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Mohamed SK, Ahsin A, Rehman HM, Mohammed HH, Mague JT, Al-Salahi R, El Bakri Y, Hussein BRM. XRD/DFT, Hirshfeld surface analysis and molecular modelling simulations for unfolding reactivity of newly synthesized vanillin derivatives: excellent optical, NLO and protein binding efficiency. J Biomol Struct Dyn 2024:1-19. [PMID: 38305762 DOI: 10.1080/07391102.2024.2308774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
New vanillin derivatives, namely, ethyl (4-formyl-2-methoxyphenoxy)acetate (2a) and 2-(4-formyl-2-methoxyphenoxy)-N-phenylacetamide (2b), respectively, were synthesized and characterized by NMR (1H and 13C), IR, mass spectra and confirmed by single-crystal X-ray analysis. Hirshfeld surface (HS) analysis was performed to probe intra- and intermolecular interactions and surface reactivity. 2D fingerprint plots (FP) were used to study the nature and percentage contribution of intermolecular interactions leading to the formation of the crystal unit. Density functional theory (DFT) simulations were used to obtain the electronic structure and reactivity of the new molecules. Natural population analysis (NPA) and frontier molecular orbital (FMO) calculations reveal significant charge transfer and a reduced HOMO-LUMO gap up to 4.34 eV for 2b. Bader's quantum theory of atoms in molecules (QTAIM) study is utilized to understand the surface topological and bonding nature of 2a and 2b. The performed molecular electrostatic potential (MESP) and density of states (DOS) study further suggest sites likely to be attractive to incoming reagents. At the same time, hyperpolarizability (βo) is used to characterize the nonlinear optical properties, and TD-DFT study shows the excitation energy and absorption behavior. In silico studies were performed, including docking, binding free energies (MMBGSA) and molecular dynamics simulations. Compounds 2a and 2b were docked with RdRp of SARS-Cov-2, and the MMBGSA for 2a and 2b were -30.70 and -28.47 kcal/mol, respectively, while MD simulation showed the stability of protein-ligand complexes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, UK
| | - Atazaz Ahsin
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Hayam H Mohammed
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Bahgat R M Hussein
- Department of Chemistry, Faculty of Science, Sohag University, Sohag, Egypt
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Al-Taifi EA, Rehman HM, Bakhite EA, Mohamed SK, Yeap GY, Lai CH, Mague JT, El Bakri Y. Synthesis, X-Ray Crystal Structure, and Identification of Potential Drug Candidate against COVID-19 Main Protease through Structure-Guided Modeling and Simulation Approach. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2165512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Elham A. Al-Taifi
- Chemistry Department, Faculty of Science, Sana’a University, Sana’a, Yemen
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Lahore, Pakistan
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, UK
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Guan-Yeow Yeap
- Liquid Crystal Research Laboratory, School of Chemical Sciences, Universiti Sains Malaysia, Minden, Malaysia
| | - Chin-Hung Lai
- Department of Medical Applied Chemistry, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Education, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
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A Combined Study on Optimization, In Silico Modeling, and Genetic Modification of Large Scale Microbial Cellulase Production. Biochem Res Int 2022; 2022:4598937. [PMID: 36589721 PMCID: PMC9797302 DOI: 10.1155/2022/4598937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Cellulase is a biocatalyst that hydrolyzes cellulosic biomass and is considered a major group of industrial enzymes for its applications. Extensive work has been done on microbial cellulase but fungi are considered a novel strain for their maximum cellulase production. Production cost and novel microbial strains are major challenges for its improvement where cheap agro wastes can be essential sources of cellulose as substrates. The researcher searches for more cellulolytic microbes from natural sources but the production level of isolated strains is comparatively low. So genetic modification or mutation can be employed for large-scale cellulase production before optimization. After genetic modification than in silico molecular modeling can be evaluated for substrate molecule's binding affinity. In this review, we focus not only on the conventional methods of cellulase production but also on modern biotechnological approaches applied to cellulase production by a sequential study on common cellulase-producing microbes, modified microbes, culture media, carbon sources, substrate pretreatment process, and the importance of optimum pH and temperature on fermentation. In this review, we also compare different cellulase activity determination methods. As a result, this review provides insights into the interrelationship between the characteristics of optimizing different culture conditions, genetic modification, and in silico enzyme modeling for the production of cellulase enzymes, which may aid in the advancement of large-scale integrated enzyme manufacturing of substrate-specific enzymes.
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Winkelman DC, Nikolau BJ. The Effects of Carbon Source and Growth Temperature on the Fatty Acid Profiles of Thermobifida fusca. Front Mol Biosci 2022; 9:896226. [PMID: 35720111 PMCID: PMC9198275 DOI: 10.3389/fmolb.2022.896226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The aerobic, thermophilic Actinobacterium, Thermobifida fusca has been proposed as an organism to be used for the efficient conversion of plant biomass to fatty acid-derived precursors of biofuels or biorenewable chemicals. Despite the potential of T. fusca to catabolize plant biomass, there is remarkably little data available concerning the natural ability of this organism to produce fatty acids. Therefore, we determined the fatty acids that T. fusca produces when it is grown on different carbon sources (i.e., glucose, cellobiose, cellulose and avicel) and at two different growth temperatures, namely at the optimal growth temperature of 50°C and at a suboptimal temperature of 37°C. These analyses establish that T. fusca produces a combination of linear and branched chain fatty acids (BCFAs), including iso-, anteiso-, and 10-methyl BCFAs that range between 14- and 18-carbons in length. Although different carbon sources and growth temperatures both quantitatively and qualitatively affect the fatty acid profiles produced by T. fusca, growth temperature is the greater modifier of these traits. Additionally, genome scanning enabled the identification of many of the fatty acid biosynthetic genes encoded by T. fusca.
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Affiliation(s)
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology and the Center of Metabolic Biology, Iowa State University, Ames, IA, United States
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Paul M, Mohapatra S, Kumar Das Mohapatra P, Thatoi H. Microbial cellulases - An update towards its surface chemistry, genetic engineering and recovery for its biotechnological potential. BIORESOURCE TECHNOLOGY 2021; 340:125710. [PMID: 34365301 DOI: 10.1016/j.biortech.2021.125710] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The inherent resistance of lignocellulosic biomass makes it impervious for industrially important enzymes such as cellulases to hydrolyze cellulose. Further, the competitive absorption behavior of lignin and hemicellulose for cellulases, due to their electron-rich surfaces augments the inappropriate utilization of these enzymes. Hence, modification of the surface charge of the cellulases to reduce its non-specific binding to lignin and enhance its affinity for cellulose is an urgent necessity. Further, maintaining the stability of cellulases by the preservation of their secondary structures using immobilization techniques will also play an integral role in its industrial production. In silico approaches for increasing the catalytic activity of cellulase enzymes is also significant along with a range of substrate specificity. In addition, enhanced productivity of cellulases by tailoring the related genes through the process of genetic engineering and higher cellulase recovery after saccharification seems to be promising areas for efficient and large-scale enzyme production concepts.
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Affiliation(s)
- Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India
| | - Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Bhubaneswar 751003, Odisha, India
| | - Pradeep Kumar Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India; PAKB Environment Conservation Centre, Raiganj University, Raiganj - 733134, Uttar Dinajpur, West Bengal, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Takatpur, Baripada 757003, Odisha, India.
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Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications. Int J Biol Macromol 2021; 188:226-244. [PMID: 34371052 DOI: 10.1016/j.ijbiomac.2021.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.
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