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Wadood A, Shareef A, Ur Rehman A, Muhammad S, Khurshid B, Khan RS, Shams S, Afridi SG. In Silico Drug Designing for ala438 Deleted Ribosomal Protein S1 (RpsA) on the Basis of the Active Compound Zrl15. ACS OMEGA 2022; 7:397-408. [PMID: 35036709 PMCID: PMC8756442 DOI: 10.1021/acsomega.1c04764] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/21/2021] [Indexed: 05/10/2023]
Abstract
Pyrazinoic acid-resistant tuberculosis is a severe chronic disorder. First-line drugs specifically target the ribosomal protein subunit-1 (RpsA) and stop trans-translation in the wild-type bacterium, causing bacterial cell death. In mutant bacterial strain, the deletion of ala438 does not let the pyrazinoic acid to bind to the active site of RpsA and ensures that the bacterium survives. Hence, such tuberculosis cases require an immediate and successful regime. The current study was designed to identify inhibitors that could bind to the mutant state of the RpsA protein. Initially, a pharmacophore model was generated based on the recently published most potent inhibitor for the mutant state of RpsA, i.e., zrl15. The validated pharmacophore model was further used for virtual screening of two chemical libraries, i.e., ZINC and ChemBridge. After applying the Lipinski rule of five (Ro5), a total of 260 and 749 hits from the ChemBridge and ZINC libraries, respectively, were identified using pharmacophore mapping. These hits were then docked into the active site of the mutant state of the RpsA protein, and later, the top 150 compounds from each library were chosen based on the docking score. A total of 21 compounds were shortlisted from each library based on the best protein-ligand interactions. Finally, a total of 05 compounds were subjected to molecular dynamics study to examine the dynamic behavior of each compound in the active site of the mutant state of the RpsA protein. The results revealed that all compounds had good chemical properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET), and there was no Pan Assay Interference (PAINS) or deviation from Ro5, indicating that these compounds could be useful antagonists for the mutant state of the RpsA protein.
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Affiliation(s)
- Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Azam Shareef
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, Irvine, California 92697, United States
| | - Shabbir Muhammad
- Department
of Physics, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Beenish Khurshid
- Woman
College, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Raham Sher Khan
- Department
of Biotechnology, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Sulaiman Shams
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Sahib Gul Afridi
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
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Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
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Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Zhi Y, Dai Y, Yang J, Tan S, Lin D, Lin K. Lead compounds and key residues of ribosomal protein S1 in drug-resistant Mycobacterium tuberculosis. Bioorg Chem 2018; 82:58-67. [PMID: 30268974 DOI: 10.1016/j.bioorg.2018.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal protein S1 (RpsA) has been identified as a novel target of pyrazinoic acid (POA), which is the active form of pyrazinamide (PZA), in vivo. RpsA plays a crucial role in trans-translation, which is widespread in microbes. In our investigation, we first described the discovery of promising RpsA antagonists for drug-resistant mycobacterium (MtRpsAd438A) and M. smegmatis, as well as wild-type M. tuberculosis. These antagonists were discovered via structure/ligand-based virtual screening approaches. A total of 21 targeted compounds were selected by virtual screening, combined scores, affinity, similarities and rules for potential as drugs. Next, the affinities of these compounds for three targeted proteins were tested in vitro by applying various technologies, including fluorescence quenching titration (FQT), saturation transfer difference (STD), and chemical shift perturbation (CSP) assays. The results showed that seven compounds had a high affinity for the targeted proteins. Our discovery set the stage for discovering new chemical entities (NCEs) for PZA-resistant tuberculosis and providing key residues for rational drug design to target RpsA.
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Affiliation(s)
- Yunbao Zhi
- China Pharmaceutical University, Nanjing 210009, China; Shandong New Time Pharmaceutical Company, Lunan Pharmaceutical Group, Linyi 273400, China
| | - Yazhuang Dai
- China Pharmaceutical University, Nanjing 210009, China; Hangzhou Ipharmacare Information Technology Co., Ltd, Hangzhou 310000, China
| | - Juanjuan Yang
- College of Biological Science and Biotechnology, Fuzhou University, Fuzhou 350000, China
| | - Shuhua Tan
- China Pharmaceutical University, Nanjing 210009, China
| | | | - Kejiang Lin
- China Pharmaceutical University, Nanjing 210009, China.
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Shang F, Chen J, Wang L, Jin L, Zou L, Bu T, Dong Y, Ha NC, Nam KH, Quan C, Xu Y. Crystal structure of the nicotinamidase/pyrazinamidase PncA from Bacillus subtilis. Biochem Biophys Res Commun 2018; 503:2906-2911. [PMID: 30107912 DOI: 10.1016/j.bbrc.2018.08.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 11/30/2022]
Abstract
The nicotinamidase/pyrazinamidase PncA is a member of a large family of hydrolase enzymes that catalyze the deamination of nicotinamide to nicotinic acid. PncA also functions as a pyrazinamidase in a wide variety of eubacteria and is an essential coenzyme in many cellular redox reactions in living systems. We report the crystal structure of substrate-free PncA from Bacillus subtilis (BsPncA) at 2.0 Å resolution to improve our understanding of the PncA family. The structure of BsPncA consists of an α/β domain and a subdomain. The subdomain of BsPncA has a different conformation than that of PncA enzymes from other organisms. The B-factor analysis revealed a rigid structure of the α/β domain, while the subdomain is highly flexible. Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. Our results provide useful information that will further enhance our understanding of the molecular functions of PncA family members.
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Affiliation(s)
- Fei Shang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Jinli Chen
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Lulu Wang
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China; School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China
| | - Liming Jin
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China
| | - Linhai Zou
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China
| | - Tingting Bu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China
| | - Yuesheng Dong
- School of Life Science and Biotechnology, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024, Liaoning, China
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Ki Hyun Nam
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.
| | - Chunshan Quan
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.
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Pazhang M, Mardi N, Mehrnejad F, Chaparzadeh N. The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase: Methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds. Int J Biol Macromol 2017; 108:1339-1347. [PMID: 29129628 DOI: 10.1016/j.ijbiomac.2017.11.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/08/2017] [Indexed: 11/24/2022]
Abstract
Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Narges Mardi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Nader Chaparzadeh
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
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Khadem-Maaref M, Mehrnejad F, Phirouznia A. Effects of metal-ion replacement on pyrazinamidase activity: A quantum mechanical study. J Mol Graph Model 2017; 73:24-29. [PMID: 28214629 DOI: 10.1016/j.jmgm.2017.01.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 11/26/2022]
Abstract
Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co2+, Mn2+, and Zn2+, are able to reactivate metal-depleted PZase, while others including Cu2+, Fe2+, and Mg2+, cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations. We calculated the metal-ligand (residue) binding energy and the atomic partial charges in the presence of various ions. The results indicated that the tendency of alkaline earth metals to bind to PZase MCS is very low and not suitable for enzyme structural and catalytic function. In contrast, Co2+ and Ni2+ ions have very high binding affinity and are favorable to the structural and functional properties of the enzyme. Furthermore, we observed that the rate at which Ni2+, Co2+ and Fe2+ ions in PZase MCS polarize the OH bond of coordinated water molecules is much higher than the polarization rate created by other ions. This finding suggests that the coordination of Ni2+, Co2+, or Fe2+ to PZase facilitates the deprotonation of coordinated water molecules to generate a nucleophile that catalyzes the enzymatic reaction.
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Affiliation(s)
- Mahmoud Khadem-Maaref
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
| | - Arash Phirouznia
- Department of Physics, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
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