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Article: Editorial: Novel drug-designing approaches to combat antimicrobial resistance.

Muteeb, Ghazala / Rehman, Md Tabish / Pani, Bibhusita / Khan, Rizwan Hasan

2024 Volume 10, Page(s) 1342702

Language	English
Publishing date	2024-01-11
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1342702
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Article: Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review.

Muteeb, Ghazala / Rehman, Md Tabish / Shahwan, Moayad / Aatif, Mohammad

Pharmaceuticals (Basel, Switzerland)

2023 Volume 16, Issue 11

Abstract: Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the ... ...

Abstract	Antibiotics have revolutionized medicine, saving countless lives since their discovery in the early 20th century. However, the origin of antibiotics is now overshadowed by the alarming rise in antibiotic resistance. This global crisis stems from the relentless adaptability of microorganisms, driven by misuse and overuse of antibiotics. This article explores the origin of antibiotics and the subsequent emergence of antibiotic resistance. It delves into the mechanisms employed by bacteria to develop resistance, highlighting the dire consequences of drug resistance, including compromised patient care, increased mortality rates, and escalating healthcare costs. The article elucidates the latest strategies against drug-resistant microorganisms, encompassing innovative approaches such as phage therapy, CRISPR-Cas9 technology, and the exploration of natural compounds. Moreover, it examines the profound impact of antibiotic resistance on drug development, rendering the pursuit of new antibiotics economically challenging. The limitations and challenges in developing novel antibiotics are discussed, along with hurdles in the regulatory process that hinder progress in this critical field. Proposals for modifying the regulatory process to facilitate antibiotic development are presented. The withdrawal of major pharmaceutical firms from antibiotic research is examined, along with potential strategies to re-engage their interest. The article also outlines initiatives to overcome economic challenges and incentivize antibiotic development, emphasizing international collaborations and partnerships. Finally, the article sheds light on government-led initiatives against antibiotic resistance, with a specific focus on the Middle East. It discusses the proactive measures taken by governments in the region, such as Saudi Arabia and the United Arab Emirates, to combat this global threat. In the face of antibiotic resistance, a multifaceted approach is imperative. This article provides valuable insights into the complex landscape of antibiotic development, regulatory challenges, and collaborative efforts required to ensure a future where antibiotics remain effective tools in safeguarding public health.
Language	English
Publishing date	2023-11-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16111615
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Article ; Online: Probing the interaction mechanisms between sunset yellow dye and trypsin protein leading to amorphous aggregation under low pH conditions.

Al-Shabib, Nasser Abdulatif / Khan, Javed Masood / Malik, Ajamaluddin / Alamri, Abdulaziz / Rehman, Md Tabish / AlAjmi, Mohamed F / Husain, Fohad Mabood

International journal of biological macromolecules

2024 Volume 265, Issue Pt 1, Page(s) 130442

Abstract: Protein aggregation poses a significant concern in the field of food sciences, and various factors, such as synthetic food dyes, can contribute to protein aggregation. One such dye, Sunset Yellow (SY), is commonly employed in the food industry. Trypsin ... ...

Abstract	Protein aggregation poses a significant concern in the field of food sciences, and various factors, such as synthetic food dyes, can contribute to protein aggregation. One such dye, Sunset Yellow (SY), is commonly employed in the food industry. Trypsin was used as a model protein to assess the impact of SY. We employed several biophysical techniques to examine the binding and aggregation mechanisms between SY and trypsin at different pHs. Results from intrinsic fluorescence measurements indicate a stronger interaction between SY and trypsin at pH 2.0 compared to pH 6.0. Turbidity data reveal trypsin aggregation in the presence of 0.05-3.0 mM SY at pH 2.0, while no aggregation was observed at pH 6.0. Kinetic data demonstrate a rapid, lag-phase-free SY-induced aggregation of trypsin. Circular dichroism analysis reveals that trypsin adopts a secondary structure in the presence of SY at pH 6.0, whereas at pH 2.0, the secondary structure was nearly lost with increasing SY concentrations. Furthermore, turbidity and kinetics data suggest that trypsin aggregation depends on trypsin concentrations and pH. Our study highlights potential health risks associated with the consumption of SY, providing insights into its impact on human health and emphasizing the necessity for further research in this field.
MeSH term(s)	Humans ; Coloring Agents/chemistry ; Trypsin ; Protein Aggregates ; Azo Compounds/chemistry
Chemical Substances	Coloring Agents ; 6-hydroxy-5-((p- sulfophenyl)azo)-2-naphthalenesulfonic acid disodium salt (H77VEI93A8) ; Trypsin (EC 3.4.21.4) ; Protein Aggregates ; Azo Compounds
Language	English
Publishing date	2024-02-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.130442
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Article: An Electroanalytical Enzymeless α-Fe

Ahmad, Rafiq / Abdullah / Rehman, Md Tabish / AlAjmi, Mohamed F / Alam, Shamshad / Bhat, Kiesar Sideeq / Mishra, Prabhash / Lee, Byeong-Il

Nanomaterials (Basel, Switzerland)

2024 Volume 14, Issue 8

Abstract: Nitrite monitoring serves as a fundamental practice for protecting public health, preserving environmental quality, ensuring food safety, maintaining industrial safety standards, and optimizing agricultural practices. Although many nitrite sensing ... ...

Abstract	Nitrite monitoring serves as a fundamental practice for protecting public health, preserving environmental quality, ensuring food safety, maintaining industrial safety standards, and optimizing agricultural practices. Although many nitrite sensing methods have been recently developed, the quantification of nitrite remains challenging due to sensitivity and selectivity limitations. In this context, we present the fabrication of enzymeless iron oxide nanoparticle-modified zinc oxide nanorod (α-Fe
Language	English
Publishing date	2024-04-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano14080706
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Article ; Online: Celecoxib, Glipizide, Lapatinib, and Sitagliptin as potential suspects of aggravating SARS-CoV-2 (COVID-19) infection: a computational approach.

AlAjmi, Mohamed F / Rehman, Md Tabish / Hussain, Afzal

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 24, Page(s) 13747–13758

Abstract: COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α ... ...

Abstract	COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α converting enzyme), which is responsible for the shedding of membrane-bound ACE2 (angiotensin-converting enzyme2) receptors into soluble ACE2. The inhibition of TACE would lead to an increased population of membrane-bound ACE2, which would facilitate ACE2-Spike protein interaction and viral entry. A total of 50 drugs prescribed in treating various chronic diseases in Saudi Arabia were screened by performing molecular docking using AutoDock4.2. Based on docking energy (≤ -9.00 kcal mol
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Celecoxib/pharmacology ; Glipizide ; Lapatinib ; Sitagliptin Phosphate ; Angiotensin-Converting Enzyme 2 ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding
Chemical Substances	Celecoxib (JCX84Q7J1L) ; Glipizide (X7WDT95N5C) ; Lapatinib (0VUA21238F) ; Sitagliptin Phosphate (TS63EW8X6F) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2021-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1994013
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Article ; Online: Study of Amiloride Binding to Human Serum Albumin: Insights from Thermodynamic, Spectroscopic, and Molecular Docking Investigations.

Rahman, Safikur / Iram, Sana / Rehman, Md Tabish / Hussain, Afzal / Jan, Arif Tasleem / Kim, Jihoe

Molecules (Basel, Switzerland)

2023 Volume 28, Issue 23

Abstract: This study was undertaken to investigate the interaction between the sodium channel blocker amiloride (AML) and human serum albumin (HSA). A combination of multi-spectroscopic techniques and computational methods were employed to identify the AML binding ...

Abstract	This study was undertaken to investigate the interaction between the sodium channel blocker amiloride (AML) and human serum albumin (HSA). A combination of multi-spectroscopic techniques and computational methods were employed to identify the AML binding site on HSA and the forces responsible for the formation of the HSA-AML complex. Our findings revealed that AML specifically binds to Sudlow's site II, located in subdomain IIIA of HSA, and that the complex formed is stabilized using van der Waals hydrogen-bonding and hydrophobic interactions. FRET analysis showed that the distance between AML and Trp214 was optimal for efficient quenching. UV-Vis spectroscopy and circular dichroism indicated minor changes in the structure of HSA after AML binding, and molecular dynamics simulations (MDS) conducted over 100 ns provided additional evidence of stable HSA-AML-complex formation. This study enhances understanding of the interaction between AML and HSA and the mechanism responsible.
MeSH term(s)	Humans ; Serum Albumin, Human/chemistry ; Molecular Docking Simulation ; Amiloride/pharmacology ; Protein Binding ; Binding Sites ; Circular Dichroism ; Thermodynamics ; Leukemia, Myeloid, Acute ; Spectrometry, Fluorescence
Chemical Substances	Serum Albumin, Human (ZIF514RVZR) ; Amiloride (7DZO8EB0Z3)
Language	English
Publishing date	2023-11-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules28237688
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Article ; Online: Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Molecular Docking and Simulation Approach to Combat COVID-19.

Rehman, Md Tabish / AlAjmi, Mohamed F / Hussain, Afzal

Current pharmaceutical design

2020 Volume 27, Issue 33, Page(s) 3577–3589

Abstract: Background: The emergence and dissemination of SARS-CoV-2 has caused high mortality and enormous economic loss. Rapid development of new drug molecules is the need of hour to fight COVID-19. However, the conventional approaches of drug development are ... ...

Abstract	Background: The emergence and dissemination of SARS-CoV-2 has caused high mortality and enormous economic loss. Rapid development of new drug molecules is the need of hour to fight COVID-19. However, the conventional approaches of drug development are time consuming and expensive. Here, we have adopted a computational approach to identify lead molecules from nature. Ligands from natural compounds library available at Selleck Inc (L1400) have been screened for their ability to bind and inhibit the main protease (3CLpro) of SARS-CoV-2. Methods: The natural compounds library of Selleck Inc. (Catalog No. L1400) were retrieved from www.selleckchem.com. It contains 2230 compounds in sdf format, curated from natural sources. Prior to molecular docking, all the ligands were prepared by adding hydrogen atoms and merging them with non-polar hydrogen atoms. Gasteiger partial charges were added, rotatable bonds were defined, and the energies were minimized using MMFF94 forcefield (11,12). The three-dimensional coordinates of the main protease (Mpro), also known as 3C-like protein (3CLpro), was downloaded from the protein databank available at https://www.rcsb.org/structure/6LU7. The structure was solved to a resolution of 2.16 Å and is bound with a peptide-like inhibitor (N3)(8). The structure of target was prepared for molecular docking by adding hydrogen atoms, Kollman united atom type charges and solvation parameters using AutoDock Tool (ADT) (13). Results: We found that Kaempferol, Quercetin, and Rutin were bound at the substrate binding pocket of 3CLpro with high affinity (105-106 M-1) and interact with the active site residues such as His41 and Cys145 through hydrogen bonding and hydrophobic interactions. In fact, the binding affinity of Rutin (~106 M-1) was much higher than Chloroquine (~103 M-1) and Hydroxychloroquine (~104 M-1), and the reference drug Remdesivir (~105 M-1). Conclusion: The results suggest that natural compounds such as flavonoids have the potential to be developed as novel inhibitors of SARS-CoV-2 with a comparable/higher potency as that of Remdesivir. However, their clinical usage on COVID-19 patients is a subject of further investigations and clinical trials.
MeSH term(s)	COVID-19 ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2
Chemical Substances	Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-11-16
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1304236-1
ISSN	1873-4286 ; 1381-6128
ISSN (online)	1873-4286
ISSN	1381-6128
DOI	10.2174/1381612826999201116195851
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Article ; Online: Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches.

Muteeb, Ghazala / Rehman, Md Tabish / AlAjmi, Mohamed F / Aatif, Mohammad / Farhan, Mohd / Shafi, Sheeba

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 18

Abstract: New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in ... ...

Abstract	New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e.,
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Captopril ; Carbapenems/pharmacology ; Cephalosporins ; Humans ; Molecular Docking Simulation ; Penicillins ; beta-Lactamases/chemistry ; beta-Lactams
Chemical Substances	Anti-Bacterial Agents ; Carbapenems ; Cephalosporins ; Penicillins ; beta-Lactams ; Captopril (9G64RSX1XD) ; beta-Lactamases (EC 3.5.2.6) ; beta-lactamase NDM-1 (EC 3.5.2.6)
Language	English
Publishing date	2022-09-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27185930
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Article ; Online: Spectroscopic and Molecular Docking Investigation on the Interaction of Cumin Components with Plasma Protein: Assessment of the Comparative Interactions of Aldehyde and Alcohol with Human Serum Albumin.

Ali, Mohd Sajid / Rehman, Md Tabish / Al-Lohedan, Hamad / AlAjmi, Mohamed Fahad

International journal of molecular sciences

2022 Volume 23, Issue 8

Abstract: The interaction of the important plasma protein, human serum albumin (HSA), with two monoterpenes found in cumin oil, i.e., cuminaldehyde (4-isopropylbenzaldehyde) and cuminol (4-isopropylbenzyl alcohol), was studied in this paper. Both experimental and ... ...

Abstract	The interaction of the important plasma protein, human serum albumin (HSA), with two monoterpenes found in cumin oil, i.e., cuminaldehyde (4-isopropylbenzaldehyde) and cuminol (4-isopropylbenzyl alcohol), was studied in this paper. Both experimental and computational methods were utilized to understand the mechanism of binding. The UV absorption profile of HSA changes in the presence of both cuminaldehyde and cuminol, due to the interaction between HSA with both monoterpenes. The intrinsic fluorescence intensity of HSA was also quenched on the sequential addition of both ligands, due to change in the microenvironment of the fluorophore present in the former. Quenching of HSA by cuminaldehyde was much higher in comparison to that in the presence of cuminol. Fluorescence quenching data were analyzed using modified Stern-Volmer and Lineweaver-Burk methods, which suggested that the binding mechanism was of a static type for both ligands. In both cases, the binding was favored by the domination of hydrophobic as well as hydrogen bonding/Van der Waals forces. Both ligands partially unfolded the secondary structure of HSA, although the effect of cuminaldehyde was more pronounced, as compared to cuminol. The preferred binding site of cuminaldehyde and cuminol inside HSA was also the same; namely, drug binding site 1, located in subdomain IIA. The study showed that cuminaldehyde binds strongly with albumin as compared to its alcohol counterpart, which is due to the more hydrophobic nature of the former.
MeSH term(s)	Aldehydes ; Binding Sites ; Circular Dichroism ; Cuminum ; Humans ; Ligands ; Molecular Docking Simulation ; Monoterpenes ; Protein Binding ; Serum Albumin, Human/chemistry ; Spectrometry, Fluorescence ; Thermodynamics
Chemical Substances	Aldehydes ; Ligands ; Monoterpenes ; Serum Albumin, Human (ZIF514RVZR)
Language	English
Publishing date	2022-04-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23084078
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Article ; Online: Prioritization of bioactive compounds envisaging yohimbine as a multi targeted anticancer agent: insight from molecular docking and molecular dynamics simulation.

Jabir, Nasimudeen R / Rehman, Md Tabish / AlAjmi, Mohamed F / Ahmed, Bakrudeen Ali / Tabrez, Shams

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 20, Page(s) 10463–10477

Abstract: Recently, multi-targeted drugs have attracted much attention in cancer therapy where several therapeutic proteins are targeted by a single agent. Using the published scientific literature, we selected sixteen well-known anticancer targets and seven ... ...

Abstract	Recently, multi-targeted drugs have attracted much attention in cancer therapy where several therapeutic proteins are targeted by a single agent. Using the published scientific literature, we selected sixteen well-known anticancer targets and seven potential phytobioactive chemicals to find a multitargeted compound by screening through molecular docking. The feasible protein-ligand interaction was further predicted by protein-ligand interaction analysis and molecular dynamic simulation. The phytochemical yohimbine exhibited the lowest docking score in the range of -8.3 to -10.0 kcal/mol over other ligands with all the studied protein targets. Molecular interaction data also revealed the feasible binding of yohimbine with all targets. Moreover, the molecular simulation data also confirmed the stability of protein-ligand complexes with three most scored targets viz. ERK2, PARP1 and PIK3α. Based on our results, yohimbine seems to be the most potent compound out of those selected compounds and can be considered as effective lead molecule against the studied target proteins.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Molecular Docking Simulation ; Molecular Dynamics Simulation ; Ligands ; Antineoplastic Agents/pharmacology ; Yohimbine/pharmacology
Chemical Substances	Ligands ; Antineoplastic Agents ; Yohimbine (2Y49VWD90Q)
Language	English
Publishing date	2022-12-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2158137
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