), N-terminal biotinylation, acetylation, and substitutions of Orn for Arg and/or d-Arg by l-Arg. The molecules were synthesized using manual solid-phase peptide synthesis (SPPS), and their synthetic feasibility (SAScore) ranged from 6.2 to 7.6. The chromatographic purities of the synthesized peptides were greater than 89%. We found that Ahx-RWQWRWQWR and RWQWRWQW-Orn showed activity against both Caco-2 and HT-29 cell lines and decreased IC50 values by approx. 50% in Caco-2 cells (IC50: 40 μM) when compared to the parent peptide RWQWRWQWR. Moreover, the modified peptides demonstrated lower hemolytic effects, with values <10% at 200 μg/mL. Toxicity was assessed using the Galleria mellonella model and the half-maximal lethal dose (LD50) for the best peptides was >100 mg/kg, indicating that their toxicity is classified as moderately toxic or lower. In contrast, cisplatin showed an LD50 of 13 mg/Kg. The designed anticancer peptides presented good in vitro activity and low toxicity, making them promising molecules for future drug development studies.
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Affiliation(s)
- Karen
J. Cárdenas-Martínez
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Andrea C. Barragán-Cárdenas
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Manuela de la Rosa-Arbeláez
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Claudia M. Parra-Giraldo
- Proteomics
and Human Mycosis Unit, Infectious Diseases Research Group, Department
of Microbiology, Pontificia Universidad
Javeriana, Bogotá 110231, Colombia
| | - Alejandra Ochoa-Zarzosa
- Multidisciplinary
Centre for Studies in Biotechnology, Universidad
Michoacana de San Nicolas de Hidalgo, Km 9.5, Carretera Morelia, Zinapécuaro, Tarímbaro 58880, México
| | - Joel E. Lopez-Meza
- Multidisciplinary
Centre for Studies in Biotechnology, Universidad
Michoacana de San Nicolas de Hidalgo, Km 9.5, Carretera Morelia, Zinapécuaro, Tarímbaro 58880, México
| | - Zuly J. Rivera-Monroy
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Ricardo Fierro-Medina
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
| | - Javier E. García-Castañeda
- Department
of Pharmacy, Department of Biotechnology, Deparment of Chemistry, Universidad Nacional de Colombia, Carrera 45#26-85, Bogotá 111321, Colombia
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36
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Chenna A, Khan WH, Dash R, Saraswat S, Chugh A, Rathore AS, Goel G. An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins. Proteins 2023; 91:1222-1234. [PMID: 37283297 DOI: 10.1002/prot.26511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25μM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.
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Affiliation(s)
- Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Virology Unit, Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rozaleen Dash
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
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37
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Stincarelli MA, Quagliata M, Di Santo A, Pacini L, Fernandez FR, Arvia R, Rinaldi S, Papini AM, Rovero P, Giannecchini S. SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein. Virus Res 2023; 334:199170. [PMID: 37422270 PMCID: PMC10384657 DOI: 10.1016/j.virusres.2023.199170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
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Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Andrea Di Santo
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Feliciana Real Fernandez
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Silvia Rinaldi
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy.
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38
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Gholami S, Mafakher L, Fotouhi F, Bambai B, Cohan RA, Mehrbod P, Shokouhi H, Farahmand B. Computational peptide engineering approach for selection of the new C05 antibody-driven peptide with potency to blocking influenza a virus attachment; from in silico to in vivo. J Biomol Struct Dyn 2023:1-17. [PMID: 37553776 DOI: 10.1080/07391102.2023.2241554] [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: 05/04/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Antiviral drugs are currently used to prevent or treat viral infections like influenza A Virus (IAV). Nonetheless, annual genetic mutations of influenza viruses make them resistant to efficient treatment by current medications. Antiviral peptides have recently attracted researchers' attention and can potentially supplant the current medications. This study aimed to design peptides against IAV propagation. For this purpose, P2 and P3 peptides were computationally designed based on the HCDR3 region of the C05 antibody (a monoclonal antibody that neutralizes influenza HA protein and inhibits the virus attachment). The synthesized peptides were tested against the influenza A virus (A/Puerto Rico/8/34 (H1N1)) in vitro, and the most efficient peptide was selected for in vivo experiments. It was shown that the designed peptide shows much more prophylactic and therapeutic effects against the virus. These findings demonstrated that the designed peptide can control the virus infection without any cytotoxicity effect. Antiviral peptide design is acknowledged as a critical tactic to manage viral infections by preventing viral binding to the host cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shima Gholami
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Mafakher
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Fatemeh Fotouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Bijan Bambai
- Department of Systems Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Parvaneh Mehrbod
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Hadiseh Shokouhi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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Machera SJ, Niedziółka-Jönsson J, Jönsson-Niedziółka M, Szot-Karpińska K. Determination of the Dissociation Constant for Polyvalent Receptors Using ELISA: A Case of M13 Phages Displaying Troponin T-Specific Peptides. ACS OMEGA 2023; 8:26253-26262. [PMID: 37521637 PMCID: PMC10373194 DOI: 10.1021/acsomega.3c02551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (Kd). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to five copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating Kd values from ELISA experiments was developed and is presented. The determined Kd values are in the picomolar range.
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Wolf K, Kosinski J, Gibson TJ, Wesch N, Dötsch V, Genuardi M, Cordisco EL, Zeuzem S, Brieger A, Plotz G. A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation. Nucleic Acids Res 2023; 51:6307-6320. [PMID: 37224528 PMCID: PMC10325900 DOI: 10.1093/nar/gkad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.
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Affiliation(s)
- Karla Wolf
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Centre for Structural Systems Biology (CSSB), Hamburg, 22607, Germany
| | - Toby J Gibson
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, 69117, Germany
| | - Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, 60438, Germany
| | - Maurizio Genuardi
- UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome00168, Italy
| | - Emanuela Lucci Cordisco
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome00168, Italy
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Angela Brieger
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
| | - Guido Plotz
- Department of Internal Medicine 1, University Hospital, Goethe University, Frankfurt am Main, 60590, Germany
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Heidarinia H, Tajbakhsh E, Rostamian M, Momtaz H. Two peptides derivate from Acinetobacter baumannii outer membrane protein K as vaccine candidates: a comprehensive in silico study. BMC Res Notes 2023; 16:128. [PMID: 37391796 DOI: 10.1186/s13104-023-06409-9] [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: 02/11/2023] [Accepted: 06/20/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND The lack of appropriate vaccines is an obstacle to the effective management of A. baumannii infections. Peptide vaccines offer an attractive and promising preventive strategy against A. baumannii. OBJECTIVE In this study, we identified specific T cell epitopes of A. baumannii outer membrane protein K (OMPK) using comprehensive bioinformatics and detailed molecular docking analysis. METHODS Both class-I and class-II T cell epitopes of A. baumannii OMPK were predicted by three tools namely IEDB, SYFPEITHI, and ProPred. The predicted epitopes were shortlisted based on several analyses including prediction scoring, clustering, exclusion of human similarity, considering immunogenicity and cytokine production, and removal of toxic and/or allergen epitopes. The epitopic peptides with high prediction scores and appropriate properties containing both class-I and class-II T cell epitopes were selected. Two of these class I/II epitopic peptides were chosen for molecular docking studies and assessing their physicochemical properties as vaccine candidates. RESULTS The results showed many T-cell epitopes of OMPK that could be evaluated for possible immunogenicity. Two of these epitopes (containing both class-I and II epitopes) had high prediction scores, were predicted by several tools, attached to several HLAs, and had the best docking score. They had different physicochemical properties and were conserved among Acinetobacter species. DISCUSSION We identified the A. baumannii OMPK high immunogenic class-I and class-II T cell epitopes and introduced two promising high immunogenic peptides as vaccine candidates. It is recommended to perform in vitro/in vivo investigation of these peptides to determine their true efficacy and efficiency.
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Affiliation(s)
- Hana Heidarinia
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Elahe Tajbakhsh
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Imam Reza Hospital, Parastar Blvd, Kermanshah, 6714415333, Iran.
| | - Hassan Momtaz
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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Wasilewski T, Neubauer D, Wojciechowski M, Szulczyński B, Gębicki J, Kamysz W. Evaluation of Linkers' Influence on Peptide-Based Piezoelectric Biosensors' Sensitivity to Aldehydes in the Gas Phase. Int J Mol Sci 2023; 24:10610. [PMID: 37445789 DOI: 10.3390/ijms241310610] [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: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Recent findings qualified aldehydes as potential biomarkers for disease diagnosis. One of the possibilities is to use electrochemical biosensors in point-of-care (PoC), but these need further development to overcome some limitations. Currently, the primary goal is to enhance their metrological parameters in terms of sensitivity and selectivity. Previous findings indicate that peptide OBPP4 (KLLFDSLTDLKKKMSEC-NH2) is a promising candidate for further development of aldehyde-sensitive biosensors. To increase the affinity of a receptor layer to long-chain aldehydes, a structure stabilization of the peptide active site via the incorporation of different linkers was studied. Indeed, the incorporation of linkers improved sensitivity to and binding of aldehydes in comparison to that of the original peptide-based biosensor. The tendency to adopt disordered structures was diminished owing to the implementation of suitable linkers. Therefore, to improve the metrological characteristics of peptide-based piezoelectric biosensors, linkers were added at the C-terminus of OBPP4 peptide (KLLFDSLTDLKKKMSE-linker-C-NH2). Those linkers consist of proteinogenic amino acids from group one: glycine, L-proline, L-serine, and non proteinogenic amino acids from group two: β-alanine, 4-aminobutyric acid, and 6-aminohexanoic acid. Linkers were evaluated with in silico studies, followed by experimental verification. All studied linkers enhanced the detection of aldehydes in the gas phase. The highest difference in frequency (60 Hz, nonanal) was observed between original peptide-based biosensors and ones based on peptides modified with the GSGSGS linker. It allowed evaluation of the limit of detection for nonanal at the level of 2 ppm, which is nine times lower than that of the original peptide. The highest sensitivity values were also obtained for the GSGSGS linker: 0.3312, 0.4281, and 0.4676 Hz/ppm for pentanal, octanal, and nonanal, respectively. An order of magnitude increase in sensitivity was observed for the six linkers used. Generally, the linker's rigidity and the number of amino acid residues are much more essential for biosensors' metrological characteristics than the amino acid sequence itself. It was found that the longer the linkers, the better the effect on docking efficiency.
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Affiliation(s)
- Tomasz Wasilewski
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Damian Neubauer
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Bartosz Szulczyński
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jacek Gębicki
- Department of Process Engineering and Chemical Technology, Chemical Faculty, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Wojciech Kamysz
- Department of Inorganic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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Sanchis I, Spinelli R, Dias J, Brazzolotto X, Rietmann Á, Aimaretti F, Siano ÁS. Inhibition of Human Cholinesterases and in vitro β-Amyloid Aggregation by Rationally Designed Peptides. ChemMedChem 2023; 18:e202200691. [PMID: 36995341 DOI: 10.1002/cmdc.202200691] [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: 12/19/2022] [Revised: 03/08/2023] [Accepted: 03/29/2023] [Indexed: 03/31/2023]
Abstract
The multifactorial nature of Alzheimer's disease (AD) is now widely recognized, which has increased the interest in compounds that can address more than one AD-associated targets. Herein, we report the inhibitory activity on the human cholinesterases (acetylcholinesterase, hAChE and butyrylcholinesterase, hBChE) and on the AChE-induced β-amyloid peptide (Aβ) aggregation by a series of peptide derivatives designed by mutating aliphatic residues for aromatic ones. We identified peptide W3 (LGWVSKGKLL-NH2 ) as an interesting scaffold for the development of new anti-AD multitarget-directed drugs. It showed the lowest IC50 value against hAChE reported for a peptide (0.99±0.02 μM) and inhibited 94.2 %±1.2 of AChE-induced Aβ aggregation at 10 μM. Furthermore, it inhibited hBChE (IC50 , 15.44±0.91 μM), showed no in vivo toxicity in brine shrimp and had shown moderated radical scavenging and Fe2+ chelating capabilities in previous studies. The results are in line with multiple reports showing the utility of the indole moiety for the development of cholinesterase inhibitors.
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Affiliation(s)
- Ivan Sanchis
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Roque Spinelli
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - José Dias
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées (IRBA) 1, Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées (IRBA) 1, Place du Général Valérie André, 91220, Brétigny-sur-Orge, France
| | - Álvaro Rietmann
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Florencia Aimaretti
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
| | - Álvaro S Siano
- Department of Organic Chemistry, Faculty of Biochemistry and Biological Sciences, National University of the Littoral, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
- National Scientific and Technical Research Council (CONICET), Ministry of Science, Technology and Innovation, Godoy Cruz, 2290, Ciudad de Buenos Aires, Argentina
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Goyal N, Hajare SN, Gautam S. Release of an encrypted, highly potent ACE-inhibitory peptide by enzymatic hydrolysis of moth bean ( Vigna aconitifolia) protein. Front Nutr 2023; 10:1167259. [PMID: 37360301 PMCID: PMC10288869 DOI: 10.3389/fnut.2023.1167259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023] Open
Abstract
Aim Dietary approaches for the regulation of blood pressure are the need of the hour. Hence, identifying the foods possessing such activity is gaining importance. With this aim, moth bean (Vigna aconitifolia), an underutilized pulse, was explored for the presence of antihypertensive activity in terms of angiotensin converting enzyme (ACE)-inhibition bioactivity. Methods Defatted moth bean protein concentrate was hydrolyzed by using different proteases including Alcalase, papain, and trypsin, to identify the enzyme producing highly potent ACE inhibitory peptides. The hydrolysate showing the highest ACE inhibitory activity was further fractionated using an ultrafiltration membrane (10, 3 and 1 kDa) based on ACE inhibitory activity. The active fraction was further subjected to the ion-exchange chromatography followed by RP-HPLC and LC-MS/MS analysis for the enrichment and identification of ACE inhibitory peptides. Finally, based on the bioinformatic analysis, few peptides were synthesized and evaluated for ACE inhibitory activity, followed by docking study and molecular dynamic simulation of a peptide with the highest ACE inhibitory activity. Results and discussion Out of the three proteases, Alcalase-derived hydrolysate showed the highest (~59%) ACE inhibition activity. Molecular weight-based fractionation revealed that <1 kDa fraction possessed the highest ACE inhibitory activity. Activity guided separation of 1 kDa fraction using ion-exchange chromatography, RP-HPLC and LC-MS/MS showed the presence of about 45 peptides. Based on the bioinformatic analysis, 15 peptides were synthesized and evaluated for ACE inhibitory activity. Among these, a novel octapeptide FPPPKVIQ showed the highest ACE inhibitory activity (93.4%) with an IC50 of 0.24 μM. This peptide retained about 59% activity post gastrointestinal digestion simulation. A Dixon plot as well as docking studies revealed the uncompetitive inhibitory nature of this peptide with a Ki value of 0.81 μM. Molecular dynamic simulation studies till 100 ns ensured the stability of the ACE-peptide complex. Conclusion Thus, present study identified a novel potent ACE inhibitory peptide from moth bean that can be incorporated in a functional dietary formulation for regulation of hypertension.
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Affiliation(s)
- Nancy Goyal
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sachin N. Hajare
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences Department, Homi Bhabha National Institute, Mumbai, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences Department, Homi Bhabha National Institute, Mumbai, India
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45
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Salama R, DiLoreto E, Srinivasan J. The Architect of Neurotransmission in C. elegans : How FLP-3 Neuropeptides' Structures Direct their Function. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000829. [PMID: 37396794 PMCID: PMC10310453 DOI: 10.17912/micropub.biology.000829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023]
Abstract
Neuropeptides direct functions in the nervous, endocrine, and immune systems of all animals by altering the activity at neural synapses. A single neuropeptide gene can be post-translationally modified to create multiple active peptides. These individual active peptides can have unique functions and drive discrete binding partners. We have previously shown that specific peptides encoded by the C. elegans neuropeptide gene, flp- 3, have sex-specific roles in response to a pheromone released by hermaphrodite C. elegans, ascaroside #8 (ascr#8). Using structural predictions of select FLP-3 neuropeptides, we identify individual amino acids within specific neuropeptides that regulate specific behaviors suggesting structure-function relationships of neuropeptides in regulate sex-specific behaviors.
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Affiliation(s)
- Rehab Salama
- Biology and Biotechnology, Worcester Polytechnic Institute
| | | | - Jagan Srinivasan
- Biology and Biotechnology, Worcester Polytechnic Institute
- Neuroscience Program, Worcester Polytechnic Institute
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46
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Masoudi-Sobhanzadeh Y, Pourseif MM, Khalili-Sani A, Jafari B, Salemi A, Omidi Y. Deciphering anti-biofilm property of Arthrospira platensis-origin peptides against Staphylococcusaureus. Comput Biol Med 2023; 160:106975. [PMID: 37146493 DOI: 10.1016/j.compbiomed.2023.106975] [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: 12/06/2022] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 05/07/2023]
Abstract
Arthrospira platensis is a valuable natural health supplement consisting of various types of vitamins, dietary minerals, and antioxidants. Although different studies have been conducted to explore the hidden benefits of this bacterium, its antimicrobial property has been poorly understood. To decipher this important feature, here, we extended our recently introduced optimization algorithm (Trader) for aligning amino acid sequences associated with the antimicrobial peptides (AMPs) of Staphylococcus aureus and A.platensis. As a result, similar amino acid sequences were identified, and several candidate peptides were generated accordingly. The obtained peptides were then filtered based on their potential biochemical and biophysical properties, and their 3D structures were simulated based on homology modeling techniques. Next, to investigate how the generated peptides can interact with S. aureus proteins (i.e., heptameric state of the hly and homodimeric form of the arsB), molecular docking approaches were used. The results indicated that four peptides included better molecular interactions relative to the other generated ones in terms of the number/average length of hydrogen bonds and hydrophobic interactions. Based on the outcomes, it can be concluded that the antimicrobial property of A.platensis might be associated with its capability in disturbing the membrane of pathogens and their functions.
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Affiliation(s)
- Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ava Khalili-Sani
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Computer Engineering, University College of Nabi Akram, Tabriz, Iran
| | - Behzad Jafari
- Department of Medicinal Chemistry, School of Pharmacy, Urmia University of Medical Sciences, Urmia, Iran
| | - Aysan Salemi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Florida, 33328, USA.
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47
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Noble JE, Vila-Gómez P, Rey S, Dondi C, Briones A, Aggarwal P, Hoose A, Baran M, Ryadnov MG. Folding-Mediated DNA Delivery by α-Helical Amphipathic Peptides. ACS Biomater Sci Eng 2023; 9:2584-2595. [PMID: 37014978 DOI: 10.1021/acsbiomaterials.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The renaissance gene therapy experiences these days requires specialist biomaterials and a systemic understanding of major factors influencing their ability to deliver genetic material. Peptide transfection systems represent a major class of such biomaterials. Several peptidic reagents have been commercialized to date. However, a comparative assessment of peptide sequences alone without auxiliary support or excipients against a common determinant for their ability to complex and deliver DNA has been lacking. This study cross-compares commercial and experimental transfection reagents from the same family of helical amphiphiles. Factors defining the efficacy of DNA delivery including cell uptake and gene expression are assessed along with cytotoxicity and DNA complexation. The results show that despite differences in sequence composition, length, and origin, peptide reagents of the same structural family exhibit similar characteristics and limitations with common variability trends. The cross-comparison revealed that functional DNA delivery is independent of the peptide sequence used but is mediated by the ability of the reagents to co-fold with DNA. Peptide folding proved to be the common determinant for DNA complexation and delivery by peptidic transfection reagents.
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Affiliation(s)
- James E Noble
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Paula Vila-Gómez
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Brain Sciences, Imperial College London, London W12 0TR, U.K
| | - Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Andrea Briones
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Purnank Aggarwal
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maryana Baran
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Physics, King's College London, London WC2R 2LS, U.K
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De Oliveira DH, Biler M, Mim C, Enstedt L, Kvick M, Norman P, Linares M, Hedhammar M. Silk Assembly against Hydrophobic Surfaces─Modeling and Imaging of Formation of Nanofibrils. ACS APPLIED BIO MATERIALS 2023; 6:1011-1018. [PMID: 36791416 PMCID: PMC10031558 DOI: 10.1021/acsabm.2c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, β-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of ∼7 nm and a width of ∼11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.
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Affiliation(s)
- Danilo Hirabae De Oliveira
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Michal Biler
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute (KTH), Hälsovägen 11C, SE-141 27 Huddinge, Sweden
| | - Linnea Enstedt
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | | | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Mathieu Linares
- Laboratory of Organic Electronics and Scientific Visualization Group, ITN, Linköping University, SE-581 83 Linköping, Sweden
| | - My Hedhammar
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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Exploring the Potential of Black Soldier Fly Larval Proteins as Bioactive Peptide Sources through in Silico Gastrointestinal Proteolysis: A Cheminformatic Investigation. Catalysts 2023. [DOI: 10.3390/catal13030605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Despite their potential as a protein source for human consumption, the health benefits of black soldier fly larvae (BSFL) proteins following human gastrointestinal (GI) digestion are poorly understood. This computational study explored the potential of BSFL proteins to release health-promoting peptides after human GI digestion. Twenty-six proteins were virtually proteolyzed with GI proteases. The resultant peptides were screened for high GI absorption and non-toxicity. Shortlisted peptides were searched against the BIOPEP-UWM and Scopus databases to identify their bioactivities. The potential of the peptides as inhibitors of myeloperoxidase (MPO), NADPH oxidase (NOX), and xanthine oxidase (XO), as well as a disruptor of Keap1–Nrf2 protein–protein interaction, were predicted using molecular docking and dynamics simulation. Our results revealed that about 95% of the 5218 fragments generated from the proteolysis of BSFL proteins came from muscle proteins. Dipeptides comprised the largest group (about 25%) of fragments arising from each muscular protein. Screening of 1994 di- and tripeptides using SwissADME and STopTox tools revealed 65 unique sequences with high GI absorption and non-toxicity. A search of the databases identified 16 antioxidant peptides, 14 anti-angiotensin-converting enzyme peptides, and 17 anti-dipeptidyl peptidase IV peptides among these sequences. Results from molecular docking and dynamic simulation suggest that the dipeptide DF has the potential to inhibit Keap1–Nrf2 interaction and interact with MPO within a short time frame, whereas the dipeptide TF shows promise as an XO inhibitor. BSFL peptides were likely weak NOX inhibitors. Our in silico results suggest that upon GI digestion, BSFL proteins may yield high-GI-absorbed and non-toxic peptides with potential health benefits. This study is the first to investigate the bioactivity of peptides liberated from BSFL proteins following human GI digestion. Our findings provide a basis for further investigations into the potential use of BSFL proteins as a functional food ingredient with significant health benefits.
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Ranjbarian P, Goudarzi F, Akya A, Heidarinia H, Farasat A, Rostamian M. Finding epitopes of Klebsiella pneumoniae outer membrane protein-K17 (OMPK17) and introducing a 25-mer peptide of it as a vaccine candidate. Biologia (Bratisl) 2023; 78:1-11. [PMID: 37363641 PMCID: PMC10012306 DOI: 10.1007/s11756-023-01371-0] [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: 08/14/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023]
Abstract
No approved vaccine exists for Klebsiella pneumoniae yet. Outer membrane protein-K17 (OMPK17) is involved in K. pneumoniae pathogenesis. No information has been found about OMPK17 dominant epitopes in the literature. Therefore, this study aimed to predict both T cell and B cell epitopes of K. pneumoniae OMPK17 via immunoinformatics approaches. Both T cell (class-I and II) and B cell (linear and discontinuous) epitopes of OMPK17 were predicted. Several screening analyses were performed including clustering, immunogenicity, human similarity, toxicity, allergenicity, conservancy, docking, and structural/physicochemical suitability. The results showed that some regions of OMPK17 have more potential as epitopes. The most possible epitopes were found via several analyses including the selection of higher-scoring epitopes, the epitopes predicted with more tools, more immunogenic epitopes, the epitopes capable of producing interferon-gamma, the epitopes with more dissimilarity to human peptides, and non-toxic and non-allergenic epitopes. By comparing the best T cell and B cell epitopes, we reached a 25-mer peptide containing both T cell (class-I and class-II) and B cell (linear) epitopes and comprising appropriate physicochemical characteristics that are required for K. pneumoniae vaccine development. The in vitro/in vivo study of this peptide is recommended to clarify its actual efficiency and efficacy. Supplementary information The online version contains supplementary material available at 10.1007/s11756-023-01371-0.
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Affiliation(s)
- Parivash Ranjbarian
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farjam Goudarzi
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alisha Akya
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Parastar Blvd, Imam Reza Hospital, Kermanshah, 6714415333 Iran
| | - Hana Heidarinia
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch of Islamic Azad University, Shahrekord, Iran
| | - Alireza Farasat
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Parastar Blvd, Imam Reza Hospital, Kermanshah, 6714415333 Iran
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