Pub Date : 2024-04-01Epub Date: 2023-10-04DOI: 10.1007/s10930-023-10161-1
Supratik Das, Hilal Ahmad Parray, Adarsh Kumar Chiranjivi, Prince Kumar, Abhishek Goswami, Manish Bansal, Deepak Kumar Rathore, Rajesh Kumar, Sweety Samal
Efficiently cleaved HIV-1 Envs are the closest mimics of functional Envs as they specifically expose only bNAb (broadly neutralizing antibody) epitopes and not non-neutralizing ones, making them suitable for developing vaccine immunogens. We have previously identified several efficiently cleaved Envs from clades A, B, C and B/C. We also described that truncation of the CT (C-terminal tail) of a subset of these Envs, but not others, impairs their ectodomain conformation/antigenicity on the cell surface in a CT conserved hydrophilic domain (CHD) or Kennedy epitope (KE)-dependent manner. Here, we report that those Envs (4 - 2.J41 and JRCSF), whose native-like ectodomain conformation/antigenicity on the cell surface is disrupted upon CT truncation, but not other Envs like JRFL, whose CT truncation does not have an effect on ectodomain integrity on the cell surface, are also defective in retrograde transport from early to late endosomes. Restoration of the CHD/KE in the CT of these Envs restores wild-type levels of distribution between early and late endosomes. In the presence of retrograde transport inhibitor Retro 2, cell surface expression of 4 - 2.J41 and JRCSF Envs increases [as does in the presence of Rab7a DN and Rab7b DN (DN: dominant negative)] but particle formation decreases for 4 - 2.J41 and JRCSF Env pseudotyped viruses. Our results show for the first time a correlation between CT-dependent, CHD/KE regulated retrograde transport and cell surface expression/viral particle formation of these efficiently cleaved Envs. Based on our results we hypothesize that a subset of these efficiently cleaved Envs use a CT-dependent, CHD/KE-mediated mechanism for assembly and release from late endosomes.
{"title":"Kennedy Epitope (KE)-dependent Retrograde Transport of Efficiently Cleaved HIV-1 Envelopes (Envs) and its Effect on Env Cell Surface Expression and Viral Particle Formation.","authors":"Supratik Das, Hilal Ahmad Parray, Adarsh Kumar Chiranjivi, Prince Kumar, Abhishek Goswami, Manish Bansal, Deepak Kumar Rathore, Rajesh Kumar, Sweety Samal","doi":"10.1007/s10930-023-10161-1","DOIUrl":"10.1007/s10930-023-10161-1","url":null,"abstract":"<p><p>Efficiently cleaved HIV-1 Envs are the closest mimics of functional Envs as they specifically expose only bNAb (broadly neutralizing antibody) epitopes and not non-neutralizing ones, making them suitable for developing vaccine immunogens. We have previously identified several efficiently cleaved Envs from clades A, B, C and B/C. We also described that truncation of the CT (C-terminal tail) of a subset of these Envs, but not others, impairs their ectodomain conformation/antigenicity on the cell surface in a CT conserved hydrophilic domain (CHD) or Kennedy epitope (KE)-dependent manner. Here, we report that those Envs (4 - 2.J41 and JRCSF), whose native-like ectodomain conformation/antigenicity on the cell surface is disrupted upon CT truncation, but not other Envs like JRFL, whose CT truncation does not have an effect on ectodomain integrity on the cell surface, are also defective in retrograde transport from early to late endosomes. Restoration of the CHD/KE in the CT of these Envs restores wild-type levels of distribution between early and late endosomes. In the presence of retrograde transport inhibitor Retro 2, cell surface expression of 4 - 2.J41 and JRCSF Envs increases [as does in the presence of Rab7a DN and Rab7b DN (DN: dominant negative)] but particle formation decreases for 4 - 2.J41 and JRCSF Env pseudotyped viruses. Our results show for the first time a correlation between CT-dependent, CHD/KE regulated retrograde transport and cell surface expression/viral particle formation of these efficiently cleaved Envs. Based on our results we hypothesize that a subset of these efficiently cleaved Envs use a CT-dependent, CHD/KE-mediated mechanism for assembly and release from late endosomes.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-03-15DOI: 10.1007/s10930-024-10188-y
Nguyen Thai Huynh, Thao N T Ho, Yen N D Pham, Le Hang Dang, Son H Pham, Tien T Dang
The immune system maintains constant surveillance to prevent the infiltration of both endogenous and exogenous threats into host organisms. The process is regulated by effector immune cells that combat external pathogens and regulatory immune cells that inhibit excessive internal body inflammation, ultimately establishing a state of homeostasis within the body. Disruption to this process could lead to autoimmunity, which is often associated with the malfunction of both T cells and B cells with T cells playing a more major role. A number of therapeutic mediators for autoimmune diseases are available, from conventional disease-modifying drugs to biologic agents and small molecule inhibitors. Recently, ribosomally synthesized peptides, specifically cyclotides from plants are currently attracting more attention as potential autoimmune disease therapeutics due to their decreased toxicity compared to small molecules inhibitors as well as their remarkable stability against a number of factors. This review provides a concise overview of various cyclotides exhibiting immunomodulatory properties and their potential as therapeutic interventions for autoimmune diseases.
免疫系统保持持续监控,以防止内源性和外源性威胁渗入宿主机体。这一过程由对抗外部病原体的效应免疫细胞和抑制身体内部过度炎症的调节免疫细胞调节,最终在体内建立起一种平衡状态。这一过程的破坏会导致自身免疫,而自身免疫通常与 T 细胞和 B 细胞的功能失常有关,其中 T 细胞的作用更大。目前有许多治疗自身免疫疾病的介质,从传统的疾病调节药物到生物制剂和小分子抑制剂。最近,核糖体合成的多肽,特别是来自植物的环肽,作为潜在的自身免疫性疾病治疗药物受到越来越多的关注,这是因为与小分子抑制剂相比,它们的毒性更低,而且对多种因素具有显著的稳定性。本综述简要概述了具有免疫调节特性的各种环肽及其作为自身免疫疾病治疗干预措施的潜力。
{"title":"Immunosuppressive Cyclotides: A Promising Approach for Treating Autoimmune Diseases.","authors":"Nguyen Thai Huynh, Thao N T Ho, Yen N D Pham, Le Hang Dang, Son H Pham, Tien T Dang","doi":"10.1007/s10930-024-10188-y","DOIUrl":"10.1007/s10930-024-10188-y","url":null,"abstract":"<p><p>The immune system maintains constant surveillance to prevent the infiltration of both endogenous and exogenous threats into host organisms. The process is regulated by effector immune cells that combat external pathogens and regulatory immune cells that inhibit excessive internal body inflammation, ultimately establishing a state of homeostasis within the body. Disruption to this process could lead to autoimmunity, which is often associated with the malfunction of both T cells and B cells with T cells playing a more major role. A number of therapeutic mediators for autoimmune diseases are available, from conventional disease-modifying drugs to biologic agents and small molecule inhibitors. Recently, ribosomally synthesized peptides, specifically cyclotides from plants are currently attracting more attention as potential autoimmune disease therapeutics due to their decreased toxicity compared to small molecules inhibitors as well as their remarkable stability against a number of factors. This review provides a concise overview of various cyclotides exhibiting immunomodulatory properties and their potential as therapeutic interventions for autoimmune diseases.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140133728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent's immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in E. coli TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS-PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.
{"title":"Engineering Human Pancreatic RNase 1 as an Immunotherapeutic Agent for Cancer Therapy Through Computational and Experimental Studies.","authors":"Mohammadreza Nassiri, Shahrokh Ghovvati, Marzieh Gharouni, Mojtaba Tahmoorespur, Ahmad Reza Bahrami, Hesam Dehghani","doi":"10.1007/s10930-023-10171-z","DOIUrl":"10.1007/s10930-023-10171-z","url":null,"abstract":"<p><p>Most plant and bacterial toxins are highly immunogenic with non-specific toxic effects. Human ribonucleases are thought to provide a promising basis for reducing the toxic agent's immunogenic properties, which are candidates for cancer therapy. In the cell, the ribonuclease inhibitor (RI) protein binds to the ribonuclease enzyme and forms a tight complex. This study aimed to engineer and provide a gene construct encoding an improved version of Human Pancreatic RNase 1 (HP-RNase 1) to reduce connection to RI and modulate the immunogenic effects of immunotoxins. To further characterize the interaction complex of HP-RNase 1 and RI, we established various in silico and in vitro approaches. These methods allowed us to specifically monitor interactions within native and engineered HP-RNase 1/RI complexes. In silico research involved molecular dynamics (MD) simulations of native and mutant HP-RNase 1 in their free form and when bound to RI. For HP-RNase 1 engineering, we designed five mutations (K8A/N72A/N89A/R92D/E112/A) based on literature studies, as this combination proved effective for the intended investigation. Then, the cDNA encoding HP-RNase 1 was generated by RT-PCR from blood and cloned into the pSYN2 expression vector. Consequently, wild-type and the engineered HP-RNase 1 were over-expressed in E. coli TG1 and purified using an IMAC column directed against a poly-his tag. The protein products were detected by SDS-PAGE and Western blot analysis. HP-RNase 1 catalytic activity, in the presence of various concentrations of RI, demonstrated that the mutated version of the protein is able to escape the ribonuclease inhibitor and target the RNA substrate 2.5 folds more than that of the wild type. From these data, we tend to suggest the engineered recombinant HP-RNase 1 potentially as a new immunotherapeutic agent for application in human cancer therapy.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139033143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-02-12DOI: 10.1007/s10930-023-10175-9
Erika Maria Gomes Ferreira Teixeira, Dario Eluam Kalume, Patrícia Fernandes Ferreira, Thayane Aparecida Alves, Ana Paula G A Fontão, André Luís Franco Sampaio, Danilo Ribeiro de Oliveira, José Andrés Morgado-Díaz, Raquel Elisa Silva-López
A novel trypsin inhibitor from Cajanus cajan (TIC) fresh leaves was partially purified by affinity chromatography. SDS-PAGE revealed one band with about 15 kDa with expressive trypsin inhibitor activity by zymography. TIC showed high affinity for trypsin (Ki = 1.617 μM) and was a competitive inhibitor for this serine protease. TIC activity was maintained after 24 h of treatment at 70 °C, after 1 h treatments with different pH values, and β-mercaptoethanol increasing concentrations, and demonstrated expressive structural stability. However, the activity of TIC was affected in the presence of oxidizing agents. In order to study the effect of TIC on secreted serine proteases, as well as on the cell culture growth curve, SK-MEL-28 metastatic human melanoma cell line and CaCo-2 colon adenocarcinoma was grown in supplemented DMEM, and the extracellular fractions were submitted salting out and affinity chromatography to obtain new secreted serine proteases. TIC inhibited almost completely, 96 to 89%, the activity of these serine proteases and reduced the melanoma and colon adenocarcinoma cells growth of 48 and 77% respectively. Besides, it is the first time that a trypsin inhibitor was isolated and characterized from C. cajan leaves and cancer serine proteases were isolated and partial characterized from SK-MEL-28 and CaCo-2 cancer cell lines. Furthermore, TIC shown to be potent inhibitor of tumor protease affecting cell growth, and can be one potential drug candidate to be employed in chemotherapy of melanoma and colon adenocarcinoma.
{"title":"A Novel Trypsin Kunitz-Type Inhibitor from Cajanus cajan Leaves and Its Inhibitory Activity on New Cancer Serine Proteases and Its Effect on Tumor Cell Growth.","authors":"Erika Maria Gomes Ferreira Teixeira, Dario Eluam Kalume, Patrícia Fernandes Ferreira, Thayane Aparecida Alves, Ana Paula G A Fontão, André Luís Franco Sampaio, Danilo Ribeiro de Oliveira, José Andrés Morgado-Díaz, Raquel Elisa Silva-López","doi":"10.1007/s10930-023-10175-9","DOIUrl":"10.1007/s10930-023-10175-9","url":null,"abstract":"<p><p>A novel trypsin inhibitor from Cajanus cajan (TIC) fresh leaves was partially purified by affinity chromatography. SDS-PAGE revealed one band with about 15 kDa with expressive trypsin inhibitor activity by zymography. TIC showed high affinity for trypsin (Ki = 1.617 μM) and was a competitive inhibitor for this serine protease. TIC activity was maintained after 24 h of treatment at 70 °C, after 1 h treatments with different pH values, and β-mercaptoethanol increasing concentrations, and demonstrated expressive structural stability. However, the activity of TIC was affected in the presence of oxidizing agents. In order to study the effect of TIC on secreted serine proteases, as well as on the cell culture growth curve, SK-MEL-28 metastatic human melanoma cell line and CaCo-2 colon adenocarcinoma was grown in supplemented DMEM, and the extracellular fractions were submitted salting out and affinity chromatography to obtain new secreted serine proteases. TIC inhibited almost completely, 96 to 89%, the activity of these serine proteases and reduced the melanoma and colon adenocarcinoma cells growth of 48 and 77% respectively. Besides, it is the first time that a trypsin inhibitor was isolated and characterized from C. cajan leaves and cancer serine proteases were isolated and partial characterized from SK-MEL-28 and CaCo-2 cancer cell lines. Furthermore, TIC shown to be potent inhibitor of tumor protease affecting cell growth, and can be one potential drug candidate to be employed in chemotherapy of melanoma and colon adenocarcinoma.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The paper introduces a novel probability descriptor for genome sequence comparison, employing a generalized form of Jensen-Shannon divergence. This divergence metric stems from a one-parameter family, comprising fractions up to a maximum value of half. Utilizing this metric as a distance measure, a distance matrix is computed for the new probability descriptor, shaping Phylogenetic trees via the neighbor-joining method. Initial exploration involves setting the parameter at half for various species. Assessing the impact of parameter variation, trees drawn at different parameter values (half, one-fourth, one-eighth). However, measurement scales decrease with parameter value increments, with higher similarity accuracy corresponding to lower scale values. Ultimately, the highest accuracy aligns with the maximum parameter value of half. Comparative analyses against previous methods, evaluating via Symmetric Distance (SD) values and rationalized perception, consistently favor the present approach's results. Notably, outcomes at the maximum parameter value exhibit the most accuracy, validating the method's efficacy against earlier approaches.
{"title":"Choice of Metric Divergence in Genome Sequence Comparison.","authors":"Soumen Ghosh, Jayanta Pal, Bansibadan Maji, Carlo Cattani, Dilip Kumar Bhattacharya","doi":"10.1007/s10930-024-10189-x","DOIUrl":"10.1007/s10930-024-10189-x","url":null,"abstract":"<p><p>The paper introduces a novel probability descriptor for genome sequence comparison, employing a generalized form of Jensen-Shannon divergence. This divergence metric stems from a one-parameter family, comprising fractions up to a maximum value of half. Utilizing this metric as a distance measure, a distance matrix is computed for the new probability descriptor, shaping Phylogenetic trees via the neighbor-joining method. Initial exploration involves setting the parameter at half for various species. Assessing the impact of parameter variation, trees drawn at different parameter values (half, one-fourth, one-eighth). However, measurement scales decrease with parameter value increments, with higher similarity accuracy corresponding to lower scale values. Ultimately, the highest accuracy aligns with the maximum parameter value of half. Comparative analyses against previous methods, evaluating via Symmetric Distance (SD) values and rationalized perception, consistently favor the present approach's results. Notably, outcomes at the maximum parameter value exhibit the most accuracy, validating the method's efficacy against earlier approaches.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140141340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called "superbugs", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.
{"title":"Heterologous Production of Antimicrobial Peptides: Notes to Consider.","authors":"Masoumeh Kordi, Parnian Ghaedi Talkhounche, Helia Vahedi, Naser Farrokhi, Maryam Tabarzad","doi":"10.1007/s10930-023-10174-w","DOIUrl":"10.1007/s10930-023-10174-w","url":null,"abstract":"<p><p>Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called \"superbugs\", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139099450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2023-11-08DOI: 10.1007/s10930-023-10163-z
Muhammad Sarfraz, Mubashir Aziz, Saira Afzal, Pervaiz Ali Channar, Bshra A Alsfouk, Ghulam Abbas Kandhro, Sidra Hassan, Ahlam Sultan, Asad Hamad, Mosab Arafat, Muhammad Naeem Qaiser, Aftab Ahmed, Farhan Siddique, Syeda Abida Ejaz
AKR1B1 and AKR1B10 are important members of aldo-keto reductase family which plays a significant role in cancer progression by modulating cellular metabolism. These enzymes are involved in various metabolic processes, including the synthesis and metabolism of hormones, detoxification of reactive aldehydes, and the reduction of various endogenous and exogenous compounds. This study aimed to explore the potential of strychnine as an anticancer agent by targeting AKR1B1 and AKR1B10 via drug repurposing approach. To assess the drug-like properties of strychnine, a physiologically based pharmacokinetic (PKPB) model and High Throughput Pharmacokinetics (HTPK) approach were employed. The obtained results fell within the expected range for drug molecules, confirming its suitability for further investigation. Additionally, density functional theory (DFT) studies were conducted to gain insight into the electronic properties contributing to the drug molecule's reactivity. Building upon the promising DFT results, molecular docking analysis using the AutoDock tool was performed to examine the binding interactions between strychnine and the proposed targets, AKR1B1 and AKR1B10. Findings from the molecular docking studies suggested a higher probability of strychnine acting as an inhibitor of AKR1B1 and AKR1B10 with docking scores of - 30.84 and - 29.36 kJ/mol respectively. To validate the stability of the protein-ligand complex, Molecular Dynamic Simulation (MDS) studies were conducted, revealing the formation of a stable complex between the enzymes and strychnine. This comprehensive approach sheds light on the potential effectiveness of strychnine as a treatment for breast, lung, liver, and pancreatic cancers, as well as related malignancies. The novel insights gained from the physiologically based pharmacokinetic modeling, density functional theory, molecular docking, and molecular dynamics simulations collectively support the prospect of strychnine as a promising molecule for anticancer therapy. Further investigations are warranted to validate these findings and explore the therapeutic potential of strychnine in preclinical and clinical settings.
{"title":"Repurposing of Strychnine as the Potential Inhibitors of Aldo-keto Reductase Family 1 Members B1 and B10: Computational Modeling and Pharmacokinetic Analysis.","authors":"Muhammad Sarfraz, Mubashir Aziz, Saira Afzal, Pervaiz Ali Channar, Bshra A Alsfouk, Ghulam Abbas Kandhro, Sidra Hassan, Ahlam Sultan, Asad Hamad, Mosab Arafat, Muhammad Naeem Qaiser, Aftab Ahmed, Farhan Siddique, Syeda Abida Ejaz","doi":"10.1007/s10930-023-10163-z","DOIUrl":"10.1007/s10930-023-10163-z","url":null,"abstract":"<p><p>AKR1B1 and AKR1B10 are important members of aldo-keto reductase family which plays a significant role in cancer progression by modulating cellular metabolism. These enzymes are involved in various metabolic processes, including the synthesis and metabolism of hormones, detoxification of reactive aldehydes, and the reduction of various endogenous and exogenous compounds. This study aimed to explore the potential of strychnine as an anticancer agent by targeting AKR1B1 and AKR1B10 via drug repurposing approach. To assess the drug-like properties of strychnine, a physiologically based pharmacokinetic (PKPB) model and High Throughput Pharmacokinetics (HTPK) approach were employed. The obtained results fell within the expected range for drug molecules, confirming its suitability for further investigation. Additionally, density functional theory (DFT) studies were conducted to gain insight into the electronic properties contributing to the drug molecule's reactivity. Building upon the promising DFT results, molecular docking analysis using the AutoDock tool was performed to examine the binding interactions between strychnine and the proposed targets, AKR1B1 and AKR1B10. Findings from the molecular docking studies suggested a higher probability of strychnine acting as an inhibitor of AKR1B1 and AKR1B10 with docking scores of - 30.84 and - 29.36 kJ/mol respectively. To validate the stability of the protein-ligand complex, Molecular Dynamic Simulation (MDS) studies were conducted, revealing the formation of a stable complex between the enzymes and strychnine. This comprehensive approach sheds light on the potential effectiveness of strychnine as a treatment for breast, lung, liver, and pancreatic cancers, as well as related malignancies. The novel insights gained from the physiologically based pharmacokinetic modeling, density functional theory, molecular docking, and molecular dynamics simulations collectively support the prospect of strychnine as a promising molecule for anticancer therapy. Further investigations are warranted to validate these findings and explore the therapeutic potential of strychnine in preclinical and clinical settings.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-03-01DOI: 10.1007/s10930-024-10181-5
T Idhaya, A Suruliandi, S P Raja
Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves identifying evolutionary relationships between proteins by examining similarities in their sequences or structures. This approach holds great potential for applications such as drug discovery and functional annotation of genomes. However, current methods for protein family prediction have certain limitations, including limited accuracy, high false positive rates, and challenges in handling large datasets. Some methods also rely on homologous sequences or protein structures, which introduce biases and restrict their applicability to specific protein families or structures. To overcome these limitations, researchers have turned to machine learning (ML) approaches that can identify connections between protein features and simplify complex high-dimensional datasets. This paper presents a comprehensive survey of articles that employ various ML techniques for predicting protein families. The primary objective is to explore and improve ML techniques specifically for protein family prediction, thus advancing future research in the field. Through qualitative and quantitative analyses of ML techniques, it is evident that multiple methods utilizing a range of classifiers have been applied for protein family prediction. However, there has been limited focus on developing novel classifiers for protein family classification, highlighting the urgent need for improved approaches in this area. By addressing these challenges, this research aims to enhance the accuracy and effectiveness of protein family prediction, ultimately facilitating advancements in proteomics and its diverse applications.
蛋白质组学是一个致力于分析细胞、组织和生物体内蛋白质的领域,旨在深入了解它们的结构、功能和相互作用。蛋白质组学的一个重要方面是蛋白质家族预测,即通过研究蛋白质序列或结构的相似性来确定蛋白质之间的进化关系。这种方法在药物发现和基因组功能注释等应用领域具有巨大潜力。然而,目前的蛋白质家族预测方法有一定的局限性,包括准确性有限、假阳性率高以及在处理大型数据集时面临挑战。有些方法还依赖于同源序列或蛋白质结构,这会带来偏差并限制其对特定蛋白质家族或结构的适用性。为了克服这些局限性,研究人员转向了机器学习(ML)方法,这种方法可以识别蛋白质特征之间的联系并简化复杂的高维数据集。本文对采用各种 ML 技术预测蛋白质家族的文章进行了全面调查。其主要目的是探索和改进专门用于蛋白质家族预测的 ML 技术,从而推动该领域的未来研究。通过对 ML 技术的定性和定量分析,我们可以明显看出,利用一系列分类器的多种方法已被用于蛋白质家族预测。然而,人们对开发用于蛋白质家族分类的新型分类器的关注还很有限,这凸显了该领域对改进方法的迫切需求。通过应对这些挑战,本研究旨在提高蛋白质族预测的准确性和有效性,最终促进蛋白质组学及其各种应用的发展。
{"title":"A Comprehensive Review on Machine Learning Techniques for Protein Family Prediction.","authors":"T Idhaya, A Suruliandi, S P Raja","doi":"10.1007/s10930-024-10181-5","DOIUrl":"10.1007/s10930-024-10181-5","url":null,"abstract":"<p><p>Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves identifying evolutionary relationships between proteins by examining similarities in their sequences or structures. This approach holds great potential for applications such as drug discovery and functional annotation of genomes. However, current methods for protein family prediction have certain limitations, including limited accuracy, high false positive rates, and challenges in handling large datasets. Some methods also rely on homologous sequences or protein structures, which introduce biases and restrict their applicability to specific protein families or structures. To overcome these limitations, researchers have turned to machine learning (ML) approaches that can identify connections between protein features and simplify complex high-dimensional datasets. This paper presents a comprehensive survey of articles that employ various ML techniques for predicting protein families. The primary objective is to explore and improve ML techniques specifically for protein family prediction, thus advancing future research in the field. Through qualitative and quantitative analyses of ML techniques, it is evident that multiple methods utilizing a range of classifiers have been applied for protein family prediction. However, there has been limited focus on developing novel classifiers for protein family classification, highlighting the urgent need for improved approaches in this area. By addressing these challenges, this research aims to enhance the accuracy and effectiveness of protein family prediction, ultimately facilitating advancements in proteomics and its diverse applications.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139998771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-01Epub Date: 2024-02-12DOI: 10.1007/s10930-023-10179-5
Angshu Dutta, Shankar Prasad Kanaujia
The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.
{"title":"The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry.","authors":"Angshu Dutta, Shankar Prasad Kanaujia","doi":"10.1007/s10930-023-10179-5","DOIUrl":"10.1007/s10930-023-10179-5","url":null,"abstract":"<p><p>The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. \"asymmetric protomer movement (APM)\". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Therapeutic proteins are potent, fast-acting drugs that are highly effective in treating various conditions. Medicinal protein usage has increased in the past 10 years, and it will evolve further as we better understand disease molecular pathways. However, it is associated with high processing costs, limited stability, difficulty in being administered as an oral medication, and the inability of large proteins to penetrate tissue and reach their target locations. Many methods have been developed to overcome the problems with the stability and chaperone activity of therapeutic proteins, viz., the addition of external agents (changing the properties of the surrounding solvent by using stabilizing excipients, e.g., amino acids, sugars, polyols) and internal agents (chemical modifications that influence its structural properties, e.g., mutations, glycosylation). However, these methods must completely clear protein instability and chaperone issues. There is still much work to be done on finetuning chaperone proteins to increase their biological efficacy and stability. Methylglyoxal (MGO), a potent dicarbonyl compound, reacts with proteins and forms covalent cross-links. Much research on MGO scavengers has been conducted since they are known to alter protein structure, which may result in alterations in biological activity and stability. MGO is naturally produced within our body, however, its impact on chaperones and protein stability needs to be better understood and seems to vary based on concentration. This review highlights the efforts of several research groups on the effect of MGO on various proteins. It also addresses the impact of MGO on a client protein, α-crystallin, to understand the potential solutions to the protein's chaperone and stability problems.
{"title":"Methylglyoxal Induced Modifications to Stabilize Therapeutic Proteins: A Review.","authors":"Nainika Prashant Kotian, Anusha Prabhu, Tenzin Tender, Hariharapura Raghu Chandrashekar","doi":"10.1007/s10930-023-10166-w","DOIUrl":"10.1007/s10930-023-10166-w","url":null,"abstract":"<p><p>Therapeutic proteins are potent, fast-acting drugs that are highly effective in treating various conditions. Medicinal protein usage has increased in the past 10 years, and it will evolve further as we better understand disease molecular pathways. However, it is associated with high processing costs, limited stability, difficulty in being administered as an oral medication, and the inability of large proteins to penetrate tissue and reach their target locations. Many methods have been developed to overcome the problems with the stability and chaperone activity of therapeutic proteins, viz., the addition of external agents (changing the properties of the surrounding solvent by using stabilizing excipients, e.g., amino acids, sugars, polyols) and internal agents (chemical modifications that influence its structural properties, e.g., mutations, glycosylation). However, these methods must completely clear protein instability and chaperone issues. There is still much work to be done on finetuning chaperone proteins to increase their biological efficacy and stability. Methylglyoxal (MGO), a potent dicarbonyl compound, reacts with proteins and forms covalent cross-links. Much research on MGO scavengers has been conducted since they are known to alter protein structure, which may result in alterations in biological activity and stability. MGO is naturally produced within our body, however, its impact on chaperones and protein stability needs to be better understood and seems to vary based on concentration. This review highlights the efforts of several research groups on the effect of MGO on various proteins. It also addresses the impact of MGO on a client protein, α-crystallin, to understand the potential solutions to the protein's chaperone and stability problems.</p>","PeriodicalId":94249,"journal":{"name":"The protein journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138453441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}