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Potential Application of Small Molecules in Molecular Medicine–an In Vitro and In-Silico Approach

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 10623

Special Issue Editors

Dr. Kulandaisamy Arulsamy

E-Mail Website
Guest Editor
Basic and Translational Research Division, Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
Interests: protein structure and function; mutation-specific drug design; databases and tools; machine learning
Dr. Muralikannan Maruthamuthu

E-Mail Website
Guest Editor
UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599, USA
Interests: bioremediation; synthetic biotechnology; microbial cell-surface display
Special Issues, Collections and Topics in MDPI journals
Dr. Nagendran Tharmalingam

E-Mail Website
Guest Editor
Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School, and Brown University, Providence, RI 02903, USA
Interests: antimicrobials; colon cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Small molecules administered during therapy play a significant role in regulating biological functions when a dysfunction is diagnosed. Small molecules mainly interact with host macromolecules, such as DNA, protein, lipid moieties, etc. These small molecules are drug-like chemical compounds with a low molecular weight (less than 500 Da) that are derived from either a chemical synthesis or natural resources of bacteria, plant, and animal origin. Notably, in the past five years, more than 200 small molecules have been approved for the treatment of several diseases by the U.S. Food and Drug Administration (FDA). Therefore, it is essential to design and develop a potential small molecule that can act against different drug targets/proteins. In addition, numerous in vitro and in silico approaches can be used to study the underlying mechanisms of protein–small-molecule (ligand) interactions. This Special Issue will provide further insight into new developments in the design of small molecules and their molecular mechanisms to elucidate their potential applications in treatments for a wide range of diseases.

For this Special Issue, we intend to collect contributions, including reviews and original articles, concerning successful stories related to potential applications of small molecules in molecular medicine. Topics of interest include but are not limited to the following:

  • Small-molecule synthesis and extraction from natural sources for biological applications;
  • Determination of efficacy for small molecules using in vitro biological approaches;
  • Design of new molecules or derivatives from existing ones for biological applications;
  • Density functional theory (DFT) studies on small or drug-like molecules;
  • Influence of mutations on protein–small molecule interactions
  • Relationship between small molecules’ structural properties and their activities against drug targets;
  • Exploration of protein–small molecule interactions using molecular docking, and molecular dynamics;
  • Natural/synthetic antimicrobial compounds for bacteria and fungi;
  • New trends in developing small molecules as an antimicrobial agent;
  • Active small molecules for antimicrobial resistance microbes.    

Dr. Kulandaisamy Arulsamy
Dr. Muralikannan Maruthamuthu
Dr. Nagendran Tharmalingam
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chemical synthesis
  • protein interactions
  • efficacy
  • small-molecule inhibitors
  • drug targets
  • molecular docking
  • drug design
  • molecular medicine

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Published Papers (4 papers)

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Research

10 pages, 1702 KiB  
Article
Phytosynthesis of Silver Nanoparticle (AgNPs) Using Aqueous Leaf Extract of Knoxia sumatrensis (Retz.) DC. and Their Multi-Potent Biological Activity: An Eco-Friendly Approach
by Settu Loganathan, Kuppusamy Selvam, Muthugounder Subaramanian Shivakumar, Sengottayan Senthil-Nathan, Prabhakaran Vasantha-Srinivasan, Dhakshinamoorthy Gnana Prakash, Sengodan Karthi, Fahad Al-Misned, Shahid Mahboob, Ahmed Abdel-Megeed, Aml Ghaith and Patcharin Krutmuang
Molecules 2022, 27(22), 7854; https://doi.org/10.3390/molecules27227854 - 14 Nov 2022
Cited by 8 | Viewed by 2011
Abstract
Green synthesis of silver nanoparticles (AgNPs) has gained greater interest among chemists and researchers in this current scenario. The present research investigates the larvicidal and anti-proliferation activity of AgNPs derived from Knoxia sumatrensis aqueous leaf extract (K. sumatrensis-ALE) as a potential [...] Read more.
Green synthesis of silver nanoparticles (AgNPs) has gained greater interest among chemists and researchers in this current scenario. The present research investigates the larvicidal and anti-proliferation activity of AgNPs derived from Knoxia sumatrensis aqueous leaf extract (K. sumatrensis-ALE) as a potential capping and reducing candidate. The synthesized AgNPs were characterized through-UV-spectra absorption peak at 425 nm. The XRD and FT-IR studied displayed the crystalline nature and presence of functional groups in prepared samples. FE-SEM showed the hexagonal shape of NPs with the size of 7.73 to 32.84 nm. The synthesized AgNPs displayed superior antioxidant and anti-proliferative activity (IC50 53.29 µg/mL) of breast cancer cell line (MCF-7). Additionally, larvicidal activity against mosquito vector Culex quinquefasciatus larvae delivered (LC50-0.40, mg/L, and LC90-15.83) significant mortality rate post treatment with synthesized AgNPs. Overall, the present research illustrates that the synthesized AgNPs have high biological potential and present a perfect contender in the pharmacological and mosquitocidal arena. Full article
(This article belongs to the Special Issue Potential Application of Small Molecules in Molecular Medicine–an In Vitro and In-Silico Approach)
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16 pages, 2301 KiB  
Article
Small Molecule BRD4 Inhibitors Apabetalone and JQ1 Rescues Endothelial Cells Dysfunction, Protects Monolayer Integrity and Reduces Midkine Expression
by Sidra Shahid, Marlena Pantakani, Lutz Binder, Andreas Fischer, Krishna Pantakani and Abdul R. Asif
Molecules 2022, 27(21), 7453; https://doi.org/10.3390/molecules27217453 - 2 Nov 2022
Cited by 6 | Viewed by 2320
Abstract
NF-κB signaling is a key regulator of inflammation and atherosclerosis. NF-κB cooperates with bromodomain-containing protein 4 (BRD4), a transcriptional and epigenetic regulator, in endothelial inflammation. This study aimed to investigate whether BRD4 inhibition would prevent the proinflammatory response towards TNF-α in endothelial cells. [...] Read more.
NF-κB signaling is a key regulator of inflammation and atherosclerosis. NF-κB cooperates with bromodomain-containing protein 4 (BRD4), a transcriptional and epigenetic regulator, in endothelial inflammation. This study aimed to investigate whether BRD4 inhibition would prevent the proinflammatory response towards TNF-α in endothelial cells. We used TNF-α treatment of human umbilical cord-derived vascular endothelial cells to create an in vitro inflammatory model system. Two small molecule inhibitors of BRD4—namely, RVX208 (Apabetalone), which is in clinical trials for the treatment of atherosclerosis, and JQ1—were used to analyze the effect of BRD4 inhibition on endothelial inflammation and barrier integrity. BRD4 inhibition reduced the expression of proinflammatory markers such as SELE, VCAM-I, and IL6 in endothelial cells and prevented TNF-α-induced endothelial tight junction hyperpermeability. Endothelial inflammation was associated with increased expression of the heparin-binding growth factor midkine. BRD4 inhibition reduced midkine expression and normalized endothelial permeability upon TNF-α treatment. In conclusion, we identified that TNF-α increased midkine expression and compromised tight junction integrity in endothelial cells, which was preventable by pharmacological BRD4 inhibition. Full article
(This article belongs to the Special Issue Potential Application of Small Molecules in Molecular Medicine–an In Vitro and In-Silico Approach)
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17 pages, 3819 KiB  
Article
In Silico Evaluation of Bioactive Compounds of Artemisia pallens Targeting the Efflux Protein of Multidrug-Resistant Acinetobacter baumannii (LAC-4 Strain)
by Suvaiyarasan Suvaithenamudhan, Sivapunniyam Ananth, Vanitha Mariappan, Victor Violet Dhayabaran, Subbiah Parthasarathy, Pitchaipillai Sankar Ganesh and Esaki Muthu Shankar
Molecules 2022, 27(16), 5188; https://doi.org/10.3390/molecules27165188 - 15 Aug 2022
Cited by 2 | Viewed by 2212
Abstract
Acinetobacter baumannii (A. baumannii) is one of the major representative aetiologies of recalcitrant nosocomial infections. Genotypic and phenotypic alterations in A. baumannii have resulted in a significant surge in multidrug resistance (MDR). Of all the factors responsible for the development of [...] Read more.
Acinetobacter baumannii (A. baumannii) is one of the major representative aetiologies of recalcitrant nosocomial infections. Genotypic and phenotypic alterations in A. baumannii have resulted in a significant surge in multidrug resistance (MDR). Of all the factors responsible for the development of antimicrobial resistance (AMR), efflux protein pumps play a paramount role. In pursuit of a safe alternative for the prevention and control of A. baumannii infections, bioactive compounds from the aerial parts of the medicinal plant Artemisia pallens were studied. GC-MS analysis of the ethanol extract of A. pallens detected five major compounds: lilac alcohol A, spathulenol, lilac alcohol C, n-hexadecanoic acid, and vulgarin. In silico examinations were performed using the Schrödinger suite. Homology modelling was performed to predict the structure of the efflux protein of A. baumannii-LAC-4 strain (MDR Ab-EP). The identified bioactive compounds were analysed for their binding efficiency with MDR Ab-EP. High binding efficiency was observed with vulgarin with a glide score of −4.775 kcal/mol and stereoisomers of lilac alcohol A (−3.706 kcal/mol) and lilac alcohol C (−3.706 kcal/mol). Our molecular dynamic simulation studies unveiled the stability of the ligand–efflux protein complex. Vulgarin and lilac alcohol A possessed strong and stable binding efficiency with MDR Ab-EP. Furthermore, validation of the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of the ligands strongly suggested that these compounds could serve as a lead molecule in the development of an alternate drug from A. pallens. Full article
(This article belongs to the Special Issue Potential Application of Small Molecules in Molecular Medicine–an In Vitro and In-Silico Approach)
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27 pages, 7538 KiB  
Article
QSAR, Molecular Docking, MD Simulation and MMGBSA Calculations Approaches to Recognize Concealed Pharmacophoric Features Requisite for the Optimization of ALK Tyrosine Kinase Inhibitors as Anticancer Leads
by Rahul D. Jawarkar, Praveen Sharma, Neetesh Jain, Ajaykumar Gandhi, Nobendu Mukerjee, Aamal A. Al-Mutairi, Magdi E. A. Zaki, Sami A. Al-Hussain, Abdul Samad, Vijay H. Masand, Arabinda Ghosh and Ravindra L. Bakal
Molecules 2022, 27(15), 4951; https://doi.org/10.3390/molecules27154951 - 3 Aug 2022
Cited by 14 | Viewed by 3071
Abstract
ALK tyrosine kinase ALK TK is an important target in the development of anticancer drugs. In the present work, we have performed a QSAR analysis on a dataset of 224 molecules in order to quickly predict anticancer activity on query compounds. Double cross [...] Read more.
ALK tyrosine kinase ALK TK is an important target in the development of anticancer drugs. In the present work, we have performed a QSAR analysis on a dataset of 224 molecules in order to quickly predict anticancer activity on query compounds. Double cross validation assigns an upward plunge to the genetic algorithm–multi linear regression (GA-MLR) based on robust univariate and multivariate QSAR models with high statistical performance reflected in various parameters like, fitting parameters; R2 = 0.69–0.87, F = 403.46–292.11, etc., internal validation parameters; Q2LOO = 0.69–0.86, Q2LMO = 0.69–0.86, CCCcv = 0.82–0.93, etc., or external validation parameters Q2F1 = 0.64–0.82, Q2F2 = 0.63–0.82, Q2F3 = 0.65–0.81, R2ext = 0.65–0.83 including RMSEtr < RMSEcv. The present QSAR evaluation successfully identified certain distinct structural features responsible for ALK TK inhibitory potency, such as planar Nitrogen within four bonds from the Nitrogen atom, Fluorine atom within five bonds beside the non-ring Oxygen atom, lipophilic atoms within two bonds from the ring Carbon atoms. Molecular docking, MD simulation, and MMGBSA computation results are in consensus with and complementary to the QSAR evaluations. As a result, the current study assists medicinal chemists in prioritizing compounds for experimental detection of anticancer activity, as well as their optimization towards more potent ALK tyrosine kinase inhibitor. Full article
(This article belongs to the Special Issue Potential Application of Small Molecules in Molecular Medicine–an In Vitro and In-Silico Approach)
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