1
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Amala M, Nagarajan H, Ahila M, Nachiappan M, Veerapandiyan M, Vetrivel U, Jeyakanthan J. Unveiling the intricacies of allosteric regulation in aspartate kinase from the Wolbachia endosymbiont of Brugia Malayi: Mechanistic and therapeutic insights. Int J Biol Macromol 2024; 267:131326. [PMID: 38569988 DOI: 10.1016/j.ijbiomac.2024.131326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 03/04/2024] [Accepted: 03/31/2024] [Indexed: 04/05/2024]
Abstract
Aspartate kinase (AK), an enzyme from the Wolbachia endosymbiont of Brugia malayi (WBm), plays a pivotal role in the bacterial cell wall and amino acid biosynthesis, rendering it an attractive candidate for therapeutic intervention. Allosteric inhibition of aspartate kinase is a prevalent mode of regulation across microorganisms and plants, often modulated by end products such as lysine, threonine, methionine, or meso-diaminopimelate. The intricate and diverse nature of microbial allosteric regulation underscores the need for rigorous investigation. This study employs a combined experimental and computational approach to decipher the allosteric regulation of WBmAK. Molecular Dynamics (MD) simulations elucidate that ATP (cofactor) and ASP (substrate) binding induce a closed conformation, promoting enzymatic activity. In contrast, the binding of lysine (allosteric inhibitor) leads to enzyme inactivation and an open conformation. The enzymatic assay demonstrates the optimal activity of WBmAK at 28 °C and a pH of 8.0. Notably, the allosteric inhibition study highlights lysine as a more potent inhibitor compared to threonine. Importantly, this investigation sheds light on the allosteric mechanism governing WBmAK and imparts novel insights into structure-based drug discovery, paving the way for the development of effective inhibitors against filarial pathogens.
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Affiliation(s)
- Mathimaran Amala
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Mathimaran Ahila
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Mutharasappan Nachiappan
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India
| | - Malaisamy Veerapandiyan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Umashankar Vetrivel
- Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu 600 031, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India.
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2
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Karthika A, Hemavathy N, Amala M, Rajamanikandan S, Veerapandian M, Prabhu D, Vetrivel U, Jung Chen C, Jeyaraj Pandian C, Jeyakanthan J. Structural and functional characterization of 6-phosphogluconate dehydrogenase in Plasmodium falciparum (3D7) and identification of its potent inhibitors. J Biomol Struct Dyn 2024; 42:2058-2074. [PMID: 37599457 DOI: 10.1080/07391102.2023.2248271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/09/2023] [Indexed: 08/22/2023]
Abstract
The malarial parasite Plasmodium falciparum predominantly causes severe malaria and deaths worldwide. Moreover, resistance developed by P. falciparum to frontline drugs in recent years has markedly increased malaria-related deaths in South Asian Countries. Ribulose 5-phosphate and NADPH synthesized by Pentose Phosphate Pathway (PPP) act as a direct precursor for nucleotide synthesis and P. falciparum survival during oxidative challenges in the intra-erythrocytic growth phase . In the present study, we have elucidated the structure and functional characteristics of 6-phosphogluconate dehydrogenase (6PGD) in P. falciparum and have identified potent hits against 6PGD by pharmacophore-based virtual screening with ZINC and ChemBridge databases. Molecular docking and Molecular dynamics simulation, binding free energies (MMGBSA & MMPBSA), and Density Functional Theory (DFT) calculations were integratively employed to validate and prioritize the most potential hits. The 6PGD structure was found to have an open and closed conformation during MD simulation. The apo form of 6PGD was found to be in closed conformation, while a open conformation attributed to facilitating binding of cofactor. It was also inferred from the conformational analysis that the small domain of 6PGD has a high influence in altering the conformation that may aid in open/closed conformation of 6PGD. The top three hits identified using pharmacophore hypotheses were ChemBridge_11084819, ChemBridge_80178394, and ChemBridge_17912340. Though all three hits scored a high glide score, MMGBSA, and favorable ADMET properties, ChemBridge_11084819 and ChemBrdige_17912340 showed higher stability and binding free energy. Moreover, these hits also featured stable H-bond interactions with the active loop of 6PGD with binding free energy comparable to substrate-bound complex. Therefore, the ChemBridge_11084819 and ChemBridge_17912340 moieties demonstrate to have high therapeutic potential against 6PGD in P. falciparum.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alagesan Karthika
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Nagarajan Hemavathy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Centre for Bioinformatics, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Mathimaran Amala
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sundaraj Rajamanikandan
- Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Malaisamy Veerapandian
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Dhamodharan Prabhu
- Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Umashankar Vetrivel
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi, Karnataka, India
- ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Chun Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chitra Jeyaraj Pandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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3
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Ahmad M, Jha B, Bose S, Tiwari S, Dwivedy A, Kar D, Pal R, Mariadasse R, Parish T, Jeyakanthan J, Vinothkumar KR, Biswal BK. Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis. IUCrJ 2023; 10:738-753. [PMID: 37860976 PMCID: PMC10619443 DOI: 10.1107/s2052252523008485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023]
Abstract
Enolase, a ubiquitous enzyme, catalyzes the reversible conversion of 2-phosphoglycerate (2PG) to phosphoenolpyruvate (PEP) in the glycolytic pathway of organisms of all three domains of life. The underlying mechanism of the 2PG to PEP conversion has been studied in great detail in previous work, however that of the reverse reaction remains to be explored. Here we present structural snapshots of Mycobacterium tuberculosis (Mtb) enolase in apo, PEP-bound and two 2PG-bound forms as it catalyzes the conversion of PEP to 2PG. The two 2PG-bound complex structures differed in the conformation of the bound product (2PG) viz the widely reported canonical conformation and a novel binding pose, which we refer to here as the alternate conformation. Notably, we observed two major differences compared with the forward reaction: the presence of MgB is non-obligatory for the reaction and 2PG assumes an alternate conformation that is likely to facilitate its dissociation from the active site. Molecular dynamics studies and binding free energy calculations further substantiate that the alternate conformation of 2PG causes distortions in both metal ion coordination and hydrogen-bonding interactions, resulting in an increased flexibility of the active-site loops and aiding product release. Taken together, this study presents a probable mechanism involved in PEP to 2PG catalysis that is likely to be mediated by the conformational change of 2PG at the active site.
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Affiliation(s)
- Mohammed Ahmad
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Bhavya Jha
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Zoology, GDM Mahavidyalaya, Patliputra University, Patna 800020, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Satish Tiwari
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Abhisek Dwivedy
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepshikha Kar
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravikant Pal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Richard Mariadasse
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630003, India
| | - Tanya Parish
- Infectious Disease Research Institute, 1616 Eastlake Avenue E, Suite 400, Seattle, WA 98102, USA
- Seattle Children’s Research Institute, Seattle, WA 98109, USA
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630003, India
| | - Kutti R. Vinothkumar
- National Centre for Biological Sciences, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Bichitra Kumar Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Vinita N, Devan U, Durgadevi S, Anitha S, Govarthanan M, Antony Joseph Velanganni A, Jeyakanthan J, Arul Prakash P, Mohamed Jaabir MS, Kumar P. Impact of Surface Charge-Tailored Gold Nanorods for Selective Targeting of Mitochondria in Breast Cancer Cells Using Photodynamic Therapy. ACS Omega 2023; 8:33229-33241. [PMID: 37744785 PMCID: PMC10515365 DOI: 10.1021/acsomega.2c06731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/10/2023] [Indexed: 09/26/2023]
Abstract
Herein, the impact of surface charge tailored of gold nanorods (GNRs) on breast cancer cells (MCF-7 and MDA-MB-231) upon conjugation with triphenylphosphonium (TPP) for improved photodynamic therapy (PDT) targeting mitochondria was studied. The salient features of the study are as follows: (i) positive (CTAB@GNRs) and negative (PSS-CTAB@GNRs) surface-charged gold nanorods were developed and characterized; (ii) the mitochondrial targeting efficiency of gold nanorods was improved by conjugating TPP molecules; (iii) the conjugated nanoprobes (TPP-CTAB@GNRs and TPP-PSS-CTAB@GNRs) were evaluated for PDT in the presence of photosensitizer (PS), 5-aminolevulinic acid (5-ALA) in breast cancer cells; (iv) both nanoprobes (TPP-CTAB@GNRs and TPP-PSS-CTAB@GNRs) induce apoptosis, damage DNA, generate reactive oxygen species, and decrease mitochondrial membrane potential upon 5-ALA-based PDT; and (v) 5-ALA-PDT of two nanoprobes (TPP-CTAB@GNRs and TPP-PSS-CTAB@GNRs) impact cell signaling (PI3K/AKT) pathway by upregulating proapoptotic genes and proteins. Based on the results, we confirm that the positively charged (rapid) nanoprobes are more advantageous than their negatively (slow) charged nanoprobes. However, depending on the kind and degree of cancer, both nanoprobes can serve as efficient agents for delivering anticancer therapy.
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Affiliation(s)
- Nadar
Manimaran Vinita
- Food
Chemistry and Molecular Cancer Biology Lab, Department of Animal Health
and Management, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Umapathy Devan
- Molecular
Oncology Laboratory, Department of Biochemistry, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Sabapathi Durgadevi
- Food
Chemistry and Molecular Cancer Biology Lab, Department of Animal Health
and Management, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Selvaraj Anitha
- Food
Chemistry and Molecular Cancer Biology Lab, Department of Animal Health
and Management, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Muthusamy Govarthanan
- Department
of Environmental Engineering, Kyungpook
National University, Deagu 41566, Republic
of Korea
- Department
of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, Tamil Nadu, India
| | | | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Pitchan Arul Prakash
- PG
and Research
Department of Biotechnology and Microbiology, The National College, Tiruchirappalli 620001, Tamil Nadu, India
| | - Mohamed Sultan Mohamed Jaabir
- PG
and Research
Department of Biotechnology and Microbiology, The National College, Tiruchirappalli 620001, Tamil Nadu, India
| | - Ponnuchamy Kumar
- Food
Chemistry and Molecular Cancer Biology Lab, Department of Animal Health
and Management, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
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5
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Loganathan L, Jeyakanthan J, Muthusamy K. HTNpedia: A Knowledge Base for Hypertension Research. Comb Chem High Throughput Screen 2023:CCHTS-EPUB-131917. [PMID: 37202885 DOI: 10.2174/1386207326666230518162439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Hypertension is notably a serious public health concern due to its high prevalence and strong association with cardiovascular disease and renal failure. It is reported to be the fourth leading disease that leads to death worldwide. OBJECTIVE Currently, there is no active operational knowledge base or database for hypertension or cardiovascular illness. METHOD The primary data source was retrieved from the research outputs obtained from our laboratory team working on hypertension research. We have presented a preliminary dataset and external links to the public repository for detailed analysis to readers. RESULT As a result, HTNpedia was created to provide information regarding hypertension-related proteins and genes. CONCLUSION The complete webpage is accessible via www.mkarthikeyan.bioinfoau.org/HTNpedia.
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Affiliation(s)
- Lakshmanan Loganathan
- Department of Bioinformatics, Alagappa University, Karaikudi-630003, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi-630003, Tamil Nadu, India
| | - Karthikeyan Muthusamy
- Department of Bioinformatics, Alagappa University, Karaikudi-630003, Tamil Nadu, India
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6
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Muthumanickam S, Ramachandran B, Boomi P, Jeyakanthan J, Prabu HG, Jegatheswaran S, Premkumar K. Combination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study. J Biomol Struct Dyn 2023; 41:13950-13962. [PMID: 37098715 DOI: 10.1080/07391102.2023.2203259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/28/2023] [Indexed: 04/27/2023]
Abstract
Breast cancer (BC) is the most serious and second leading cause of death in women worldwide. When breast cancer is diagnosed and treated early, the chance of long-term survival is up to 90%. On the other hand, 90% of BC patient deaths are due to metastasis and a lack of effective early diagnosis. The existing conventional chemotherapy provides negative feedback due to transportation barriers towards the action sites, multidrug resistance, poor bio-availability, non-specific delivery and systemic side effects on the healthy tissue. Syk protein Kinase has been reported in BC, as a tumor modulator, providing a pro-survival signal and also by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration. In the present study, we explored the possibility of targeting BC by attenuating Syk protein Kinase. Hence, we have conjugated the hydrophobic Bendamustine (BEN) and hydrophilic Azacitidine (AZA) anticancer drugs to evaluate their efficacy against BC. The native drugs (BEN and AZA) and designed drug-drug conjugate (BEN-AZA) were docked with Syk protein. Then, the docked complex was performed for Binding Free Energy and Molecular Dynamics Simulations. Furthermore, DFT and ADME properties were carried out. The results revealed that the designed drug-drug conjugate has a better docking score, ΔGbind and admirable stability throughout the simulation when compared with native drugs. In DFT and ADME analyses, the designed drug-drug conjugate has shown good stereo electronic features and pharmaceutical relevant parameters than that of native drugs. The overall results suggested that the designed drug-drug conjugate may be a suitable candidate for BC treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Halliah Gurumallesh Prabu
- Department of Industrial Chemistry, School of Chemical Sciences, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Kumpati Premkumar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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7
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Sindhu T, Rajamanikandan S, Jeyakanthan J, Pal D. Investigation of protein-ligand binding motions through protein conformational morphing and clustering of cytochrome bc1-aa3 super complex. J Mol Graph Model 2023; 118:108347. [PMID: 36208591 DOI: 10.1016/j.jmgm.2022.108347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022]
Abstract
Cytochrome b (QcrB) is considered an essential subunit in the electron transport chain that coordinates the action of the entire cytochrome bc1 oxidase. It has been identified as an attractive drug target for a new promising clinical candidate Q203 that depletes the intracellular ATP levels in the bacterium, Mycobacterium tuberculosis. However, single point polymorphism (T313A/I) near the quinol oxidation site of QcrB developed resistance to Q203. In the present study, we analyze the structural changes and drug-resistance mechanism of QcrB due to the point mutation in detail through conformational morphing and molecular docking studies. By morphing, we generated conformers between the open and closed state of the electron transporting cytochrome bc1-aa3 super complex. We clustered them to identify four intermediate structures and relevant intra- and intermolecular motions that may be of functional relevance, especially the binding of Q203 in wild and mutant QcrB intermediate structures and their alteration in developing drug resistance. The difference in the binding score and hydrogen bond interactions between Q203 and the wild-type and mutant intermediate structures of QcrB from molecular docking studies showed that the point mutation T313A severely affected the binding affinity of the candidate drug. Together, the findings provide an in-depth understanding of QcrB inhibition in different conformations, including closed, intermediate, and open states of cytochrome bc1-aa3 super complex in Mycobacterium tuberculosis at the atomic level. We also obtain insights for designing QcrB and cytochrome bc1-aa3 inhibitors as potential therapeutics that may combat drug resistance in tuberculosis.
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Affiliation(s)
- Thangaraj Sindhu
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Sundarraj Rajamanikandan
- Research and Development Wing, Sree Balaji Medical College and Hospital (BIHER), Chennai, Tamil Nadu, India
| | | | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, India.
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8
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Prabhu D, Rajamanikandan S, Amala M, Saritha P, Jeyakanthan J, Ramasamy P. Functional Characterization, Mechanism, and Mode of Action of Putative Streptomycin Adenylyltransferase from Serratia marcescens. Antibiotics (Basel) 2022; 11:antibiotics11121722. [PMID: 36551379 PMCID: PMC9774460 DOI: 10.3390/antibiotics11121722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Nosocomial infections are serious threats to the entire world in healthcare settings. The major causative agents of nosocomial infections are bacterial pathogens, among which Enterobacteriaceae family member Serratia marcescens plays a crucial role. It is a gram-negative opportunistic pathogen, predominantly affecting patients in intensive-care units. The presence of intrinsic genes in S. marcescens led to the development of resistance to antibiotics for survival. Complete scanning of the proteome, including hypothetical and partially annotated proteins, paves the way for a better understanding of potential drug targets. The targeted protein expressed in E. coli BL21 (DE3) pLysS cells has shown complete resistance to aminoglycoside antibiotic streptomycin (>256 MCG). The recombinant protein was purified using affinity and size-exclusion chromatography and characterized using SDS-PAGE, western blotting, and MALDI-TOF analysis. Free phosphate bound to malachite green was detected at 620 nm, evident of the conversion of adenosine triphosphate to adenosine monophosphate during the adenylation process. Similarly, in the chromatographic assay, adenylated streptomycin absorbed at 260 nm in AKTA (FPLC), confirming the enzyme-catalyzed adenylation of streptomycin. Further, the adenylated product of streptomycin was confirmed through HPLC and mass spectrometry analysis. In conclusion, our characterization studies identified the partially annotated hypothetical protein as streptomycin adenylyltransferase.
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Affiliation(s)
- Dhamodharan Prabhu
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Sundararaj Rajamanikandan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
| | - Mathimaran Amala
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Poopandi Saritha
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
| | - Palaniappan Ramasamy
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai 600 044, Tamil Nadu, India
- Correspondence: (D.P.); (J.J.); (P.R.)
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9
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Yuvaraj I, Chaudhary SK, Jeyakanthan J, Sekar K. Structure of the hypothetical protein TTHA1873 from Thermus thermophilus. Acta Crystallogr F Struct Biol Commun 2022; 78:338-346. [PMID: 36048084 PMCID: PMC9435673 DOI: 10.1107/s2053230x22008457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of an uncharacterized hypothetical protein, TTHA1873 from Thermus thermophilus, has been determined by X-ray crystallography to a resolution of 1.78 Å using the single-wavelength anomalous dispersion method. The protein crystallized as a dimer in two space groups: P43212 and P6122. Structural analysis of the hypothetical protein revealed that the overall fold of TTHA1873 has a β-sandwich jelly-roll topology with nine β-strands. TTHA1873 is a dimeric metal-binding protein that binds to two Ca2+ ions per chain, with one on the surface and the other stabilizing the dimeric interface of the two chains. A structural homology search indicates that the protein has moderate structural similarity to one domain of cell-surface proteins or agglutinin receptor proteins. Red blood cells showed visible agglutination at high concentrations of the hypothetical protein.
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Affiliation(s)
- I. Yuvaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Santosh Kumar Chaudhary
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - J. Jeyakanthan
- Structural Biology and Bio Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, India
| | - K. Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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Jayaprakash P, Biswal J, Rangaswamy R, Jeyakanthan J. Designing of potent anti-diabetic molecules by targeting SIK2 using computational approaches. Mol Divers 2022:10.1007/s11030-022-10470-0. [PMID: 35727438 DOI: 10.1007/s11030-022-10470-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
Diabetes mellitus (DM) is one of the major health problems worldwide. WHO have estimated that 439 million people may have DM by the year 2030. Several classes of drugs such as sulfonylureas, meglitinides, thiazolidinediones etc. are available to manage this disease, however, there is no cure for this disease. Salt inducible kinase 2 (SIK2) is expressed several folds in adipose tissue than in normal tissues and thus SIK2 is one of the attractive targets for DM treatment. SIK2 inhibition improves glucose homeostasis. Several analogues have been reported and experimentally proven against SIK for DM treatment. But, identifying potential SIK2 inhibitors with improved efficacy and good pharmacokinetic profiles will be helpful for the effective treatment of DM. The objective of the present study is to identify selective SIK2 inhibitors with good pharmacokinetic profiles. Due to the unavailability of SIK2 structure, the modeled structure of SIK2 will be an important to understand the atomic level of SIK2 inhibitors in the binding site pocket. In this study, different molecular modeling studies such as Homology Modeling, Molecular Docking, Pharmacophore-based virtual screening, MD simulations, Density Functional Theory calculations and WaterMap analysis were performed to identify potential SIK2 inhibitors. Five molecules from different databases such as Binding_4067, TosLab_837067, NCI_349155, Life chemicals_ F2565-0113, Enamine_7623111186 molecules were identified as possible SIK2 inhibitors.
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Affiliation(s)
- Prajisha Jayaprakash
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India
| | - Raghu Rangaswamy
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India.
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11
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Alexpandi R, Gendrot M, Abirami G, Delandre O, Fonta I, Mosnier J, Mariadasse R, Jeyakanthan J, Pandian SK, Pradines B, Ravi AV. Repurposing of Doxycycline to Hinder the Viral Replication of SARS-CoV-2: From in silico to in vitro Validation. Front Microbiol 2022; 13:757418. [PMID: 35602049 PMCID: PMC9115549 DOI: 10.3389/fmicb.2022.757418] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Since the rapid spread of coronavirus disease (COVID-19) became a global pandemic, healthcare ministries around the world have recommended specific control methods such as quarantining infected peoples, identifying infections, wearing mask, and practicing hand hygiene. Since no effective treatment for COVID-19 has yet been discovered, a variety of drugs approved by Food and Drug Administration (FDA) have been suggested for repurposing strategy. In the current study, we predicted that doxycycline could interact with the nucleotide triphosphate (NTP) entry channel, and is therefore expected to hinder the viral replication of SARS-CoV-2 RNA-dependent RNA-polymerase (RdRp) through docking analysis. Further, the molecular dynamics results revealed that the RdRp-Doxycycline complex was structurally relatively stable during the dynamic period (100 ns), and its complex maintained close contact with their active catalytic domains of SARS-CoV-2 RdRp. The molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) calculation of binding free energy also showed that the doxycycline has worthy affinities with SARS-CoV-2 RdRp. As expected, doxycycline effectively inhibited the viral replication of IHU strains of SARS-CoV-2 (IHUMI-3 and IHUMI-6), identified from the hospitalized patients in IHU Méditerranée Infection (IHUMI), Marseille, France. Moreover, doxycycline inhibited the viral load in vitro at both on-entry and after viral entry of IHU variants of SARS-CoV-2. The results suggest that doxycycline exhibits strains-dependant antiviral activity against COVID-19. As a result, the current study concludes that doxycycline may be more effective in combination with other drugs for better COVID-19 treatment efficacy.
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Affiliation(s)
- Rajaiah Alexpandi
- Laboratory in Microbiology and Marine Biotechnology, Department of Biotechnology, School of Biological Sciences, Alagappa University, Karaikudi, India
| | - Mathieu Gendrot
- Parasitology and Entomology Unit, Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute, Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Gurusamy Abirami
- Laboratory in Microbiology and Marine Biotechnology, Department of Biotechnology, School of Biological Sciences, Alagappa University, Karaikudi, India
| | - Océane Delandre
- Parasitology and Entomology Unit, Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute, Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Isabelle Fonta
- Parasitology and Entomology Unit, Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute, Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,National Reference Center for Malaria, Marseille, France
| | - Joel Mosnier
- Parasitology and Entomology Unit, Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute, Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,National Reference Center for Malaria, Marseille, France
| | - Richard Mariadasse
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Shunmugiah Karutha Pandian
- Laboratory in Microbiology and Marine Biotechnology, Department of Biotechnology, School of Biological Sciences, Alagappa University, Karaikudi, India
| | - Bruno Pradines
- Parasitology and Entomology Unit, Department of Microbiology and Infectious Diseases, French Armed Forces Biomedical Research Institute, Marseille, France.,IRD, SSA, AP-HM, VITROME, Aix-Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,National Reference Center for Malaria, Marseille, France
| | - Arumugam Veera Ravi
- Laboratory in Microbiology and Marine Biotechnology, Department of Biotechnology, School of Biological Sciences, Alagappa University, Karaikudi, India
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12
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Ramachandran B, Jeyarajpandian C, Jeyaseelan JM, Prabhu D, Rajamanikandan S, Boomi P, Venkateswari R, Jeyakanthan J. Quercetin-induced apoptosis in HepG2 cells and identification of quercetin derivatives as potent inhibitors for Caspase-3 through computational methods. Struct Chem 2022. [DOI: 10.1007/s11224-022-01933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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13
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Prajisha J, Biswal J, Jeyakanthan J. Discovery of potent Camkk1 kinase inhibitors through e-pharmacophore and molecular screening approaches. J Biomol Struct Dyn 2022; 40:2740-2756. [PMID: 33155526 DOI: 10.1080/07391102.2020.1842805] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Diabetes is recognized as a major health problem and according to WHO estimates global prevalence of diabetes is expected to increase from 171 million in 2000 to 366 million in 2030, among which 21.7% will be Indians. The chronic nature of diabetes leads to several metabolic complications like kidney failure, cardiac problems and hypertension, etc.Camkk family members are attractive and emerging targets for the development of anti-diabetic drugs. However, the selectivity of inhibitors is a crucial property as a lack of selectivity could lead to serious adverse effects. STO-609 recently reported the role of Camkks a as potent inhibitor. In this study, Combined Molecular Docking and Pharmacophore Mapping were employed to identify potent lead molecules. E-Pharmacophore based virtual screening was performed against commercially available databases to identify the best lead molecule which was docked with the targets and analyzed for the binding pattern. Also, ADME and density function theory (DFT) studies of the compound were performed and the hits that showed good binding to the active sites and that matched with the pharmacophore models were considered as possible functional molecules against Camkk1. The results from e-pharmacophore based virtual screening and MD simulations evidenced that the top three compounds namely (Lifechemicals_1, Zinc_0910993 and Binding_10131) will be a promising inhibitor for Camkk1 family.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jayaprakash Prajisha
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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14
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Sureshan M, Rajamanikandan S, Srimari S, Prabhu D, Jeyakanthan J, Saraboji K. Designing specific inhibitors against dihydrofolate reductase of W. bancrofti towards drug discovery for lymphatic filariasis. Struct Chem 2022. [DOI: 10.1007/s11224-022-01896-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Affiliation(s)
- Jeyaraman Jeyakanthan
- Department of Bioinformatics Alagappa University Karaikudi-630 003, Tamil Nadu, India
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16
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021; 17:e1009384. [PMID: 34516563 PMCID: PMC8478224 DOI: 10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 09/28/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2. The on-going coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is significantly affecting the world health. Unfortunately, over 180 million cases of COVID-19 resulting in nearly 4 million deaths have been reported till June, 2021. In this study, using a combination of bioinformatics, biochemical and mass spectrometry methods, we show that the Nidovirus RdRp associated Nucleotidyl transferase (NiRAN) domain of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 exhibits a kinase like activity. Additionally, we also show that few broad spectrum anti-cancer and anti-microbial drugs dampen this kinase like activity. Of note, Sorafenib, an FDA approved anti-cancer kinase inhibiting drug significantly reduces the SARS-CoV-2 load in cell lines. Our study suggests that NiRAN domain of the SARS-CoV-2 RdRp is indispensible for the successful viral life cycle and shows that abolishing this enzymatic function of RdRp by small molecule inhibitors may open novel avenues for COVID-19 therapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Sudipta Sonar
- Translational Health Science and Technology Institute, Faridabad, India
| | - Shailendra Mani
- Translational Health Science and Technology Institute, Faridabad, India
| | | | - Tanmay Majumdar
- National Institute of Immunology, New Delhi, India
- * E-mail: (TM); (JJ); (BKB)
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Tamil Nadu, India
- * E-mail: (TM); (JJ); (BKB)
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17
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Dwivedy A, Mariadasse R, Ahmad M, Chakraborty S, Kar D, Tiwari S, Bhattacharyya S, Sonar S, Mani S, Tailor P, Majumdar T, Jeyakanthan J, Biswal BK. Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2. PLoS Comput Biol 2021. [DOI: https://doi.org/10.1371/journal.pcbi.1009384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, a well-known kinase inhibitor- Sorafenib showed a significant inhibition and dampened viral load in SARS-CoV-2 infected cells. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.
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18
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Karthika A, Ramachandran B, Chitra J, Prabhu D, Rajamanikandan S, Veerapandiyan M, Jeyakanthan J. Molecular dynamics simulation of Toxin-Antitoxin (TA) system in Acinetobacter baumannii to explore the novel mechanism for inhibition of cell wall biosynthesis: Zeta Toxin as an effective therapeutic target. J Cell Biochem 2021; 122:1832-1847. [PMID: 34448250 DOI: 10.1002/jcb.30137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 01/15/2023]
Abstract
The majority of bacteria and archaea contains Toxin-Antitoxin system (TA) that codes for the stable Toxin and unstable Antitoxin components forming a complex. The Antitoxin inhibits the catalytic activities of the Toxin. In general, the Antitoxin will be degraded by the proteases leading to the Toxin activation that subsequently targets essential cellular processes, including transcription, translation, replication, cell division, and cell wall biosynthesis. The Zeta Toxin-Epsilon Antitoxin system in ESKAPE pathogen stabilizes the resistance plasmid and promotes pathogenicity. The known TA system in Acinetobacter baumannii are known to be involved in the replication and translation, however, the mechanism of Zeta Toxin-Epsilon Antitoxin in cell wall biosynthesis remains unknown. In the present study, molecular docking and molecular dynamic (MD) simulations were employed to demonstrate whether Zeta Toxin can impair cell wall synthesis in A. baumannii. Further, the degradation mechanism of Antitoxin in the presence and absence of adenosine triphosphate (ATP) molecules are explained through MD simulation. The result reveals that the cleavage of Antitoxin could be possible with the presence of ATP by displaying its response from 20 ns, whereas the Zeta Toxin/Epsilon was unstable after 90 ns. The obtained results demonstrate that Zeta Toxin is "temporarily favorable" for ATP to undergo phosphorylation at UNAG kinase through the substrate tunneling process. The study further evidenced that phosphorylated UNAG prevents the binding of MurA, the enzyme that catalyzes the initial step of bacterial peptidoglycan biosynthesis. Therefore, the present study explores the binding mechanism of Zeta Toxin/Epsilon Antitoxin, which could be beneficial for preventing cell wall biosynthesis as well as for unveiling the alternative treatment options to antibiotics.
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Affiliation(s)
- Alagesan Karthika
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Balajee Ramachandran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jeyarajpandian Chitra
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
| | - Dhamodharan Prabhu
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sundaraj Rajamanikandan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Malaisamy Veerapandiyan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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19
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Murugan NA, Pandian CJ, Jeyakanthan J. Computational investigation on Andrographis paniculata phytochemicals to evaluate their potency against SARS-CoV-2 in comparison to known antiviral compounds in drug trials. J Biomol Struct Dyn 2021; 39:4415-4426. [PMID: 32543978 PMCID: PMC7309306 DOI: 10.1080/07391102.2020.1777901] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022]
Abstract
The outbreak due to SARS-CoV-2 (or Covid-19) is spreading alarmingly and number of deaths due to infection is aggressively increasing every day. Due to the rapid human to human transmission of Covid-19, we are in need to find a potent drug at the earliest by ruling-out the traditional time-consuming approach of drug development. This is only possible if we use reliable computational approaches for screening compounds from chemical space or by drug repurposing or by finding the phytochemicals and nutraceuticals from plants as they can be immediately used without the need for carrying out drug-trials to test safety and efficacy. A number of plant products were routinely suggested as drugs in traditional Indian and Chinese medicine. Here using molecular docking approach, and combined molecular dynamics and MM-GBSA based free energy calculations approach, we study the potency of the four selected phytochemicals namely andrographolide (AGP1), 14-deoxy 11,12-didehydro andrographolide (AGP2), neoandrographolide (AGP3) and 14-deoxy andrographolide (AGP4) from A. paniculata plant against the four key targets including three non-structural proteins (3 L main protease (3CLpro), Papain-like proteinase (PLpro) and RNA-directed RNA polymerase (RdRp)) and a structural protein (spike protein (S)) of the virus which are responsible for replication, transcription and host cell recognition. The therapeutic potential of the selected phytochemicals against Covid-19 were also evaluated in comparison with a few commercially available drugs. The binding free energy data suggest that AGP3 could be used as a cost-effective drug-analog for treating covid-19 infection in developing countries.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Natarajan Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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20
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Mohanrasu K, Guru Raj Rao R, Dinesh GH, Zhang K, Sudhakar M, Pugazhendhi A, Jeyakanthan J, Ponnuchamy K, Govarthanan M, Arun A. Production and characterization of biodegradable polyhydroxybutyrate by Micrococcus luteus isolated from marine environment. Int J Biol Macromol 2021; 186:125-134. [PMID: 34246666 DOI: 10.1016/j.ijbiomac.2021.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/26/2022]
Abstract
Marine microorganisms are reported to produce polyhydroxybutyrate (PHB) that has wide range of medical and industrial applications with the advantage of biodegradability. PHBs are synthesized as an energy and carbon storage element under metabolic pressure. The scope of this work is enhancing PHB production using marine microbial isolate, Micrococcus luteus by selectively optimizing various growth conditions such as different media components and growth parameters that influence the cell growth and PHB production were sampled. Micrococcus luteus produced 7.54 g/L of PHB utilizing glucose as a carbon source and ammonium sulphate as a nitrogen source with maximum efficiency. The same optimized operational conditions were further employed in batch fermentation over a time span of 72 h. Interestingly higher cell dry weight of 21.52 g/L with PHB yield of 12.18 g/L and 56.59% polymer content was observed in batch fermentation studies at 64 h. The chemical nature of the extracted polymer was validated with physio-chemical experiments and was at par with the commercially available PHB. This study will spotlight M. luteus as a potential source for large-scale industrial production of PHB with reducing environmental pollutions.
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Affiliation(s)
- K Mohanrasu
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - R Guru Raj Rao
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - G H Dinesh
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Kunyu Zhang
- School of Chemical Engineering and Technology, Tianjin University, China
| | - Muniyasamy Sudhakar
- CSIR Chemical Cluster, Advanced Polymers and Composites Research, Pretoria, South Africa; Dept of Chemistry, Nelson Mandela University, Port Elizabeth, South Africa
| | - A Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Viet Nam
| | - J Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Kumar Ponnuchamy
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu 630003, India
| | - M Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea.
| | - A Arun
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India.
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21
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Mariadasse R, Rajmichael R, Dwivedy A, Amala M, Ahmad M, Mutharasappan N, Biswal BK, Jeyakanthan J. Characterization of putative transcriptional regulator (PH0140) and its distal homologue. Cell Signal 2021; 84:110031. [PMID: 33932498 DOI: 10.1016/j.cellsig.2021.110031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
In this study, a phylogenetic tree was constructed using 1854 sequences of various Lrp/AnsC (FFRPs) and ArsR proteins from pathogenic and non-pathogenic organisms. Despite having sequence similarities, FFRPs and ArsR proteins functioning differently as a transcriptional regulator and de-repressor in the presence of exogenous amino acids and metal ions, respectively. To understand these functional differences, the structures of various FFRPs and ArsR proteins (134 sequences) were modeled. Several ArsR proteins exhibited high similarity to the FFRPs while in few proteins, unusual structural folds were observed. However, the Helix-turn-Helix (HTH) domains are common among them and the ligand-binding domains are structurally dissimilar suggest the differences in their binding preferences. Despite low sequence conservation, most of these proteins revealed negatively charged surfaces in the active site pockets. Representative structures (PH0140 and TtArsR protein) from FFRPs and ArsR protein families were considered and evaluated for their functional differences using molecular modeling studies. Our earlier study has explained the binding preference of exogenous Tryptophan and the related transcriptional regulatory mechanism of PH0140 protein. In this study, a Cu2+ ion-induced de-repression mechanism of the TtArsR-DNA complex was characterized through docking and molecular dynamics. Further, the proteins were purified and their efficiency for sensing Tryptophan and Cu2+ ions were analyzed using cyclic voltammetry. Overall, the study explores the structural evolution and functional difference of FFRPs and ArsR proteins that present the possibilities of PH0140 and TtArsR as potential bio-sensory molecules.
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Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | - Raji Rajmichael
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Mathimaran Amala
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Nachiappan Mutharasappan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India
| | | | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 004, India.
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22
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Premnath N, Mohanrasu K, Guru Raj Rao R, Dinesh GH, Siva Prakash G, Pugazhendhi A, Jeyakanthan J, Govarthanan M, Kumar P, Arun A. Effect of C/N substrates for enhanced extracellular polymeric substances (EPS) production and Poly Cyclic Aromatic Hydrocarbons (PAHs) degradation. Environ Pollut 2021; 275:116035. [PMID: 33581631 DOI: 10.1016/j.envpol.2020.116035] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 05/22/2023]
Abstract
Extracellular Polymeric Substances (EPS) influenced Poly Cyclic Aromatic Hydrocarbons (PAHs) degrading Klebsiella pneumoniae was isolated from the marine environment. To increase the EPS production by Klebsiella pneumoniae, several physicochemical parameters were tweaked such as different carbon sources (arabinose, glucose, glycerol, lactose, lactic acid, mannitol, sodium acetate, starch, and sucrose at 20 g/L), nitrogen sources (ammonium chloride, ammonium sulphate, glycine, potassium nitrate, protease peptone and urea at 2 g/L), different pH, carbon/nitrogen ratio, temperature, and salt concentration were examined. Maximum EPS growth and biodegradation of Anthracene (74.31%), Acenaphthene (67.28%), Fluorene (62.48%), Naphthalene (57.84%), and mixed PAHs (55.85%) were obtained using optimized conditions such as glucose (10 g/L) as carbon source, potassium nitrate (2 g/L) as the nitrogen source at pH 8, growth temperature of 37 °C, 3% NaCl concentration and 72 h incubation period. The Klebsiella pneumoniae biofilm architecture was studied by confocal laser scanning microscopy (CLSM) and scanning electron microscope (SEM). The present study demonstrates the EPS influenced PAHs degradation of Klebsiella pneumoniae.
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Affiliation(s)
- N Premnath
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - K Mohanrasu
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - R Guru Raj Rao
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - G H Dinesh
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India; Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India
| | - G Siva Prakash
- Department of Energy Science, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Arivalagan Pugazhendhi
- Innovative Green Product Synthesis and Renewable Environment Development Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho, Chi Minh City, Viet Nam.
| | - J Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ponnuchamy Kumar
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - A Arun
- Department of Microbiology, Alagappa University, Karaikudi, Tamil Nadu, India.
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Biswal J, Jayaprakash P, Rayala SK, Venkatraman G, Rangasamy R, Poopandi S, Jeyakanthan J. Water Mapping and Scoring approaches to predict the role of Hydration sites in Binding Affinity of PAK1 inhibitors. Comb Chem High Throughput Screen 2021; 25:660-676. [PMID: 33687876 DOI: 10.2174/1386207324666210308110646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/11/2020] [Accepted: 02/18/2021] [Indexed: 11/22/2022]
Abstract
AIM This study aims to develop and establish a computational model that can identify potent molecules for p21-activating kinase 1 (PAK1). BACKGROUND PAK1 is a well-established drug target that has been explored for various therapeutic interventions. Control of this protein requires an indispensable inhibitor to curb the structural changes and subsequent activation of signalling effectors responsible for the progression of diseases, such as cancer, inflammatory, viral, and neurological disorders. OBJECTIVE To establish a computational model that could identify active molecules which will further provide a platform for developing potential PAK1 inhibitors. METHOD A congeneric series of 27 compounds was considered for this study with Ki (nm) covering a minimum of 3 log range. The compounds were developed based on a previously reported Group-I PAK inhibitor, namely G-5555. The 27 compounds were subjected to the SP and XP mode of docking, to understand the binding mode, its conformation and interaction patterns. To understand the relevance of biological activity from computational approaches, the compounds were scored against generated water maps to obtain WM/MM ΔG binding energy. Moreover, molecular dynamics analysis was performed for the highly active compound, to understand the conformational variability and complex's stability. We then evaluate the predictable binding pose obtained from the docking studies. RESULT From the SP and XP modes of docking, the common interaction pattern with the amino acid residues Arg299 (cation-π), Glu345 (Aromatic hydrogen bond), hinge region Leu347, salt bridges Asp393 and Asp407 was observed, among the congeneric compounds. The interaction pattern was compared with the co-crystal inhibitor FRAX597 of the PAK1 crystal structure (PDB id: 4EQC). The correlation with different docking parameters in the SP and XP modes was insignificant and thereby revealed that the SP and XP's scoring functions could not predict the active compounds. This was due to the limitations in the docking methodology that neglected the receptor flexibility and desolvation parameters. Hence, to recognise the desolvation and explicit solvent effects, as well as to study the Structure-Activity Relationships (SARs) extensively, WaterMap (WM) calculations were performed on the congeneric compounds. Based on displaceable unfavourable hydration sites (HS) and their associated thermodynamic properties, the WM calculations facilitated to understand the significance of correlation in the folds of activity of highly (19 and 17), moderate (16 and 21) and less active (26 and 25) compounds. Furthermore, the scoring function from WaterMap, namely WM/MM, led to a significant R2 value of 0.72, due to a coupled conjunction with MM treatment and displaced unfavourable waters at the binding site. To check the "optimal binding conformation", molecular dynamics simulation was carried out with the highly active compound 19 to explain the binding mode, stability, interactions, solvent accessible area, etc., which could support the predicted conformation with bioactive conformation. CONCLUSION This study determined the best scoring function, established SARs and predicted active molecules through a computational model. This will contribute towards development of the most potent PAK1 inhibitors.
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Affiliation(s)
- Jayashree Biswal
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Prajisha Jayaprakash
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Suresh Kumar Rayala
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Ganesh Venkatraman
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Raghu Rangasamy
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Saritha Poopandi
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Science Block, Alagappa University, Karaikudi - 630 004, Tamil Nadu. India
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24
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Rajamanikandan S, Soundarya S, Paramasivam A, Prabhu D, Jeyakanthan J, Ramasamy V. Computational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae. J Biomol Struct Dyn 2021; 40:6415-6425. [PMID: 33590810 DOI: 10.1080/07391102.2021.1885491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Gonorrhea, one of the sexually transmitted disease caused by a gram negative diplococcus bacteria Neisseria gonorrhoeae. Rho protein is indispensable for bacterial viability due to its versatile functions in physiology apart from RNA dependent transcription termination. Based on conserved function and wider role in several cellular processes, inhibitors specifically targeting Rho proteins are largely in use these days to treat various bacterial infections. In this study, three dimensional structure of Rho protein was modeled using the template protein from E. coli and further the optimized model was simulated for 100 ns to understand the structural stability and compactness. Owing to the therapeutic potential of Rho, traditional structure-based virtual screening was applied to identify potential inhibitors for the selected target. Based on empirical glide scoring functions two potent lead molecules (ChemBridge_6121956 and ChemBridge_5232688) were selected from ChemBridge database. The pharmacokinetic properties of these lead molecules are within the permissible range. DFT descriptor revealed that the lead molecules are more reactive, which also supports the molecular docking studies. The stability of Rho and Rho-inhibitor complexes was studied using molecular dynamics simulation. Parameters include binding free energy calculation, RMSD, RMSF and hydrogen bond analysis depicts the stability of Rho and Rho-inhibitors throughout the simulation. Altogether, the identified lead molecules require further optimization towards the design and development of new antibiotics against N. gonorrhoeae.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Anandhi Paramasivam
- Department of Biotechnology and Bioinformatics, Bishop Herber College, Trichy, Tamil Nadu, India
| | - Dhamodharan Prabhu
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
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25
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Ramachandran B, Srinivasadesikan V, Chou TM, Jeyakanthan J, Lee SL. Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus. J Biomol Struct Dyn 2020; 40:4314-4327. [PMID: 33308046 DOI: 10.1080/07391102.2020.1856184] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against Staphylococcus aureus using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N - H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of S. aureus that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Venkatesan Srinivasadesikan
- Division of Chemistry, Department of Sciences & Humanities, Vignan's Foundation for Science, Technology and Research, Vadlamudi, Andhra Pradesh, India
| | - Tsz-Min Chou
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan
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26
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Amala M, Richard M, Saritha P, Prabhu D, Veerapandiyan M, Surekha K, Jeyakanthan J. Molecular evolution, binding site interpretation and functional divergence of aspartate semialdehyde dehydrogenase. J Biomol Struct Dyn 2020; 40:3223-3241. [DOI: 10.1080/07391102.2020.1846619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mathimaran Amala
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Mariadasse Richard
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Poopandi Saritha
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Dhamodharan Prabhu
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Malaisamy Veerapandiyan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Kangarajan Surekha
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Laboratory, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
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27
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Chaudhary SK, Elayappan M, Jeyakanthan J, Kanagaraj S. Structural and functional characterization of oligomeric states of proteins in RecFOR pathway. Int J Biol Macromol 2020; 163:943-953. [DOI: 10.1016/j.ijbiomac.2020.07.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 11/30/2022]
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Lokesh R, Jeyakanthan J, Kannabiran K. Targeting VEGFR2 protein by marine Streptomyces globosus VITLGK011-derived compound BECA: An in vitro and in silico analysis. J Basic Microbiol 2020; 60:983-993. [PMID: 33103250 DOI: 10.1002/jobm.202000461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022]
Abstract
This study investigates the anticancer cytotoxic mechanism of action of benzoyloxy-ethyl-carbamic acid (BECA) produced by Streptomyces globosus VITLGK011. Flow cytometry analysis confirmed that BECA (at IC50 : 3.12 µg/ml) treatment for 24 h induced apoptosis in 60% of cells. Schrodinger Maestro tools such as QikProp and DFT were used to confirm that BECA is an eligible drug-like molecule, with suitable physiochemical properties. Glide XP tool was used to perform induced-fit docking between BECA and 30 cancer drug target proteins. The highest significance was observed for VEGFR2 protein (-6.7 kcal/mol). GROMACS tool was used to perform molecular dynamic simulation between BECA and VEGFR2 protein for 40 ns. Root mean square deviation, root mean square fluctuation, H-bond, and trajectory analysis, confirmed that BECA is a suitable inhibitor of VEGFR2 protein. Results conclude that BECA is a valid VEGFR2 inhibitor, and it thus exerts the observed anticancer cytotoxicity against MCF-7 cells.
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Affiliation(s)
- Ravi Lokesh
- Department of Botany, St. Joseph's College (Autonomous), Bengaluru, India
| | | | - Krishnan Kannabiran
- Department of Biomedical Sciences, Vellore Institute of Technology, Vellore, India
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29
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Murugan NA, Muvva C, Jeyarajpandian C, Jeyakanthan J, Subramanian V. Performance of Force-Field- and Machine Learning-Based Scoring Functions in Ranking MAO-B Protein-Inhibitor Complexes in Relevance to Developing Parkinson's Therapeutics. Int J Mol Sci 2020; 21:ijms21207648. [PMID: 33081086 PMCID: PMC7589968 DOI: 10.3390/ijms21207648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/27/2020] [Accepted: 10/08/2020] [Indexed: 01/11/2023] Open
Abstract
Monoamine oxidase B (MAOB) is expressed in the mitochondrial membrane and has a key role in degrading various neurologically active amines such as benzylamine, phenethylamine and dopamine with the help of Flavin adenine dinucleotide (FAD) cofactor. The Parkinson’s disease associated symptoms can be treated using inhibitors of MAO-B as the dopamine degradation can be reduced. Currently, many inhibitors are available having micromolar to nanomolar binding affinities. However, still there is demand for compounds with superior binding affinity and binding specificity with favorable pharmacokinetic properties for treating Parkinson’s disease and computational screening methods can be majorly recruited for this. However, the accuracy of currently available force-field methods for ranking the inhibitors or lead drug-like compounds should be improved and novel methods for screening compounds need to be developed. We studied the performance of various force-field-based methods and data driven approaches in ranking about 3753 compounds having activity against the MAO-B target. The binding affinities computed using autodock and autodock-vina are shown to be non-reliable. The force-field-based MM-GBSA also under-performs. However, certain machine learning approaches, in particular KNN, are found to be superior, and we propose KNN as the most reliable approach for ranking the complexes to reasonable accuracy. Furthermore, all the employed machine learning approaches are also computationally less demanding.
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Affiliation(s)
- Natarajan Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 10691 Stockholm, Sweden
- Correspondence:
| | | | - Chitra Jeyarajpandian
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi 630 004, India;
| | | | - Venkatesan Subramanian
- Centre for High Computing, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India;
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30
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Joseph Sahayarayan J, Soundar Rajan K, Nachiappan M, Prabhu D, Guru Raj Rao R, Jeyakanthan J, Hossam Mahmoud A, Mohammed OB, Morgan AMA. Identification of potential drug target in malarial disease using molecular docking analysis. Saudi J Biol Sci 2020; 27:3327-3333. [PMID: 33304138 PMCID: PMC7715035 DOI: 10.1016/j.sjbs.2020.10.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 11/27/2022] Open
Abstract
Malaria caused by genus Plasmodium, is a parasite which is the main health issue for humans and about half of the population were suffered. An every year, approximately 1.2–2.7 million people died due to malaria globally. Therefore to prevent the spreading of malaria from the glob novel active drugs with specific activities are necessary. The present study aimed to identify novel drug molecule together with the bioinformatic tools for the development of active malarial drugs. As the search for latest anti malarial compound was developed, this work determined six active blends from various drug databases which possess drug-like characteristics and presents a significant anti malarial actions in in-silico level. Compound ID 300238, 889, 76569, 87324, 45678, and Z185397112are a few of the ligands were got from the Toss lab, Maybridge, Cambridge, Life chem, Bitter, and Examine drug databases and docked against hexokinase 1 protein (PDB: 1CZA) with high throughput practical screening (HTVS) using Glide v6.6. Amid the 6 compounds, compound no: 300238 from Toss lab has the greatest docking score of −9.889 kcal/mol targeting 1CZA protein. The active sites of Hexokinase I of protein were determine by using superimposition of the destination and template structure showed similar structural folds and active sites which were decidedly conserved. The quality of hexokinase I protein was considered to be sterically stable where the protein was prepared by utilizing the software protein preparation execute in the Schrodinger suite. Prepared proteins were evaluated using SAVES and the studies of molecular dynamics of the hexokinase, and the GROMACS were performed for protein–ligand complex. The low HOMO-LUMO energy gaps of the compound verified the greater stability of the molecule. Here, the tested drug candidates have good absorption, distribution, metabolism, and excretion (ADME) properties which were established by using QikProp, version 3.4 of Schrodinger.
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Affiliation(s)
| | | | | | - Dhamodharan Prabhu
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630 003, India
| | - Ravi Guru Raj Rao
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630 003, India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630 003, India
| | - Ahmed Hossam Mahmoud
- Department Zoology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia
| | - Osama B Mohammed
- Department Zoology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia
| | - Abubaker M A Morgan
- Faculty of Agricultural Sciences, University of Gezira, Wad-Medani, P.O Box 20, Sudan
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Muthumanickam S, Indhumathi T, Boomi P, Balajee R, Jeyakanthan J, Anand K, Ravikumar S, Kumar P, Sudha A, Jiang Z. In silico approach of naringin as potent phosphatase and tensin homolog (PTEN) protein agonist against prostate cancer. J Biomol Struct Dyn 2020; 40:1629-1638. [PMID: 33034258 DOI: 10.1080/07391102.2020.1830855] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Prostate cancer (PC) is one of the major impediments affecting men, which leads approximately 31,620 deaths in both developing and developed countries. Although some chemotherapy drugs have been reported for prostate cancer, they are not effective due to the lack of safety, efficacy and low selectivity. Hence, the novel alternative anticancer agents with remarkable effect are highly appreciable. Natural plants contain several bio-active compounds which have been traditionally used for the various medical treatments. Particularly, naringin is a natural bio-active compound commonly found in the citrus fruits, which have shown numerous biological activities. Phosphatase and tensin homolog (PTEN) is a tumor suppressor gene, which activates both lipid phosphates and protein phosphates. The PTEN gene is negative regulator of PI3K/AKT/mTOR pathways, since, this signaling pathway play an essential role in the cell survival, proliferation and migration. In the present in silico investigation, structure based virtual screening, molecular docking, molecular dynamics simulation and Adsorption, Distribution, Metabolism, Excretion (ADME) prediction were employed to determine the binding affinity, stability and drug likeness properties of top ranked screened compounds and naringin, respectively. The results revealed that the complex has good molecular interactions, binding stability (peak between 0.3 and 0.4 nm) and no violations in the Lipinski Rule of 5 in naringin, but the screened compounds violated the drug likeness properties. From the in silico analyses, it is identified that naringin compound might assist in the development of novel therapeutic candidate against prostate cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | | | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Sundaram Ravikumar
- Department of Biomedical Science, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ponnuchamy Kumar
- Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Arumugam Sudha
- Department of Biotechnology, Dr. Umayal Ramanathan College for Women, Karaikudi, Tamil Nadu, India
| | - Zhihui Jiang
- School of life Science, Department of Biotechnology, Anyang Institute of Technology, Henan, China
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Boomi P, Ganesan R, Prabu Poorani G, Jegatheeswaran S, Balakumar C, Gurumallesh Prabu H, Anand K, Marimuthu Prabhu N, Jeyakanthan J, Saravanan M. Phyto-Engineered Gold Nanoparticles (AuNPs) with Potential Antibacterial, Antioxidant, and Wound Healing Activities Under in vitro and in vivo Conditions. Int J Nanomedicine 2020; 15:7553-7568. [PMID: 33116487 PMCID: PMC7548233 DOI: 10.2147/ijn.s257499] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Background A diabetic ulcer is one of the major causes of illness among diabetic patients that involves severe and intractable complications associated with diabetic wounds. Hence, a suitable wound-healing agent is urgently needed at this juncture. Greener nanotechnology is a very promising and emerging technology currently employed for the development of alternative medicines. Plant-mediated synthesis of metal nanoparticles has been intensively investigated and regarded as an alternative strategy for overcoming various diseases and their secondary complications like microbial infections. Hence, we are interested in developing phyto-engineered gold nanoparticles as useful therapeutic agents for the treatment of infectious diseases and wounds effectively. Methods and Results We have synthesized phyto-engineered gold nanoparticles from the aqueous extract of Acalypha indica and characterized using advanced bio-analytical techniques. The surface plasmon resonance feature and crystalline behavior of gold nanoparticles were revealed by ultraviolet-visible spectroscopy and X-ray diffraction, respectively. High-performance liquid chromatography analysis of the extract demonstrated the presence of different constituents, while major functional groups were interpreted by the Fourier-transform infrared spectroscopy as the various stretching vibrations appeared for important O-H (3443 cm−1), C=O (1644 cm−1) and C-O (1395 cm−1) groups. Scanning electron microscopy, high-resolution transmission electron microscopy results revealed a distribution of spherical and rod-like nanostructures with 20 nm of size. The gold nanoparticle-coated cotton fabric was evaluated for the antibacterial activity against Staphylococcus epidermidis and Escherichia coli bacterial strains which revealed remarkable inhibition at the zone of inhibition of 31 mm diameter against S. epidermidis. Further, antioxidant activity was tested for their free radical scavenging property, and the maximum antioxidant activity of the extract containing gold nanoparticles was found to be 80% at 100 µg/mL. The potent free radical scavenging property of the nanoparticles is observed at IC50 value 16.25 µg/mL. Moreover, in vivo wound-healing activity was carried out using BALB/c mice model with infected diabetic wounds and observed the stained microscopic images at different time intervals (day 2, day 7 and day 15). It was noted that in 15 days, the wound area is completely re-epithelialized due to the presence of different morphologies such as spherical, needle and triangle nanoparticles. The re-epithelialization layer is fully covered by nanoparticles on the wound area and also collagen filled in the scar tissue when compared with the control group. Conclusion The pharmacological evaluation results of the study indicated an encouraging antibacterial and antioxidant activity of the greener synthesized gold nanoparticles tethered with aqueous extract of Acalypha indica. Moreover, we demonstrated enhanced in vivo wound-healing efficiency of the synthesized gold nanoparticles through the animal model. Thus, the outcome of this work revealed that the phyto-engineered gold nanoparticles could be useful for biomedical applications, especially in the development of promising antibacterial and wound-healing agents.
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Affiliation(s)
- Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Ramalingam Ganesan
- Department of Chemistry, Arumugam Seethaiyammal Arts and Science College, Tiruppattur, Tamil Nadu, India
| | | | - Sonamuthu Jegatheeswaran
- The Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textile, Zhejiang Sci-Tech University, Hangzhou, People's Republic of China
| | | | - Halliah Gurumallesh Prabu
- Department of Industrial Chemistry, School of Chemical Sciences, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Narayanasamy Marimuthu Prabhu
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Muthupandian Saravanan
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, School of Medicine, College of Health Science, Mekelle University, Mekelle, Ethiopia
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Choubey SK, Nachiappan M, Richard M, Chitra JP, Jeyakanthan J. Structural and functional insights of STAT2-NS5 interaction for the identification of NS5 antagonist – An approach for restoring interferon signaling. Comput Biol Chem 2020; 88:107332. [DOI: 10.1016/j.compbiolchem.2020.107332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
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Ramachandran B, Jeyakanthan J, Lopes BS. Molecular docking, dynamics and free energy analyses of Acinetobacter baumannii OXA class enzymes with carbapenems investigating their hydrolytic mechanisms. J Med Microbiol 2020; 69:1062-1078. [PMID: 32773005 DOI: 10.1099/jmm.0.001233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction. Acinetobacter baumannii is a critical priority pathogen listed by the World Health Organization due to increasing levels of resistance to carbapenem classes of antibiotics. It causes wound and other nosocomial infections, which can be life-threatening. Hence, there is an urgent need for the development of new classes of antibiotics.Aim. To study the interaction of carabapenems with class D beta-lactamases (oxacillinases) and analyse drug resistance by studying enzyme-substrate complexes using modelling approaches as a means of establishing correlations with the phenotypic data.Methodology. The three-dimensional structures of carbapenems (doripenem, ertapenem, imipenem and meropenem) were obtained from DrugBank and screened against class D beta-lactamases. Further, the study was extended with their variants. The variants' structure was homology-modelled using the Schrödinger Prime module (Schrödinger LLC, NY, USA).Results. The first discovered intrinsic beta-lactamase of Acinetobacter baumannii, OXA-51, had a binding energy value of -40.984 kcal mol-1, whereas other OXA-51 variants, such as OXA-64, OXA-110 and OXA-111, have values of -60.638, -66.756 and -67.751 kcal mol-1, respectively. The free energy values of OXA-51 variants produced better results than those of other groups.Conclusions. Imipenem and meropenem showed MIC values of 2 and 8 µg ml-1, respectively against OXA-51 in earlier studies, indicating that these are the most effective drugs for treatment of A. baumannii infection. According to our results, OXA-51 is an active enzyme that shows better interactions and is capable of hydrolyzing carbapenems. When correlating the hydrogen-bonding interaction with MIC values, the predicted results are in good agreement and might provide initial insights into performing similar studies related to OXA variants or other antibiotic-enzyme-based studies.
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Affiliation(s)
- Balajee Ramachandran
- Structural Biology and Bio-computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi - 630 004, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi - 630 004, Tamil Nadu, India
| | - Bruno S Lopes
- School of Medicine, Medical Sciences and Nutrition, 0:025 Polwarth building, Foresterhill, Aberdeen AB25 2ZD, UK
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Prabhu D, Rajamanikandan S, Anusha SB, Chowdary MS, Veerapandiyan M, Jeyakanthan J. In silico Functional Annotation and Characterization of Hypothetical Proteins from Serratia marcescens FGI94. BIOL BULL+ 2020; 47:319-331. [PMID: 32834707 PMCID: PMC7394047 DOI: 10.1134/s1062359020300019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/28/2019] [Accepted: 09/30/2019] [Indexed: 01/16/2023]
Abstract
Serratia marcescens, rod-shaped Gram-negative bacteria is classified as an opportunistic pathogen in the family Enterobacteriaceae. It causes a wide variety of infections in humans, including urinary, respiratory, ocular lens and ear infections, osteomyelitis, endocarditis, meningitis and septicemia. Unfortunately, over the past decade, antibiotic resistance has become a serious health care issue; the effective means to control and dissemination of S. marcescens resistance is the need of hour. The whole genome sequencing of S. marcescens FGI94 strain contains 4434 functional proteins, among which 690 (15.56%) proteins were classified under hypothetical. In the present study, we applied the power of various bioinformatics tools on the basis of protein family comparison, motifs, functional properties of amino acids and genome context to assign the possible functions for the HPs. The pseudo sequences (protein sequence that contain ≤100 amino acid residues) are eliminated from the study. Although we have successfully predicted the function for 483 proteins, we were able to infer the high level of confidence only for 108 proteins. The predicted HPs were classified into various classes such as enzymes, transporters, binding proteins, cell division, cell regulatory and other proteins. The outcome of the study could be helpful to understand the molecular mechanism in bacterial pathogenesis and also provide an insight into the identification of potential targets for drug and vaccine development.
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Affiliation(s)
- D Prabhu
- Department of Bioinformatics, Alagappa University, Science Campus, 630004 Karaikudi, Tamil Nadu India
| | - S Rajamanikandan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, 560064 Yelahanka, Bengaluru India
| | - S Baby Anusha
- Department of Bioinformatics, Sathyabama University, 600119 Chennai, Tamil Nadu India
| | - M Sushma Chowdary
- Department of Bioinformatics, Sathyabama University, 600119 Chennai, Tamil Nadu India
| | - M Veerapandiyan
- Department of Bioinformatics, Alagappa University, Science Campus, 630004 Karaikudi, Tamil Nadu India
| | - J Jeyakanthan
- Department of Bioinformatics, Alagappa University, Science Campus, 630004 Karaikudi, Tamil Nadu India
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Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS Omega 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
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Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
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Santhosh R, Bankoti N, Gurudarshan M, Jeyakanthan J, Sekar K. IMRPS: Inserted and Modified Residues in Protein Structures. A database. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576720001880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Modified residues present in proteins are the result of post-translational modifications (PTMs). These PTMs increase the functional diversity of the proteome and influence various biological processes and diseased conditions. Therefore, identification and understanding of PTMs in various protein structures is of great significance. In view of this, an online database, Inserted and Modified Residues in Protein Structures (IMRPS), has been developed. IMRPS is a derived database that furnishes information on the residues modified and inserted in the protein structures available in the Protein Data Bank (PDB). The database is equipped with a graphical user interface and has an option to view the data for non-redundant protein structures (25 and 90%) as well. A quality criteria cutoff has been incorporated to assist in displaying the specific set of PDB codes. The entire protein structure along with the inserted or modified residues can be visualized in JSmol. This database will be updated regularly (presently, every three months) and can be accessed through the URL http://cluster.physics.iisc.ac.in/imrps/.
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Nanda H, Ponnusamy N, Odumpatta R, Jeyakanthan J, Mohanapriya A. Exploring genetic targets of psoriasis using genome wide association studies (GWAS) for drug repurposing. 3 Biotech 2020; 10:43. [PMID: 31988837 PMCID: PMC6954159 DOI: 10.1007/s13205-019-2038-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
Psoriasis is a chronic inflammatory disease causing itching in the body and pain in the joints. Currently, no permanent cure is available at a commercial level for this disease. Genome wide association studies (GWAS) provide a deeper insight that helps in better understanding this disease and further possible cure of this disease. The major goal of the present study is to identify potent genetic targets of psoriasis disease using GWAS approach and identify drugs for repurposing. The methods used include GWAS catalogue, GeneAnalytics, canSAR protein annotation tool, VarElect, Drug bank, Proteomics database, ProTox software. By exploring GWAS catalogue, 126 psoriasis associated genes (PAG) were identified. 68 genes found to be druggable were obtained from canSAR protein annotation tool. Localization results depict that maximum genes are present in cytoplasmic cellular components. The superpathways obtained from GeneAnalytics resulted in involvement of these genes in the immune system, Jak/Stat pathway, Th17 and Wnt pathways. Two genes Interleukin 13 (IL13) and POLI are Food and Drug Administration (FDA) approved targets. Small compounds for these targets were analysed for drug-likeliness, toxicity and mutagenecity properties. The FDA approved drug pandel was found to possess desirable properties. The medications used for psoriasis causes mild to severe side effects and does not work well always. Hence we propose drug repurposing strategy to use existing drugs for new therapies. Therefore, the drug pandel could be explored further and repurposed to treat psoriasis.
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Affiliation(s)
- Harshit Nanda
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Rajasree Odumpatta
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004 India
| | - Arumugam Mohanapriya
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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Mariadasse R, Choubey SK, Jeyakanthan J. Insights into Exogenous Tryptophan-Mediated Allosteric Communication and Helical Transition of TRP Protein for Transcription Regulation. J Chem Inf Model 2019; 60:175-191. [DOI: 10.1021/acs.jcim.9b00755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Mariadasse
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Sanjay Kumar Choubey
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, 630 004 Tamil Nadu, India
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Gowri M, Jayashree B, Jeyakanthan J, Girija EK. Sertraline as a promising antifungal agent: inhibition of growth and biofilm of Candida auris with special focus on the mechanism of action in vitro. J Appl Microbiol 2019; 128:426-437. [PMID: 31621139 DOI: 10.1111/jam.14490] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 01/18/2023]
Abstract
AIM The aim of this present study was to investigate the antifungal mechanism of sertraline against Candida auris (C. auris) and its effect on biofilm formation. METHODS AND RESULTS Sertraline, a repurposing drug with a history of human use for the treatment of depression was screened against three different isolates of C. auris, and was found to possess efficient antifungal activity. The antifungal activity of sertraline was further confirmed by killing kinetics assay and post-antifungal effect (PAFE). Sertraline inhibited C. auris yeast to hyphae conversion and further the inhibition of biofilm formation showed 71% inhibition upon treatment. Cell damage caused due to C. auris after treatment with sertraline was observed using SEM and cell membrane damage was ascertained using flow cytometry by Propidium Iodide (PI) uptake assay. The results of sorbitol protection assay and ergosterol effect assay suggested that sertraline did not affect the cell wall and did not act by binding to membrane ergosterol. The mechanism of action of sertraline against C. auris was understood through in silico docking studies that revealed the binding nature of sertraline to the sterol 14 alpha demethylase which is involved in ergosterol biosynthesis. Ergosterol that was quantified from treated cells showed a 5·5-fold decrease in ergosterol production. CONCLUSION Sertraline displayed promising antifungal activity against C. auris involved in candidiasis infection and the mechanism of action was predicted. SIGNIFICANCE AND IMPACT OF THIS STUDY The results of this study can encourage for the development of new antifungal agents and can be promising antifungal agent against C. auris infection.
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Affiliation(s)
- M Gowri
- Department of Physics, Periyar University, Salem, Tamil Nadu, India
| | - B Jayashree
- Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - J Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - E K Girija
- Department of Physics, Periyar University, Salem, Tamil Nadu, India
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Prabhu D, Rajamanikandan S, Saritha P, Jeyakanthan J. Evolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens. J Biomol Struct Dyn 2019; 38:4418-4431. [PMID: 31635545 DOI: 10.1080/07391102.2019.1682046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Complete functional annotations of proteins are essential to understand the role and mechanisms in pathogenesis. Aminoglycoside nucleotidyltransferases are the subclasses of aminoglycosides modifying enzymes conferring resistance to organisms. Insight into the structural and functional understanding of nucleotidyltransferase family protein provides vital information to combat pathogenesis. Phylogenetic analysis is employed to identify the evolutionary significance and common motif's present among the homologs of nucleotidyltransferase family protein. Structure, sequence based approaches and molecular docking were implemented to predict the exact function of the protein. Wide distribution of the nucleotidyltransferase family protein in gram-positive and gram-negative organisms are evidenced from phylogenetic analysis. Five common motifs were present in all the homolog's of nucleotidyltransferase family protein. Sequence-structure based functional annotations predicts that the targeted protein function as ATP-Mg dependent streptomycin adenylyltransferase. Structural comparisons and docking studies correlate well with the identified function. The complete function of nucleotidyltransferase family protein was identified as Streptomycin adenylyltransferase and it could be targeted as a potential therapeutic target to overcome antibiotic resistance.Communicated by Ramaswamy H. SarmaAbbreviationsAACaminoglycoside acetyltransferasesAMEaminoglycoside modifying enzymeANTaminoglycoside nucleotidyltransferasesAPHaminoglycoside phosphotransferasesATPadenosine triphosphateCASTpcomputer atlas and surface topography of proteinsDUFdomains of unknown functionGlidegrid-based ligand docking with energeticHMMhidden Markov modelMASTmotif alignment and search toolMEGAmolecular evolutionary genetics analysisMEMEmultiple Em for motif elicitationMSAmultiple sequence alignmentNMPnucleoside monophosphateNTPnucleoside triphosphateNTnucleotidyltransferaseOPLSoptimized potential for liquid simulationXPextra precision.
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Affiliation(s)
- Dhamodharan Prabhu
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sundaraj Rajamanikandan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru, India
| | - Poopandi Saritha
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Santhosh R, Bankoti N, Padmashri AM, Michael D, Jeyakanthan J, Sekar K. MRPC (Missing Regions in Polypeptide Chains): a knowledgebase. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719012330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Missing regions in protein crystal structures are those regions that cannot be resolved, mainly owing to poor electron density (if the three-dimensional structure was solved using X-ray crystallography). These missing regions are known to have high B factors and could represent loops with a possibility of being part of an active site of the protein molecule. Thus, they are likely to provide valuable information and play a crucial role in the design of inhibitors and drugs and in protein structure analysis. In view of this, an online database, Missing Regions in Polypeptide Chains (MRPC), has been developed which provides information about the missing regions in protein structures available in the Protein Data Bank. In addition, the new database has an option for users to obtain the above data for non-homologous protein structures (25 and 90%). A user-friendly graphical interface with various options has been incorporated, with a provision to view the three-dimensional structure of the protein along with the missing regions using JSmol. The MRPC database is updated regularly (currently once every three months) and can be accessed freely at the URL http://cluster.physics.iisc.ac.in/mrpc.
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Vanajothi R, Hemamalini V, Jeyakanthan J, Premkumar K. Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors. J Biomol Struct Dyn 2019; 38:2800-2808. [PMID: 31269869 DOI: 10.1080/07391102.2019.1640132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
AbbreviationsADMEabsorption, distribution, metabolism, and excretionMMGB/SAmolecular mechanics generalized born surface areaIFDinduced fit dockingRTKreceptor tyrosine kinaseNSCLCnon-small-cell lung cancerATPadenosine triphosphateOPLSoptimized potential for liquid stimulationRMSDroot mean square deviationHTVShigh-throughput virtual screeningSPstandard precisionXPextra precisionOPLS-AAoptimized potential for liquid stimulation-all atomMDmolecular simulationMMEmolecular mechanics energiesSGBsurface generalized bornPOPC membrane1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membranePDBProtein Data BankDDR1discoidin domain receptor 1DDR2discoidin domain receptor 2DDRsdiscoidin domain receptorsECMextracellular matrixTIP4Ptransferable intermolecular potential 4 pointNPTconstant particle number, pressure and temperatureRMSFroot mean square fluctuationCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramar Vanajothi
- Department of Biomedical Science, Bharathidasan University, Trichy, India
| | | | | | - Kumpati Premkumar
- Department of Biomedical Science, Bharathidasan University, Trichy, India
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Santhosh R, Chandrasekaran P, Michael D, Rangachari K, Bankoti N, Jeyakanthan J, Sekar K. ACMS: a database of alternate conformations found in the atoms of main and side chains of protein structures. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719006447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Proteins are usually dynamic biological macromolecules, thereby exhibiting a large number of conformational ensembles which influence the association with their neighbours and interacting partners. Most of the side-chain atoms and a few main-chain atoms of the high-resolution crystal structures deposited in the Protein Data Bank adopt alternate conformations. This kind of conformational behaviour prompted the authors to explore the relationship, if any, between the alternate conformations and the function of the protein molecule. Thus, a knowledge base of the alternate conformations of the main- and side-chain atoms of protein structures has been developed. It provides a detailed description of the alternate conformations of various residues for more than 60 000 high-resolution crystal structures. The proposed knowledge base is very user friendly and has various flexible options. The knowledge base will be updated periodically and can be accessed at http://iris.physics.iisc.ac.in/acms.
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Jayaprakash P, Biswal J, Kanagarajan S, Prabhu D, Gogoi P, Prasad Kanaujia S, Jeyakanthan J. Design of novel PhMTNA inhibitors, targeting neurological disorder through homology modeling, molecular docking, and dynamics approaches. J Recept Signal Transduct Res 2019; 39:28-38. [PMID: 31241401 DOI: 10.1080/10799893.2019.1567786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Vanishing white matter (VWM) is a hereditary human disease, mostly prevalent in childhood caused by the defects in the eukaryotic initiation factor beta subunits. It is the first disease involved in the translation initiation factor, eIF2B. There is no specific treatment for VWM which mainly affect the brain and ovaries. The gray matter remains normal in all characteristics while the white matter changes texture, coming to the pathophysiology, many initiation factors are involved in the initiation of translation of mRNAs into polypeptides. In this study, the three-dimensional structure of PhMTNA protein was modeled and the stability ascertained through Molecular dynamic simulation (MDS) for 100 ns. The active site residues are conserved with the reported BsMTNA structure which is also confirmed through sitemap prediction. Through virtual screening and induced fit docking, top five leads against PhMTNA protein was identified based on their binding mode and affinity. ADME properties and DFT (Density Functional Theory) studies of these compounds were studied. In addition to that, computational mutagenesis studies were performed to identify the hotspot residues involved in the protein-ligand interactions. Overall analysis showed that the compound NCI_941 has a highest binding energy of -46.256 kcal mol-1 in the Arg57Ala mutant. Thus, the results suggest that NCI_941 would act as a potent inhibitor against PhMTNA protein.
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Affiliation(s)
- Prajisha Jayaprakash
- a Structural Biology and Bio-Computing Lab, Department of Bioinformatics , Science Block, Alagappa University , Karaikudi , India
| | - Jayashree Biswal
- a Structural Biology and Bio-Computing Lab, Department of Bioinformatics , Science Block, Alagappa University , Karaikudi , India
| | - Sureka Kanagarajan
- a Structural Biology and Bio-Computing Lab, Department of Bioinformatics , Science Block, Alagappa University , Karaikudi , India
| | - Dhamodharan Prabhu
- a Structural Biology and Bio-Computing Lab, Department of Bioinformatics , Science Block, Alagappa University , Karaikudi , India
| | - Prerana Gogoi
- b Department of Biosciences and Bioengineering , Indian Institute of Technology , Guwahati , India
| | - Shankar Prasad Kanaujia
- b Department of Biosciences and Bioengineering , Indian Institute of Technology , Guwahati , India
| | - Jeyaraman Jeyakanthan
- a Structural Biology and Bio-Computing Lab, Department of Bioinformatics , Science Block, Alagappa University , Karaikudi , India
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Boomi P, Ganesan R, Poorani G, Gurumallesh Prabu H, Ravikumar S, Jeyakanthan J. Biological synergy of greener gold nanoparticles by using Coleus aromaticus leaf extract. Materials Science and Engineering: C 2019; 99:202-210. [DOI: 10.1016/j.msec.2019.01.105] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 12/24/2022]
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Nachiappan M, Jain V, Sharma A, Manickam Y, Jeyakanthan J. Conformational changes in glutaminyl-tRNA synthetases upon binding of the substrates and analogs using molecular docking and molecular dynamics approaches. J Biomol Struct Dyn 2019; 38:1575-1589. [PMID: 31084346 DOI: 10.1080/07391102.2019.1617787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are considered as important components in protein translation as they facilitate the attachment of specific transfer RNA (tRNA) to form aminoacyl-tRNAs. Our study focused on understanding the crystal structure of Glutaminyl-tRNA synthetase (GlnRS) from Thermus thermophilus HB8 (PDB ID:5ZDO) and mechanism of formation of enzyme-substrate complex using substrates and its analogs by applying molecular dynamics simulation (MDS) to investigate the conformational changes. Least energy structure of TtGlnRS was considered to dock the enzyme substrates such as glutamine (Gln), glutamic acid (Glu), adenosine monophosphate (AMP), adenosine triphosphate (ATP), QSI and various substrate analogs (2MA, 4SU and 5MU) onto the active site of the enzyme. We focused on comparative analysis of binding specificity between Gln and Glu; similarly, ATP and AMP. Active site organization as observed by MDS analysis showed interactive changes associated with substrate and catalytically important loops. Study found that when tRNAGln specific for GlnRS was docked into the active site of the TtGlnRS enzyme it interacts with 2' OH on the ribose acceptor end of the tRNA. Upon validation with 50 ns MDS, the maximum deviations and conformational changes of secondary structural elements were observed to be high in the loop regions of enzyme-substrate complexes. Binding affinity of ATP to TtGlnRS was further proved by isothermal titration calorimetry. AbbreviationsaaRSsaminoacyl-tRNA synthetasesAMPadenosine monophosphateATPadenosine triphosphateGlideGrid-based LIgand Docking with EnergeticGlnRSglutaminyl-tRNA synthetaseGRAVYGRand AVerage of hydropathicitYGROMACSGROingen Machine for Chemical SimulationsHADDOCKHigh Ambiguity Driven protein-protein DOCKingITCisothermal titration calorimetry2MA2-methyladenosine 5'-(dihydrogen phosphate)MDSmolecular dynamics simulation5MU5-methyluridine 5'-monophosphateNPTnumber of particles, pressure and temperatureNVTnumber of particles, volume and temperatureOPLS-AAoptimized potential for liquid simulation all atomPDBBrookhaven Protein DatabankPMEParticle-Mesh EwaldQSI5'-o-[n-(l-Glutaminyl)-sulfamoyl]adenosineRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuation4SU4-thiouracil 5'-monophosphateSPCsimple point chargetRNAtransfer ribo nucleic acidTtThermus thermophilusXPextra precisionCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mutharasappan Nachiappan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Vitul Jain
- Molecular Medicine - Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amit Sharma
- Molecular Medicine - Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Yogavel Manickam
- Molecular Medicine - Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
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Boomi P, Poorani GP, Palanisamy S, Selvam S, Ramanathan G, Ravikumar S, Barabadi H, Prabu HG, Jeyakanthan J, Saravanan M. Evaluation of Antibacterial and Anticancer Potential of Polyaniline-Bimetal Nanocomposites Synthesized from Chemical Reduction Method. J CLUST SCI 2019. [DOI: 10.1007/s10876-019-01530-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ravi GRR, Biswal J, Kanagarajan S, Jeyakanthan J. Exploration of N5-CAIR Mutase Novel Inhibitors from Pyrococcus horikoshii OT3: A Computational Study. J Comput Biol 2019; 26:457-472. [PMID: 30785305 DOI: 10.1089/cmb.2018.0248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In bacterial and archaeal purine biosynthetic pathways, sixth step involves utilization of enzyme PurE, catalyzing the translation of aminoimidazole ribonucleotide to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) with carbon dioxide. The formation of CAIR takes place through an unstable intermediate N5-CAIR, played by two enzymes-N5-CAIR synthetase (PurK) and N5-CAIR mutase (PurE) that further catalyzes the reaction of N5-CAIR to CAIR. In this study, N5-CAIR mutase (PH0320) from Pyrococcus horikoshii OT3 (PurE) was considered. The three-dimensional structure of Pyrococcus horikoshii OT3 was modeled based on the structure of PurE from Escherichia coli. The modeled structure was subjected to molecular dynamics simulation up to 100 ns, and least energy structure from the simulation was subjected to virtual screening and induced fit docking to identify the best potent leads. A total of five best antagonists were identified based on their affinity and mode of binding leading with conserved residues Ser18, Ser20, Asp21, Ser45, Ala46, His47, Arg48, Ala72, Gly73, Ala75, and His77 promotes the activity of Ph-N5-CAIR mutase. In addition to molecular dynamics, absorption, digestion, metabolism, and excretion properties, binding free energy and density functional theory calculations of compounds were carried out. Based on analyses, compound from National Cancer Institute (NCI) database, NCI_826 was adjudged as the best potent lead molecule and could be suggested as the suitable inhibitor of N5-CAIR mutase.
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Affiliation(s)
- Guru Raj Rao Ravi
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Sureka Kanagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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Sindhu T, Venkatesan T, Prabhu D, Jeyakanthan J, Gracy GR, Jalali SK, Rai A. Insecticide-resistance mechanism of Plutella xylostella (L.) associated with amino acid substitutions in acetylcholinesterase-1: A molecular docking and molecular dynamics investigation. Comput Biol Chem 2018; 77:240-250. [DOI: 10.1016/j.compbiolchem.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/01/2018] [Accepted: 09/03/2018] [Indexed: 01/22/2023]
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