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Li J, Khalid WA, Imtiaz H, Huang L, Ali Y, Yousaf R, Gul F, Mahmood A, Shah AA, Deng H, Khattak S. The deleterious variants of N-acetylgalactosamine-6-sulfatase (GalN6S) enzyme trigger Morquio a syndrome by disrupting protein foldings. J Biomol Struct Dyn 2024; 42:3700-3711. [PMID: 37222604 DOI: 10.1080/07391102.2023.2214234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Lysosomal enzymes degrade cellular macromolecules, while their inactivation causes human hereditary metabolic disorders. Mucopolysaccharidosis IVA (MPS IVA; Moquio A syndrome) is one of the lysosomal storage disorders caused by a defective Galactosamine-6-sulfatase (GalN6S) enzyme. In several populations, disease incidence is elevated due to missense mutations brought on by non-synonymous allelic variation in the GalN6S enzyme. Here, we studied the effect of non-synonymous single nucleotide polymorphism (nsSNPs) on the structural dynamics of the GalN6S enzyme and its binding with N-acetylgalactosamine (GalNAc) using all-atom molecular dynamics simulation and an essential dynamics approach. Consequently, in this study, we have identified three functionally disruptive mutations in domain-I and domain-II, that is, S80L, R90W, and S162F, which presumably contribute to post-translational modifications. The study delineated that both domains work cooperatively, and alteration in domain II (S80L, R90W) leads to conformational changes in the catalytic site in domain-I, while mutation S162F mainly provokes higher residual flexibility of domain II. These results show that these mutations impair the hydrophobic core, implying that Morquio A syndrome is caused by misfolding of the GalN6S enzyme. The results also show the instability of the GalN6S-GalNAc complex upon substitution. Overall, the structural dynamics resulting from point mutations give the molecular rationale for Moquio A syndrome and, more importantly, the Mucopolysaccharidoses (MPS) family of diseases, re-establishing MPS IVA as a protein-folding disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiuyi Li
- Department of Anesthesiology, The First People's Hospital of Chenzhou, Chenzhou, Hunan Province, PR China
| | - Waqas Ahmad Khalid
- Government Rana Abdul Raheem Memorial Hospital Sodiwal Lahore, Sodiwal, Punjab, Pakistan
| | - Hina Imtiaz
- Tehsil Headquarters Hospital Bhera, Sarghoda, Bhera, Punjab, Pakistan
| | - Lingkun Huang
- Department of Anesthesiology, The First People's Hospital of Chenzhou, Chenzhou, Hunan Province, PR China
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rimsha Yousaf
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fouzia Gul
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, PR China
| | - Abid Ali Shah
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, PR China
| | - Huiyin Deng
- Department of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, PR China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, China
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Ali Y, Khan AA, Alanazi AM, Abdikakharovich SA, Shah JA, Ren ZG, Khattak S. Identification of the myxobacterial secondary metabolites Aurachin A and Soraphinol A as promising inhibitors of thymidylate kinase of the Monkeypox virus. Mol Divers 2024:10.1007/s11030-023-10764-x. [PMID: 38183513 DOI: 10.1007/s11030-023-10764-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/08/2024]
Abstract
Thymidylate kinase (TMPK) of monkeypox virus (MPXV) has emerged as a promising target for potential therapeutics due to its significant role in pyrimidine metabolism. While smallpox drugs are advised for treating monkeypox, the European Medicine Agency has sanctioned Tecovirimat due to its potent nanomolar activity. Nonetheless, there is a need for monkeypox-specific therapeutic options. In this work, we employed docking-based virtual screening and molecular dynamics (MD) simulations to identify myxobacterial secondary metabolites as promising anti-viral natural compounds capable of inhibiting thymidylate kinase. The computational pharmacokinetics and manual curation of top-scoring compounds identified six lead compounds that were compared in terms of protein-ligand contacts and protein-essential dynamics. The study shows that among the six candidates, Aurachin A and the Soraphinol analogues such as Soraphinol A and Soraphinol C remain very stable compared to other compounds, enabling the active site integrity via a stable dynamics pattern. We also show that other compounds such as Phenoxan, Phenylnannolone C, and 8E-Aurafuron B remain unstable and have a negative impact on the active site integrity and may not be suitable binders for TMPK protein. Analyzing the Aurachin A and Soraphinol A binding, the established hydrogen bonds with Arg93 and the conserved hydrophobic interaction with Tyr101 are consistent with previous experimental interactions. Additionally, a deeper insight into the indole and the aromatic ring interaction through π-π stacking and π-cation interactions, as well as the background of Aurachin A and Soraphinol A as a bioactive compound, has significant implications not only for its potential as a promising drug but also for directing future drug discovery efforts targeting the TMPK protein.
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Affiliation(s)
- Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, 845 38, Bratislava, Slovakia
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | | | - Junaid Ali Shah
- Ferghana Medical Institute of Public Health, 104100, Ferghana, Uzbekistan
| | - Zhi-Guang Ren
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
| | - Saadullah Khattak
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
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Shah BM, Modi P. Breaking Barriers: Current Advances and Future Directions in Mpox Therapy. Curr Drug Targets 2024; 25:62-76. [PMID: 38151842 DOI: 10.2174/0113894501281263231218070841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Mpox, a newly discovered zoonotic infection, can be transmitted from animal to human and between humans. Serological and genomic studies are used to identify the virus. OBJECTIVE Currently, there are no proven effective treatments for Mpox. Also, the safety and efficacy of intravenous vaccinia immune globulin, oral Tecovirimat (an inhibitor of intracellular viral release), and oral Brincidofovir (a DNA polymerase inhibitor) against the Mpox virus are uncertain, highlighting the need for more effective and safe treatments. As a result, drug repurposing has emerged as a promising strategy to identify previously licensed drugs that can be repurposed to treat Mpox. RESULTS Various approaches have been employed to identify previously approved drugs that can target specific Mpox virus proteins, including thymidylate kinase, D9 decapping enzyme, E8 protein, Topoisomerase1, p37, envelope proteins (D13, A26, and H3), F13 protein, virus's main cysteine proteases, and DNA polymerase. CONCLUSION In this summary, we provide an overview of potential drugs that could be used to treat Mpox and discuss the underlying biological processes of their actions.
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Affiliation(s)
- Bhumi M Shah
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
| | - Palmi Modi
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
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Dwivedi S, Singh V, Agrawal R, Misra R, Sadashiv, Fatima G, Abidi A, Misra S. Human Monkeypox Virus and Host Immunity: New Challenges in Diagnostics and Treatment Strategies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:219-237. [PMID: 38801581 DOI: 10.1007/978-3-031-57165-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The monkeypox virus (MPXV), responsible for human disease, has historically been limited to the African countries, with only a few isolated instances reported elsewhere in the world. Nevertheless, in recent years, there have been occurrences of monkeypox in regions where the disease is typically absent, which has garnered global interest. Within a period of less than four months, the incidence of MPXV infections has surged to over 48,000 cases, resulting in a total of 13 deaths. This chapter has addressed the genetics of the pox virus, specifically the human monkeypox virus, and its interaction with the immune systems of host organisms. The present chapter is skillfully constructed, encompassing diagnostic methodologies that span from traditional to developing molecular techniques. Furthermore, the chapter provides a succinct analysis of the therapeutic methods employed, potential future developments, and the various emerging difficulties encountered in illness management.
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Affiliation(s)
- Shailendra Dwivedi
- Department of Biochemistry, All India Institute of Medical Sciences, Gorakhpur, 273008, India.
| | - Vijay Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Gorakhpur, 273008, India
| | - Ruchika Agrawal
- Department of ENT, All India Institute of Medical Sciences, Gorakhpur, 273008, India
| | - Radhieka Misra
- Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Sadashiv
- Department of Biochemistry, All India Institute of Medical Sciences, Raebareli, 229405, India
| | - Ghizal Fatima
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Afroz Abidi
- Department of Pharmacology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Sanjeev Misra
- Atal Bihari Bajpayee Medical University, Lucknow, 225001, India
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Khattak S, Ali Y, Ren Z, Ji XY. Monkeypox Entry and Emergence Preparation in Pakistan. Life (Basel) 2023; 13:2308. [PMID: 38137909 PMCID: PMC10744954 DOI: 10.3390/life13122308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Monkeypox (Mpox) is a virus that first emerged in Africa in 1970 [...].
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Affiliation(s)
- Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad 45320, Pakistan;
| | - Zhiguang Ren
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
| | - Xin-Ying Ji
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China;
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Farooq QUA, Aiman S, Ali Y, Shaukat Z, Ali Y, Khan A, Samad A, Wadood A, Li C. A comprehensive protein interaction map and druggability investigation prioritized dengue virus NS1 protein as promising therapeutic candidate. PLoS One 2023; 18:e0287905. [PMID: 37498862 PMCID: PMC10374080 DOI: 10.1371/journal.pone.0287905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023] Open
Abstract
Dengue Virus (DENV) is a serious threat to human life worldwide and is one of the most dangerous vector-borne diseases, causing thousands of deaths annually. We constructed a comprehensive PPI map of DENV with its host Homo sapiens and performed various bioinformatics analyses. We found 1195 interactions between 858 human and 10 DENV proteins. Pathway enrichment analysis was performed on the two sets of gene products, and the top 5 human proteins with the maximum number of interactions with dengue viral proteins revealed noticeable results. The non-structural protein NS1 in DENV had the maximum number of interactions with the host protein, followed by NS5 and NS3. Among the human proteins, HBA1 and UBE2I were associated with 7 viral proteins, and 3 human proteins (CSNK2A1, RRP12, and HSP90AB1) were found to interact with 6 viral proteins. Pharmacophore-based virtual screening of millions of compounds in the public databases was performed to identify potential DENV-NS1 inhibitors. The lead compounds were selected based on RMSD values, docking scores, and strong binding affinities. The top ten hit compounds were subjected to ADME profiling which identified compounds C2 (MolPort-044-180-163) and C6 (MolPort-001-742-737) as lead inhibitors against DENV-NS1. Molecular dynamics trajectory analysis and intermolecular interactions between NS1 and the ligands displayed the molecular stability of the complexes in the cellular environment. The in-silico approaches used in this study could pave the way for the development of potential specie-specific drugs and help in eliminating deadly viral infections. Therefore, experimental and clinical assays are required to validate the results of this study.
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Affiliation(s)
- Qurrat Ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zeeshan Shaukat
- Faculty of Information Technology, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdus Samad
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
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Khan HA, Asif MU, Ijaz MK, Alharbi M, Ali Y, Ahmad F, Azhar R, Ahmad S, Irfan M, Javed M, Naseer N, Aziz A. In Silico Characterization and Analysis of Clinically Significant Variants of Lipase-H (LIPH Gene) Protein Associated with Hypotrichosis. Pharmaceuticals (Basel) 2023; 16:803. [PMID: 37375751 DOI: 10.3390/ph16060803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Hypotrichosis is an uncommon type of alopecia (hair loss) characterized by coarse scalp hair caused by the reduced or fully terminated activity of the Lipase-H (LIPH) enzyme. LIPH gene mutations contribute to the development of irregular or non-functional proteins. Because several cellular processes, including cell maturation and proliferation, are inhibited when this enzyme is inactive, the hair follicles become structurally unreliable, undeveloped, and immature. This results in brittle hair, as well as altered hair shaft development and structure. Because of these nsSNPs, the protein's structure and/or function may be altered. Given the difficulty in discovering functional SNPs in genes associated with disease, it is possible to assess potential functional SNPs before conducting broader population investigations. As a result, in our in silico analysis, we separated potentially hazardous nsSNPs of the LIPH gene from benign representatives using a variety of sequencing and architecture-based bioinformatics approaches. Using seven prediction algorithms, 9 out of a total of 215 nsSNPs were shown to be the most likely to cause harm. In order to distinguish between potentially harmful and benign nsSNPs of the LIPH gene, in our in silico investigation, we employed a range of sequence- and architecture-based bioinformatics techniques. Three nsSNPs (W108R, C246S, and H248N) were chosen as potentially harmful. The present findings will likely be helpful in future large population-based studies, as well as in drug discovery, particularly in the creation of personalized medicine, since this study provides an initial thorough investigation of the functional nsSNPs of LIPH.
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Affiliation(s)
- Hamza Ali Khan
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak 27200, Pakistan
| | | | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Faisal Ahmad
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ramsha Azhar
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32611, USA
| | - Maryana Javed
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Noorulain Naseer
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Abdul Aziz
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak 27200, Pakistan
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Ajmal A, Mahmood A, Hayat C, Hakami MA, Alotaibi BS, Umair M, Abdalla AN, Li P, He P, Wadood A, Hu J. Computer-assisted drug repurposing for thymidylate kinase drug target in monkeypox virus. Front Cell Infect Microbiol 2023; 13:1159389. [PMID: 37313340 PMCID: PMC10258308 DOI: 10.3389/fcimb.2023.1159389] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
Introduction Monkeypox is a zoonotic disease caused by brick-shaped enveloped monkeypox (Mpox) virus that belongs to the family of ancient viruses known as Poxviridae. Subsequently, the viruses have been reported in various countries. The virus is transmitted by respiratory droplets, skin lesions, and infected body fluids. The infected patients experience fluid-filled blisters, maculopapular rash, myalgia, and fever. Due to the lack of effective drugs or vaccines, there is a need to identify the most potent and effective drugs to reduce the spread of monkeypox. The current study aimed to use computational methods to quickly identify potentially effective drugs against the Mpox virus. Methods In our study, the Mpox protein thymidylate kinase (A48R) was targeted because it is a unique drug target. We screened a library of 9000 FDA-approved compounds of the DrugBank database by using various in silico approaches, such as molecular docking and molecular dynamic (MD) simulation. Results Based on docking score and interaction analysis, compounds DB12380, DB13276, DB13276, DB11740, DB14675, DB11978, DB08526, DB06573, DB15796, DB08223, DB11736, DB16250, and DB16335 were predicted as the most potent. To examine the dynamic behavior and stability of the docked complexes, three compounds-DB16335, DB15796, and DB16250 -along with the Apo state were simulated for 300ns. The results revealed that compound DB16335 revealed the best docking score (-9.57 kcal/mol) against the Mpox protein thymidylate kinase. Discussion Additionally, during the 300 ns MD simulation period, thymidylate kinase DB16335 showed great stability. Further, in vitro and in vivo study is recommended for the final predicted compounds.
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Affiliation(s)
- Amar Ajmal
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chandni Hayat
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Bader S. Alotaibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Muhammad Umair
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ping Li
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Pei He
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Abdul Wadood
- Department of Biochemistry, Computational Medicinal Chemistry Laboratory, Abdul Wali Khan University, Mardan, Pakistan
| | - Junjian Hu
- Department of Central Laboratory, SSL Central Hospital of Dongguan City, Affiliated Dongguan Shilong People’s Hospital of Southern Medical University, Dongguan, China
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Al Mashud MA, Kumer A, Mukerjee N, Chandro A, Maitra S, Chakma U, Dey A, Akash S, Alexiou A, Khan AA, Alanazi AM, Ghosh A, Chen KT, Sharma R. Mechanistic inhibition of Monkeypox and Marburg virus infection by O-rhamnosides and Kaempferol-o-rhamnosides derivatives: a new-fangled computational approach. Front Cell Infect Microbiol 2023; 13:1188763. [PMID: 37293201 PMCID: PMC10245557 DOI: 10.3389/fcimb.2023.1188763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/26/2023] [Indexed: 06/10/2023] Open
Abstract
The increasing incidence of Monkeypox virus (Mpox) and Marburg virus (MARV) infections worldwide presents a significant challenge to global health, as limited treatment options are currently available. This study investigates the potential of several O-rhamnosides and Kaempferol-O-rhamnosides as Mpox and MARV inhibitors using molecular modeling methods, including ADMET, molecular docking, and molecular dynamics/MD simulation. The effectiveness of these compounds against the viruses was assessed using the Prediction of Activity Spectra for Substances (PASS) prediction. The study's primary focus is molecular docking prediction, which demonstrated that ligands (L07, L08, and L09) bind to Mpox (PDB ID: 4QWO) and MARV (PDB ID: 4OR8) with binding affinities ranging from -8.00 kcal/mol to -9.5 kcal/mol. HOMO-LUMO based quantum calculations were employed to determine the HOMO-LUMO gap of frontier molecular orbitals (FMOs) and to estimate chemical potential, electronegativity, hardness, and softness. Drug similarity and ADMET prediction assessments of pharmacokinetic properties revealed that the compounds were likely non-carcinogenic, non-hepatotoxic, and rapidly soluble. Molecular dynamic (MD) modeling was used to identify the most favorable docked complexes involving bioactive chemicals. MD simulations indicate that varying types of kaempferol-O-rhamnoside are necessary for successful docking validation and maintaining the stability of the docked complex. These findings could facilitate the discovery of novel therapeutic agents for treating illnesses caused by the Mpox and MARV viruses.
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Affiliation(s)
- Md. Abdullah Al Mashud
- Biophysics and Biomedicine Research Lab, Department of Electrical & Electronic Engineering, Islamic University, Kushtia, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Habersham, NSW, Australia
| | - Akhel Chandro
- Department of Poultry Science, Faculty of Animal Science & Veterinary Medicine, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Swastika Maitra
- Department of Microbiology, Adamas University, West Bengal, Kolkata, India
| | - Unesco Chakma
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
- School of Electronic Science and Engineering, Southeast University, Nanjing, China
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Sukrabad, Dhaka, Bangladesh
| | - Athanasiosis Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Habersham, NSW, Australia
- Department of Neuroscience, AFNP Med, Wien, Austria
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Assam, India
| | - Kow-Tong Chen
- Department of Occupational Medicine, Tainan Municipal Hospital (managed by Show Chwan Medical Care Corporation), Tainan, Taiwan
- Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Shoaib M, Shehzadi I, Asif MU, Shen Y, Ni J. Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii. Front Mol Biosci 2023; 10:1183073. [PMID: 37152898 PMCID: PMC10160657 DOI: 10.3389/fmolb.2023.1183073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
Multidrug-resistant Acinetobacter baumannii infections have become a major public health concern globally. Inhibition of its essential MurF protein has been proposed as a potential target for broad-spectrum drugs. This study aimed to evaluate the potential of a novel ecological niche of 374 fungus-growing termite associated Natural Products (NPs). The molecular docking and computational pharmacokinetics screened four compounds, i.e., Termstrin B, Fridamycin A, Maduralactomycin A, and Natalenamide C, as potential compounds that have higher binding affinities and favourable protein-ligand interactions. The compound Maduralactomycin A induced more stability based on its lowest average RMSD value (2.31 Å) and low standard deviation (0.35) supported by the consistent flexibility and β-factor during the protein's time-dependent motion. While hydrogen bond analysis indicated that Termstrin B has formed the strongest intra-protein interaction, solvent accessibility was in good agreement with Maduralactomycin A compactness. Maduralactomycin A has the strongest binding energy among all the compounds (-348.48 kcal/mol) followed by Termstrin B (-321.19 kcal/mol). Since these findings suggest Maduralactomycin A and Termstrin B as promising candidates for inhibition of MurF protein, the favourable binding energies of Maduralactomycin A make it a more important compound to warrant further investigation. However, experimental validation using animal models and clinical trials is recommended before reaching any final conclusions.
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Affiliation(s)
- Muhammad Shoaib
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
| | | | | | - Yulong Shen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
| | - Jinfeng Ni
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, Shandong, China
- *Correspondence: Yulong Shen, ; Jinfeng Ni,
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