Genome analysis of Chlamydia trachomatis for functional characterization of hypothetical proteins to discover novel drug targets

In silico analysis of a novel hypothetical protein (YP_498675.1) from Staphylococcus aureus unravels the protein of tryptophan synthase beta superfamily (Try-synth-beta_ II)

BACKGROUND

Staphylococcus aureus is a gram-positive spherical bacteria and the most common cause of nosocomial infections in the world. Given its clinical significance, the genome sequence of S. aureus has been elucidated to enhance our comprehension of its lifestyle and pathogenicity. The research aimed to summarize a potential hypothetical protein that may play an important role in S. aureus virulence and pathogenicity, covering its anticipated structure, probable biological functions, and importance in this context.

RESULTS

A hypothetical protein, YP_498675.1 with 281 amino acid residues of S. aureus, was chosen for analysis and modeling by several bioinformatics tools and databases in this work. According to primary and secondary structure analyses, YP_498675.1 is a stable hydrophilic protein with a significant proportion of α-helices. Subcellular localization predictions by CELLO, PSORTb, and SOSUI server indicate that it is a cytoplasmic protein. NCBI-CDD, Pfam, and InterProScan functional genomics research revealed that the hypothetical protein may include the pyridoxal phosphate (PLP)-dependent 2, 3-diaminopropionate biosynthesis protein SbnA domain. In the homology modeling method, the HHpred server was employed to create its 3D structure using the template structure of a Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP (PDB ID: 5D84_A), an X-ray diffraction model having 100% sequence identity with the hypothetical protein. After energy minimization, several quality assessments and validation factors determined that the generated protein model was reliable and of reasonable quality.

CONCLUSION

The present study has characterized and functionally annotated the hypothetical protein YP_498675.1 of S. aureus. Further experimental validation would aid in determining the actual function of YP_498675.1 as well as confirm the protein's value as a therapeutic target.

Potential therapeutic targets for combating Mycoplasma genitalium

Mycoplasma genitalium (M. genitalium) has emerged as a sexually transmitted infection (STI) all over the world in the last three decades. It has been identified as a cause of male urethritis, and there is now evidence that it also causes cervicitis and pelvic inflammatory disease in women. However, the precise role of M. genitalium in diseases such as pelvic inflammatory disease, and infertility is unknown, and more research is required. It is a slow-growing organism, and with the advent of the nucleic acid amplification test (NAAT), more studies are being conducted and knowledge about the pathogenicity of this organism is being elucidated. The accumulation of data has improved our understanding of the pathogen and its role in disease transmission. Despite the widespread use of single-dose azithromycin in the sexual health field, M. genitalium is known to rapidly develop antibiotic resistance. As a result, the media frequently refer to this pathogen as the "new STI superbug." Despite their rarity, antibiotics available today have serious side effects. As the cure rates for first-line antimicrobials have decreased, it is now a challenge to determine the effective antimicrobial therapy. In this review, we summarise recent M. genitalium research and investigate potential therapeutic targets for combating this pathogen.

In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target

Klebsiella pneumonia is known to cause several nosocomial infections in immunocompromised patients. It has developed resistance against a broad range of presently available antibiotics, resulting in high mortality rates in patients and declared an urgent threat. Therefore, exploration of possible novel drug targets against this opportunistic bacteria needs to be undertaken. In the present study, we performed an extensive in-silico analysis for functional and structural annotation and characterized HP CP995_08280 from K. pneumonia as a drug target and aimed to identify potent drug candidates. The functional and structural studies using several bioinformatics tools and databases predicted that HP CP995_08280 is a cytosolic protein that belongs to the β-lactamase family and shares structural similarity with FmtA protein from Staphylococcus aureus (PDB ID: 5ZH8). The structure of HP CP995_08280 was successfully modeled followed by structure-based virtual screening, docking, molecular dynamics, and Molecular mechanic/Poisson-Boltzmann surface area (MMPBSA) were performed to identify the potential compounds. We have found five potent antibacterial molecules, namely BDD 24083171, BDD 24085737, BDE 25098678, BDE 33638819, and BDE 33672484, which exhibited high binding affinity (>-7.5 kcal/mol) and were stabilized by hydrogen bonding and hydrophobic interactions with active site residues (Ser42, Lys45, Tyr126, and Asp128) of protein. Molecular dynamics and MMPBSA revealed that HP CP995_08280 - ligand(s) complexes were less dynamic and more stable than native HP CP995_08280. Hence, the present study may serve as a potential lead for developing inhibitors against drug-resistant Klebsiella pneumonia.

EbfC/YbaB: A Widely Distributed Nucleoid-Associated Protein in Prokaryotes

Genomic compaction is an essential characteristic of living organisms. Nucleoid-associated proteins (NAPs) are a group of small proteins that play crucial roles in chromosome architecture and affect DNA replication, transcription, and recombination by imposing topological alterations in genomic DNA, thereby modulating global gene expression. EbfC/YbaB was first described as a DNA-binding protein of Borrelia burgdorferi that regulates the expression of surface lipoproteins with roles in virulence. Further studies indicated that this protein binds specifically and non-specifically to DNA and colocalises with nucleoids in this bacterium. The data showed that this protein binds to DNA as a homodimer, although it can form other organised structures. Crystallography analysis indicated that the protein possesses domains responsible for protein–protein interactions and forms a “tweezer” structure probably involved in DNA binding. Moreover, sequence analysis revealed conserved motifs that may be associated with dimerisation. Structural analysis also showed that the tridimensional structure of EbfC/YbaB is highly conserved within the bacterial domain. The DNA-binding activity was observed in different bacterial species, suggesting that this protein can protect DNA during stress conditions. These findings indicate that EbfC/YbaB is a broadly distributed NAP. Here, we present a review of the existing data on this NAP.

In Silico Characterization of a Hypothetical Protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System

Shigellosis caused by Shigella dysenteriae is a major public health concern worldwide, particularly in developing countries. The bacterial genome is known, but there are many hypothetical proteins whose functions are yet to be discovered. A hypothetical protein (accession no. WP_128879999.1, 161 residues) of S. dysenteriae ATCC 12039 strain was selected in this study for comprehensive structural and functional analysis. Subcellular localization and different physicochemical properties of this hypothetical protein were estimated indicating it as a stable, soluble, and extracellular protein. Functional annotation tools, such as NCBI-CD Search, Pfam, and InterProScan, predicted our target protein to be an amidase effector protein 4 (Tae4) of type-VI secretion system (T6SS). Multiple sequence alignment of the homologous sequences coincided with previous findings. Random coil was found to be predominant in secondary structure. Three-dimensional (3D) structure of the protein was obtained using homology modeling method by SWISS-MODEL server using a template protein (PDB ID: 4J30) of 80.12% sequence identity. The 3D structure became more stable after YASARA energy minimization and was validated by several quality assessment tools like PROCHECK, QMEAN, Verify3D, and ERRAT. Superimposition of the target with the template protein by UCSF Chimera generated RMSD value of 0.115 Å, suggesting a reliable 3D structure. The active site of the modeled structure was predicted and visualized by CASTp server and PyMOL. Interestingly, similar binding affinity and key interacting residues were found for the target protein and a Salmonella enterica Tae4 protein with the ligand L-Ala D-Glu-mDAP by molecular docking analysis. Protein-protein docking was also performed between the target protein and hemolysin coregulated protein 1 of T6SS. Finally, the protein was found to be a unique protein of S. dysenteriae nonhomologous to human by comparative genomics approach indicating a potential therapeutic target. Most pathogens harboring T6SS in their system pose a significant threat to the human health. Many T6SSs and their effectors are associated with interbacterial competition, pathogenesis, and virulency; however, relationships between these effectors and pathogenicity of S. dysenteriae are yet to be determined. The study findings provide a lucrative platform for future antibacterial treatment.

Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction

The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein–protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were “novel”. Furthermore, a host–pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.

Identification of novel therapeutic target and epitopes through proteome mining from essential hypothetical proteins in Salmonella strains: An In silico approach towards antivirulence therapy and vaccine development

Salmonella strains are responsible for a huge mortality rate through foodborne ailment in the world that necessitated the discovery of novel drugs and vaccines. Essential hypothetical proteins (EHPs), whose structures and functions were previously unknown, could serve as potential therapeutic and vaccine targets. Antivirulence therapy shall emerge as a superior therapeutic approach that uses virulence factors as drug targets. This study annotated the biological functions of 96 out of total 106 essential hypothetical proteins in five strains of Salmonella and classified into nine important protein categories. 34 virulence factors were predicted among the EHPs, out of which, 11 were identified to be pathogen specific potential drug targets for antivirulence therapy. These targets were non-homologous to both human and gut microbiota proteome to avoid cross-reactivity with them. Seven identified targets had druggable property, while the rest four targets were novel targets. Four identified targets (DEG10320148, DEG10110027, DEG10110040 and DEG10110142) had antigenic properties and were further classified as: two membrane-bound Lipid-binding transmembrane proteins, a Zinc-binding membrane protein and an extracellular glycosylase. These targets could be potentially used for the development of subunit vaccines. The study further identified 11 highly conserved and exposed epitope sequences from these 4 vaccine targets. The three-dimensional structures of the vaccine targets were also elucidated along with highlighting the conformation of the epitopes. This study identified potential therapeutic targets for antivirulence therapy against Salmonella. It would therefore instigate in novel drug designing as well as provide important leads to new Salmonella vaccine development.

Functional Annotation and Curation of Hypothetical Proteins Present in A Newly Emerged Serotype 1c of Shigella flexneri: Emphasis on Selecting Targets for Virulence and Vaccine Design Studies

Shigella flexneri is the principal cause of bacillary dysentery, contributing significantly to the global burden of diarrheal disease. The appearance and increase in the multi-drug resistance among Shigella strains, necessitates further genetic studies and development of improved/new drugs against the pathogen. The presence of an abundance of hypothetical proteins in the genome and how little is known about them, make them interesting genetic targets. The present study aims to carry out characterization of the hypothetical proteins present in the genome of a newly emerged serotype of S. flexneri (strain Y394), toward their novel regulatory functions using various bioinformatics databases/tools. Analysis of the genome sequence rendered 4170 proteins, out of which 721 proteins were annotated as hypothetical proteins (HPs) with no known function. The amino acid sequences of these HPs were evaluated using a combination of latest bioinformatics tools based on homology search against functionally identified proteins. Functional domains were considered as the basis to infer the biological functions of HPs in this case and the annotation helped in assigning various classes to the proteins such as signal transducers, lipoproteins, enzymes, membrane proteins, transporters, virulence, and binding proteins. This study contributes to a better understanding of growth, survival, and disease mechanism at molecular level and provides potential new targets for designing drugs against Shigella infection.

Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa

Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.

Functional assignment for essential hypothetical proteins of Staphylococcus aureus N315

Staphylococcus aureus, the causative agent of nosocomial infections worldwide, has acquired resistance to almost all antibiotics stressing the need to develop novel drugs against this pathogen. In S. aureus N315, 302 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 40 proteins encoded by S. aureus essential genes were found to be hypothetical and thus referred as essential hypothetical proteins (EHPs). The present study aims to carry out functional characterization of EHPs using bioinformatics tools/databases, whose performance was assessed by Receiver operating characteristic curve analysis. Evaluation of physicochemical parameters, homology search against known proteins, domain analysis, subcellular localization analysis and virulence prediction assisted us to characterize EHPs. Functional assignment for 35 EHPs was made with high confidence. They belong to different functional classes like enzymes, binding proteins, miscellaneous proteins, helicases, transporters and virulence factors. Around 35% of EHPs were from hydrolases family. A group of EHPs (32.5%) were predicted as virulence factors. Of 35, 19 essential pathogen-specific proteins were considered as probable drug targets. Two targets were found to be druggable and others were novel targets. Outcome of the study could aid to identify novel drugs for better treatment of S. aureus infections.