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Drug Discovery and Molecular Docking II
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Drug Discovery and Molecular Docking II

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

Deadline for manuscript submissions: closed (15 February 2022) | Viewed by 13532

Special Issue Editor

Prof. Dr. Maria Cristina De Rosa

E-Mail Website
Guest Editor
Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) – Rome, CNR, 00185 Rome, Italy
Interests: molecular modelling; molecular dynamics simulations; molecular docking; computational drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular docking is an extremely powerful tool for drug discovery processes ranging from hit identification to lead optimization. This in silico structure-based method aims to evaluate ligand–target interactions and attempts to reproduce native binding modes, thus accelerating estimations of binding affinity and ligand optimization techniques. In the last decades, molecular docking has contributed to the design of new drug candidates in a shorter time and at lower costs. The second edition of the Special Issue “Drug Discovery and Molecular Docking” will focus not only on the numerous challenges that still remain to be addressed—from protein flexibility to the role of water molecules—but also on the most recent applications of docking in drug discovery, which include drug repurposing, target fishing, and artificial intelligence.

Prof. Dr. Maria Cristina De Rosa
Guest Editor

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Keywords

  • shape complementarity
  • binding mode
  • molecular recognition
  • virtual screening
  • hot-spot residues
  • molecular docking

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Published Papers (4 papers)

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Research

14 pages, 2763 KiB  
Article
Target Design of Novel Histone Deacetylase 6 Selective Inhibitors with 2-Mercaptoquinazolinone as the Cap Moiety
by Hue Thi Buu Bui, Phuong Hong Nguyen, Quan Minh Pham, Hoa Phuong Tran, De Quang Tran, Hosun Jung, Quang Vinh Hong, Quoc Cuong Nguyen, Quy Phu Nguyen, Hieu Trong Le and Su-Geun Yang
Molecules 2022, 27(7), 2204; https://doi.org/10.3390/molecules27072204 - 28 Mar 2022
Cited by 10 | Viewed by 3387
Abstract
Epigenetic alterations found in all human cancers are promising targets for anticancer therapy. In this sense, histone deacetylase inhibitors (HDACIs) are interesting anticancer agents that play an important role in the epigenetic regulation of cancer cells. Here, we report 15 novel hydroxamic acid-based [...] Read more.
Epigenetic alterations found in all human cancers are promising targets for anticancer therapy. In this sense, histone deacetylase inhibitors (HDACIs) are interesting anticancer agents that play an important role in the epigenetic regulation of cancer cells. Here, we report 15 novel hydroxamic acid-based histone deacetylase inhibitors with quinazolinone core structures. Five compounds exhibited antiproliferative activity with IC50 values of 3.4–37.8 µM. Compound 8 with a 2-mercaptoquinazolinone cap moiety displayed the highest antiproliferative efficacy against MCF-7 cells. For the HDAC6 target selectivity study, compound 8 displayed an IC50 value of 2.3 µM, which is 29.3 times higher than those of HDAC3, HDAC4, HDAC8, and HDAC11. Western blot assay proved that compound 8 strongly inhibited tubulin acetylation, a substrate of HDAC6. Compound 8 also displayed stronger inhibition activity against HDAC11 than the control drug Belinostat. The inhibitory mechanism of action of compound 8 on HDAC enzymes was then explored using molecular docking study. The data revealed a high binding affinity (−7.92 kcal/mol) of compound 8 toward HDAC6. In addition, dock pose analysis also proved that compound 8 might serve as a potent inhibitor of HDAC11. Full article
(This article belongs to the Special Issue Drug Discovery and Molecular Docking II)
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14 pages, 3211 KiB  
Article
Biological and Cheminformatics Studies of Newly Designed Triazole Based Derivatives as Potent Inhibitors against Mushroom Tyrosinase
by Mubashir Hassan, Balasaheb D. Vanjare, Kyou-Yeong Sim, Hussain Raza, Ki Hwan Lee, Saba Shahzadi and Andrzej Kloczkowski
Molecules 2022, 27(5), 1731; https://doi.org/10.3390/molecules27051731 - 7 Mar 2022
Cited by 14 | Viewed by 2308
Abstract
A series of nine novel 1,2,4-triazole based compounds were synthesized through a multistep reaction pathway and their structures were scrutinized by using spectral methods such as FTIR, LC-MS, 1H NMR, and 13C NMR. The synthesized derivatives were screened for inhibitory activity against the [...] Read more.
A series of nine novel 1,2,4-triazole based compounds were synthesized through a multistep reaction pathway and their structures were scrutinized by using spectral methods such as FTIR, LC-MS, 1H NMR, and 13C NMR. The synthesized derivatives were screened for inhibitory activity against the mushroom tyrosinase and we found that all the synthesized compounds demonstrated decent inhibitory activity against tyrosinase. However, among the series of compounds, N-(4-fluorophenyl)-2-(5-(2-fluorophenyl)-4-(4-fluorophenyl)-4H-1,2,4-triazol-3-ylthio) acetamide exhibited more prominent activity when accompanied with the standard drug kojic acid. Furthermore, the molecular docking studies identified the interaction profile of all synthesized derivatives at the active site of tyrosinase. Based on these results, N-(4-fluorophenyl)-2-(5-(2-fluorophenyl)-4-(4-fluorophenyl)-4H-1,2,4-triazol-3-ylthio) acetamide could be used as a novel scaffold to design some new drugs against melanogenesis. Full article
(This article belongs to the Special Issue Drug Discovery and Molecular Docking II)
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21 pages, 2187 KiB  
Article
Structural Basis of 2-Phenylamino-4-phenoxyquinoline Derivatives as Potent HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors
by Arthit Makarasen, Suwicha Patnin, Pongsit Vijitphan, Nanthawan Reukngam, Panita Khlaychan, Mayuso Kuno, Pakamas Intachote, Busakorn Saimanee, Suchada Sengsai and Supanna Techasakul
Molecules 2022, 27(2), 461; https://doi.org/10.3390/molecules27020461 - 11 Jan 2022
Cited by 8 | Viewed by 2137
Abstract
New target molecules, namely, 2-phenylamino-4-phenoxyquinoline derivatives, were designed using a molecular hybridization approach, which was accomplished by fusing the pharmacophore structures of three currently available drugs: nevirapine, efavirenz, and rilpivirine. The discovery of disubstituted quinoline indicated that the pyridinylamino substituent at the 2-position [...] Read more.
New target molecules, namely, 2-phenylamino-4-phenoxyquinoline derivatives, were designed using a molecular hybridization approach, which was accomplished by fusing the pharmacophore structures of three currently available drugs: nevirapine, efavirenz, and rilpivirine. The discovery of disubstituted quinoline indicated that the pyridinylamino substituent at the 2-position of quinoline plays an important role in its inhibitory activity against HIV-1 RT. The highly potent HIV-1 RT inhibitors, namely, 4-(2′,6′-dimethyl-4′-formylphenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6b) and 4-(2′,6′-dimethyl-4′-cyanophenoxy)-2-(5″-cyanopyridin-2″ylamino)quinoline (6d) exhibited half-maximal inhibitory concentrations (IC50) of 1.93 and 1.22 µM, respectively, which are similar to that of nevirapine (IC50 = 1.05 µM). The molecular docking results for these two compounds showed that both compounds interacted with Lys101, His235, and Pro236 residues through hydrogen bonding and interacted with Tyr188, Trp229, and Tyr318 residues through π–π stacking in HIV-1 RT. Interestingly, 6b was highly cytotoxic against MOLT-3 (acute lymphoblastic leukemia), HeLA (cervical carcinoma), and HL-60 (promyeloblast) cells with IC50 values of 12.7 ± 1.1, 25.7 ± 0.8, and 20.5 ± 2.1 µM, respectively. However, 6b and 6d had very low and no cytotoxicity, respectively, to-ward normal embryonic lung (MRC-5) cells. Therefore, the synthesis and biological evaluation of 2-phenylamino-4-phenoxyquinoline derivatives can serve as an excellent basis for the development of highly effective anti-HIV-1 and anticancer agents in the near future. Full article
(This article belongs to the Special Issue Drug Discovery and Molecular Docking II)
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13 pages, 4262 KiB  
Article
Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking
by Mateusz Zalewski, Sebastian Kmiecik and Michał Koliński
Molecules 2021, 26(11), 3293; https://doi.org/10.3390/molecules26113293 - 30 May 2021
Cited by 7 | Viewed by 4268
Abstract
One of the major challenges in the computational prediction of protein–peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In [...] Read more.
One of the major challenges in the computational prediction of protein–peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In this work, we tested the protocol for Molecular Dynamics (MD)-based scoring of protein–peptide complex models obtained from coarse-grained (CG) docking simulations. In the first step of the scoring procedure, all models generated by CABS-dock were reconstructed starting from their original C-alpha trace representations to all-atom (AA) structures. The second step included geometry optimization of the reconstructed complexes followed by model scoring based on receptor–ligand interaction energy estimated from short MD simulations in explicit water. We used two well-known AA MD force fields, CHARMM and AMBER, and a CG MARTINI force field. Scoring results for 66 different protein–peptide complexes show that the proposed MD-based scoring approach can be used to identify protein–peptide models of high accuracy. The results also indicate that the scoring accuracy may be significantly affected by the quality of the reconstructed protein receptor structures. Full article
(This article belongs to the Special Issue Drug Discovery and Molecular Docking II)
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