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  • Review
  • Open Access
158 Citations
12,432 Views
19 Pages

Application of MM-PBSA Methods in Virtual Screening

  • Giulio Poli,
  • Carlotta Granchi,
  • Flavio Rizzolio and
  • Tiziano Tuccinardi

23 April 2020

Computer-aided drug design techniques are today largely applied in medicinal chemistry. In particular, receptor-based virtual screening (VS) studies, in which molecular docking represents the gold standard in silico approach, constitute a powerful st...

  • Article
  • Open Access
6 Citations
3,309 Views
16 Pages

25 January 2021

Recent studies have identified cyclic GMP-AMP synthase (cGAS) as an important target for treating autoimmune diseases, and several inhibitors of human cGAS (hcGAS) and their structures in complexation with hcGAS have been reported. However, the mecha...

  • Article
  • Open Access
12 Citations
4,170 Views
20 Pages

31 December 2021

In this study, we investigated the binding affinities between the main protease of SARS-CoV-2 virus (Mpro) and its various ligands to identify the hot spot residues of the protease. To benchmark the influence of various force fields on hot spot resid...

  • Article
  • Open Access
20 Citations
8,595 Views
20 Pages

26 September 2014

Endo-1,4-β-xylanase (EC 3.2.1.8) is the enzyme from Ruminococcus albus 8 (R. albus 8) (Xyn10A), and catalyzes the degradation of arabinoxylan, which is a major cell wall non-starch polysaccharide of cereals. The crystallographic structure of Xyn10A...

  • Article
  • Open Access
5 Citations
2,497 Views
16 Pages

Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket

  • Valdir Ferreira de Paula Junior,
  • Mauricio Fraga van Tilburg,
  • Pablo Abreu Morais,
  • Francisco Franciné Maia Júnior,
  • Elza Gadelha Lima,
  • Victor Tabosa dos Santos Oliveira,
  • Maria Izabel Florindo Guedes,
  • Ewerton Wagner Santos Caetano and
  • Valder Nogueira Freire

3 September 2022

The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this...

  • Article
  • Open Access
79 Citations
7,824 Views
14 Pages

Folding free energy is an important biophysical characteristic of proteins that reflects the overall stability of the 3D structure of macromolecules. Changes in the amino acid sequence, naturally occurring or made in vitro, may affect the stability o...

  • Article
  • Open Access
13 Citations
6,346 Views
16 Pages

The SARS-CoV-2 virus, since its appearance in 2019, has caused millions of cases and deaths. To date, there is no effective treatment or a vaccine that is fully protective. Despite the efforts made by governments and health institutions around the gl...

  • Article
  • Open Access
21 Citations
9,899 Views
19 Pages

10 April 2012

Chitinolytic β-N-acetyl-D-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-D-hexosa...

  • Data Descriptor
  • Open Access
1 Citations
792 Views
12 Pages

Computational Dataset for Polymer–Pharmaceutical Interactions: MD/MM-PBSA and DFT Resources for Molecularly Imprinted Polymer (MIP) Design

  • David Visentin,
  • Mario Lovrić,
  • Dejan Milenković,
  • Robert Vianello,
  • Željka Maglica,
  • Kristina Tolić Čop and
  • Dragana Mutavdžić Pavlović

10 December 2025

Molecularly imprinted polymers (MIPs) are promising sorbents for selectively capturing pharmaceutically active compounds (PhACs), but design remains slow because candidate screening is largely experimental or based on computationally expensive method...

  • Article
  • Open Access
389 Views
52 Pages

The SARS-CoV-2 Omicron variant and its descendants accumulated unprecedented numbers of spike substitutions yet remained transmissible, implying compensatory mechanisms that preserve entry while eroding humoral immunity. We analyzed 32 variants for s...

  • Article
  • Open Access
6 Citations
4,029 Views
22 Pages

Structural and Energetic Affinity of Annocatacin B with ND1 Subunit of the Human Mitochondrial Respiratory Complex I as a Potential Inhibitor: An In Silico Comparison Study with the Known Inhibitor Rotenone

  • Camilo Febres-Molina,
  • Jorge A. Aguilar-Pineda,
  • Pamela L. Gamero-Begazo,
  • Haruna L. Barazorda-Ccahuana,
  • Diego E. Valencia,
  • Karin J. Vera-López,
  • Gonzalo Davila-Del-Carpio and
  • Badhin Gómez

2 June 2021

ND1 subunit possesses the majority of the inhibitor binding domain of the human mitochondrial respiratory complex I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experi...

  • Article
  • Open Access
3 Citations
2,918 Views
19 Pages

Computational Tool to Design Small Synthetic Inhibitors Selective for XIAP-BIR3 Domain

  • Marc Farag,
  • Charline Kieffer,
  • Nicolas Guedeney,
  • Anne Sophie Voisin-Chiret and
  • Jana Sopkova-de Oliveira Santos

30 June 2023

X-linked inhibitor of apoptosis protein (XIAP) exercises its biological function by locking up and inhibiting essential caspase-3, -7 and -9 toward apoptosis execution. It is overexpressed in multiple human cancers, and it plays an important role in...

  • Article
  • Open Access
352 Views
19 Pages

Decoding iNOS Inhibition: A Computational Voyage of Tavaborole Toward Restoring Endothelial Homeostasis in Venous Leg Ulcers

  • Naveen Kumar Velayutham,
  • Chitra Vellapandian,
  • Himanshu Paliwal,
  • Suhaskumar Patel and
  • Bhupendra G. Prajapati

13 January 2026

Background: Due to chronic venous insufficiency, venous leg ulcers (VLUs) develop as chronic wounds characterized by impaired healing, persistent inflammation, and endothelial dysfunction. Nitrosative stress, mitochondrial damage, and tissue apoptosi...

  • Article
  • Open Access
22 Citations
4,854 Views
18 Pages

Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation

  • Sobia Ahsan Halim,
  • Almas Gul Sikandari,
  • Ajmal Khan,
  • Abdul Wadood,
  • Muhammad Qaiser Fatmi,
  • René Csuk and
  • Ahmed Al-Harrasi

22 February 2021

Tumor necrosis factor-α (TNF-α) is a drug target in rheumatoid arthritis and several other auto-immune disorders. TNF-α binds with TNF receptors (TNFR), located on the surface of several immunological cells to exert its effect. Hence, the use of inhi...

  • Article
  • Open Access
3 Citations
2,648 Views
15 Pages

As fewer therapeutic options are available for treating toxoplasmosis, newer antiparasitic drugs that can block TgAPN2 M1 aminopeptidase are of significant value. Herein, we employed several computer-aided drug-design approaches with the objective of...

  • Article
  • Open Access
4 Citations
1,401 Views
33 Pages

Background/Objectives: Highly pathogenic coronaviruses (CoVs), including SARS-CoV, MERS-CoV, and SARS-CoV-2, continue to pose a significant threat to global public health. Therefore, this situation highlights the urgent need for effective broad-spect...

  • Article
  • Open Access
29 Citations
5,136 Views
17 Pages

Conjugated β-Cyclodextrin Enhances the Affinity of Folic Acid towards FRα: Molecular Dynamics Study

  • Mohammad G. Al-Thiabat,
  • Amirah Mohd Gazzali,
  • Noratiqah Mohtar,
  • Vikneswaran Murugaiyah,
  • Ezatul Ezleen Kamarulzaman,
  • Beow Keat Yap,
  • Noorsaadah Abd Rahman,
  • Rozana Othman and
  • Habibah A. Wahab

31 August 2021

Drug targeting is a progressive area of research with folate receptor alpha (FRα) receiving significant attention as a biological marker in cancer drug delivery. The binding affinity of folic acid (FA) to the FRα active site provides a basis for reco...

  • Article
  • Open Access
5 Citations
1,562 Views
20 Pages

12 March 2025

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural a...

  • Article
  • Open Access
3 Citations
5,451 Views
37 Pages

Structure-Based Discovery of Potential HPV E6 and EBNA1 Inhibitors: Implications for Cervical Cancer Treatment

  • Emmanuel Broni,
  • Carolyn N. Ashley,
  • Miriam Velazquez,
  • Patrick O. Sakyi,
  • Samuel K. Kwofie and
  • Whelton A. Miller

Cervical cancer is the fourth most diagnosed cancer and the fourth leading cause of cancer death in women globally. Its onset and progression have been attributed to high-risk human papillomavirus (HPV) types, especially 16 and 18, while the Epstein&...

  • Article
  • Open Access
4 Citations
2,084 Views
18 Pages

4 September 2024

This study evaluates radio-iodinated anastrozole ([125I]anastrozole) and epirubicin ([125I]epirubicin) for AKT1-targeted breast cancer therapy, utilizing radiopharmaceutical therapy (RPT) for personalized treatment. Through molecular docking and dyna...

  • Article
  • Open Access
8 Citations
1,913 Views
18 Pages

12 July 2024

Alzheimer’s disease, characterized by a decline in cognitive functions, is frequently associated with decreased levels of acetylcholine due to the overactivity of acetylcholinesterase (AChE). Inhibiting AChE has been a key therapeutic strategy...

  • Article
  • Open Access
5 Citations
2,188 Views
16 Pages

7 August 2024

This study evaluates radioiodinated anastrozole ([125I]anastrozole) and epirubicin ([125I]epirubicin) for HER2-targeted cancer therapy, utilizing radiopharmaceutical therapy (RPT) for personalized treatment of HER2-positive cancers. Through molecular...

  • Article
  • Open Access
9 Citations
4,457 Views
15 Pages

24 September 2022

Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutatio...

  • Article
  • Open Access
6 Citations
3,535 Views
20 Pages

Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents

  • Emilio Lamazares,
  • Desmond MacLeod-Carey,
  • Fernando P. Miranda and
  • Karel Mena-Ulecia

13 January 2021

The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which...

  • Article
  • Open Access
7 Citations
2,548 Views
22 Pages

An Exploration of the Inhibitory Mechanism of Rationally Screened Benzofuran-1,3,4-Oxadiazoles and-1,2,4-Triazoles as Inhibitors of NS5B RdRp Hepatitis C Virus through Pharmacoinformatic Approaches

  • Ali Irfan,
  • Shah Faisal,
  • Sajjad Ahmad,
  • Muhammad Jawwad Saif,
  • Ameer Fawad Zahoor,
  • Samreen Gul Khan,
  • Jamila Javid,
  • Sami A. Al-Hussain,
  • Muhammed Tilahun Muhammed and
  • Magdi E. A. Zaki

17 November 2023

Benzofuran, 1,3,4-oxadiazole, and 1,2,4-triazole are privileged heterocyclic moieties that display the most promising and wide spectrum of biological activities against a wide variety of diseases. In the current study, benzofuran-1,3,4-oxadiazole BF1...

  • Article
  • Open Access
11 Citations
4,033 Views
18 Pages

28 January 2021

RET (rearranged during transfection) kinase, one of the receptor tyrosine kinases, plays a crucial role in the development of the human nervous system. It is also involved in various cell signaling networks responsible for the normal cell division, g...

  • Article
  • Open Access
11 Citations
3,539 Views
19 Pages

SHP2 belongs to a cytoplasmic non-receptor protein tyrosine phosphatase class. It plays a critical role in the development of various cancers, such as gastric cancer, leukemia, and breast cancer. Thus, SHP2 has gained the interest of researchers as a...

  • Article
  • Open Access
7 Citations
9,121 Views
20 Pages

Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays

  • Huimin Liu,
  • Liangcheng Chen,
  • Quan Li,
  • Mingzhu Zheng and
  • Jingsheng Liu

11 June 2014

Cysteine protease 1 precursor from Zea mays (zmCP1) is classified as a member of the C1A family of peptidases (papain-like cysteine protease) in MEROPS (the Peptidase Database). The 3D structure and substrate specificity of the zmCP1 is still unknown...

  • Article
  • Open Access
2 Citations
3,869 Views
18 Pages

18 September 2024

YTHDC1 (YTH domain containing 1), a crucial reader protein of N6-methyladenosine (m6A) mRNA, plays a critical role in various cellular functions and is considered a promising target for therapeutic intervention in acute myeloid leukemia and other can...

  • Article
  • Open Access
28 Citations
5,726 Views
14 Pages

Ligand-Based Virtual Screening, Molecular Docking, Molecular Dynamics, and MM-PBSA Calculations towards the Identification of Potential Novel Ricin Inhibitors

  • Fernanda D. Botelho,
  • Marcelo C. dos Santos,
  • Arlan da S. Gonçalves,
  • Kamil Kuca,
  • Martin Valis,
  • Steven R. LaPlante,
  • Tanos C. C. França and
  • Joyce S. F. D. de Almeida

26 November 2020

Ricin is a toxin found in the castor seeds and listed as a chemical weapon by the Chemical Weapons Convention (CWC) due to its high toxicity combined with the easiness of obtention and lack of available antidotes. The relatively frequent episodes of...

  • Feature Paper
  • Article
  • Open Access
23 Citations
5,907 Views
15 Pages

Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies

  • Vladimir P. Berishvili,
  • Alexander N. Kuimov,
  • Andrew E. Voronkov,
  • Eugene V. Radchenko,
  • Pradeep Kumar,
  • Yahya E. Choonara,
  • Viness Pillay,
  • Ahmed Kamal and
  • Vladimir A. Palyulin

11 July 2020

Tankyrase enzymes (TNKS), a core part of the canonical Wnt pathway, are a promising target in the search for potential anti-cancer agents. Although several hundreds of the TNKS inhibitors are currently known, identification of their novel chemotypes...

  • Article
  • Open Access
9 Citations
4,123 Views
17 Pages

Non-small cell lung cancer (NSCLC) is a lethal non-immunogenic malignancy and proto-oncogene ROS-1 tyrosine kinase is one of its clinically relevant oncogenic markers. The ROS-1 inhibitor, crizotinib, demonstrated resistance due to the Gly2032Arg mut...

  • Article
  • Open Access
20 Citations
7,868 Views
14 Pages

25 February 2020

Gain-of-function mutations in PCSK9 (proprotein convertase subtilisin/kexin type 9) lead to reduced uptake of LDL (low density lipoprotein) cholesterol and, therefore, increased plasma LDL levels. However, the mechanism by which these mutants reduce...

  • Article
  • Open Access
24 Citations
8,542 Views
33 Pages

Current oral medications for type 2 diabetes target a single main physiological mechanism. They either activate or inhibit receptors to enhance insulin sensitivity, increase insulin secretion, inhibit glucose absorption, or inhibit glucose production...

  • Article
  • Open Access
1,623 Views
23 Pages

Background/Objectives: Chloroquine (CQ) and hydroxychloroquine (HCQ) have been the subject of debate in the treatment of COVID-19 due to the lack of conclusive evidence regarding their efficacy and safety. Our study aims to investigate the molecular...

  • Article
  • Open Access
146 Citations
7,785 Views
20 Pages

13 February 2020

Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase that works under acute transcriptional control by several stimuli, including serum and glucocorticoids. It plays a significant role in the cancer progression and metastas...

  • Article
  • Open Access
36 Citations
6,541 Views
15 Pages

Drug resistance of mutations in HIV-1 protease (PR) is the most severe challenge to the long-term efficacy of HIV-1 PR inhibitor in highly active antiretroviral therapy. To elucidate the molecular mechanism of drug resistance associated with mutation...

  • Article
  • Open Access
15 Citations
2,951 Views
22 Pages

Pharmacoinformatics and Breed-Based De Novo Hybridization Studies to Develop New Neuraminidase Inhibitors as Potential Anti-Influenza Agents

  • Bourougaa Lotfi,
  • Ouassaf Mebarka,
  • Bader Y. Alhatlani,
  • Emad M. Abdallah and
  • Sarkar M. A. Kawsar

18 September 2023

Influenza represents a profoundly transmissible viral ailment primarily afflicting the respiratory system. Neuraminidase inhibitors constitute a class of antiviral therapeutics employed in the management of influenza. These inhibitors impede the libe...

  • Article
  • Open Access
12 Citations
3,154 Views
22 Pages

Exploring Securigera securidaca Seeds as a Source of Potential CDK1 Inhibitors: Identification of Hippeastrine and Naringenin as Promising Hit Candidates

  • Mohamed E. M. Abdelbagi,
  • Ghassab M. Al-Mazaideh,
  • Adil Elhag Ahmed,
  • Fuad Al-Rimawi,
  • Haya Ayyal Salman,
  • Abdulrahman Almutairi,
  • Faraj Ahmad Abuilaiwi and
  • Fadel Wedian

12 May 2023

CDK1 (cyclin dependent kinase 1) is a key regulator of the cell cycle and is frequently dysregulated in cancer, making it a promising target for anticancer therapy. Securigera securidaca L. (S. securidaca) seeds, traditionally used in folk medicine f...

  • Article
  • Open Access
1,516 Views
13 Pages

10 July 2024

Phenolic environmental endocrine-disrupting chemicals (PEDCs) are persistent EDCs that are widely found in food packaging materials and environmental media and seriously threaten human health and ecological security. Human estrogen-related receptor &...

  • Article
  • Open Access
20 Citations
4,323 Views
29 Pages

Synthesis and Chemopreventive Potential of 5-FU/Genistein Hybrids on Colorectal Cancer Cells

  • Gustavo Moreno-Quintero,
  • Wilson Castrillón-Lopez,
  • Angie Herrera-Ramirez,
  • Andrés F. Yepes-Pérez,
  • Jorge Quintero-Saumeth and
  • Wilson Cardona-Galeano

21 October 2022

A series of 5-FU-Genistein hybrids were synthesized and their structures were elucidated by spectroscopic analysis. The chemopreventive potential of these compounds was evaluated in human colon adenocarcinoma cells (SW480 and SW620) and non-malignant...

  • Article
  • Open Access
32 Citations
6,232 Views
18 Pages

Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study

  • Rajveer Singh,
  • Anupam Gautam,
  • Shivani Chandel,
  • Arijit Ghosh,
  • Dhritiman Dey,
  • Syamal Roy,
  • Velayutham Ravichandiran and
  • Dipanjan Ghosh

10 October 2020

The current pandemic, caused by SARS-CoV-2 virus, is a severe challenge for human health and the world economy. There is an urgent need for development of drugs that can manage this pandemic, as it has already infected 19 million people and led to th...

  • Article
  • Open Access
43 Citations
4,691 Views
19 Pages

In Silico Development of Novel Benzofuran-1,3,4-Oxadiazoles as Lead Inhibitors of M. tuberculosis Polyketide Synthase 13

  • Ali Irfan,
  • Shah Faisal,
  • Ameer Fawad Zahoor,
  • Razia Noreen,
  • Sami A. Al-Hussain,
  • Burak Tuzun,
  • Rakshanda Javaid,
  • Ahmed A. Elhenawy,
  • Magdi E. A. Zaki and
  • Magda H. Abdellattif
  • + 1 author

Benzofuran and 1,3,4-oxadiazole are privileged and versatile heterocyclic pharmacophores which display a broad spectrum of biological and pharmacological therapeutic potential against a wide variety of diseases. This article reports in silico CADD (c...

  • Article
  • Open Access
2 Citations
2,272 Views
12 Pages

The P2Y12 receptor is an important member of the purinergic receptor family, known for its critical role in platelet activation and thrombosis. In our previously published study, the acridinone analogue NSC618159 was identified as a potent antagonist...

  • Article
  • Open Access
27 Citations
5,351 Views
28 Pages

Heterocyclic Substitutions Greatly Improve Affinity and Stability of Folic Acid towards FRα. an In Silico Insight

  • Mohammad G. Al-Thiabat,
  • Fadi G. Saqallah,
  • Amirah Mohd Gazzali,
  • Noratiqah Mohtar,
  • Beow Keat Yap,
  • Yee Siew Choong and
  • Habibah A Wahab

18 February 2021

Folate receptor alpha (FRα) is known as a biological marker for many cancers due to its overexpression in cancerous epithelial tissue. The folic acid (FA) binding affinity to the FRα active site provides a basis for designing more specific targets fo...

  • Article
  • Open Access
1,934 Views
36 Pages

Computer-Aided Discovery of Natural Compounds Targeting the ADAR2 dsRBD2-RNA Interface and Computational Modeling of Full-Length ADAR2 Protein Structure

  • Carolyn N. Ashley,
  • Emmanuel Broni,
  • Michelle Pena-Martinez,
  • Chanyah M. Wood,
  • Samuel K. Kwofie and
  • Whelton A. Miller

Mesothelioma is a rare and aggressive cancer linked to asbestos exposure and characterized by rapid metastasis and poor prognosis. Inhibition of adenosine deaminase acting on dsRNA 2 (ADAR2) RNA binding but not ADAR2 editing has shown antitumor effec...

  • Article
  • Open Access
23 Citations
3,030 Views
34 Pages

28 June 2023

The RAS gene family is one of the most frequently mutated oncogenes in human cancers. In KRAS, mutations of G12D and G12C are common. Here, 52 iridoids were selected and docked against 8AFB (KRAS G12C receptor) using Sotorasib as the standard. As per...

  • Article
  • Open Access
4 Citations
2,737 Views
20 Pages

Studies on the Selectivity Mechanism of Wild-Type E. coli Thioesterase ‘TesA and Its Mutants for Medium- and Long-Chain Acyl Substrates

  • Xinyue Zhang,
  • Hao Zhang,
  • Shanshan Guan,
  • Zhijian Luo,
  • Jingwen E,
  • Zhijie Yang,
  • Juan Du and
  • Song Wang

9 September 2022

E. coli thioesterase ‘TesA is an important enzyme in fatty acid production. Medium-chain fatty acids (MCFAs, C6-C10) are of great interest due to their similar physicochemical properties to petroleum-based oleo-chemicals. It has been shown that...

  • Article
  • Open Access
1 Citations
1,254 Views
18 Pages

Mycobacterium tuberculosis, the infectious agent behind tuberculosis (TB), underscores the significance of targeting enzymes such as arabinosyltransferases in drug development efforts. Benzothiozinone derivatives, which have been assessed for their e...

  • Article
  • Open Access
5 Citations
2,151 Views
18 Pages

In the dynamic field of radiopharmaceuticals, innovating targeted agents for cancer diagnosis and therapy is crucial. Our study enriches this evolving landscape by evaluating the potential of radioiodinated anastrozole ([125I]anastrozole) and radioio...

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