Embedded Files
of Medicinal and Toxicological Chemistry I
c/o Magna Græcia University
of Catanzaro
Dear Students of the UMG Medicinal and Toxicological Chemistry I course,
this blog belongs to You!
The MedChemBlog arises from the boundless amount of structural chemical informations available online on accredited and scientifically valid databases (Protein Data Bank, Drug Bank, PubChem and others), but above all from the desire to stimulate the participation of you students and thus, make enjoyable and interactive our current online teaching experience, due to Covid-19.
During 2020/2021 academic year, with the aim of promoting the development of skills in understanding the molecular structures and mechanisms of drug functioning, we placed at the service of the topics covered by the course, the many cues and references you proposed and discussed together during our lessons.
Your insights and cues will then be the ones to design this blog and color our palette with new and different
shades .. the chemist's laboratory, besides, is not so far from that of the artist!
Have a good job but mainly, have fun!
Gentili Studenti del corso di Chimica Farmaceutica e Tossicologica I dell'UMG,
questo blog Vi appartiene!
Il MedChemBlog nasce dalla sconfinata mole di informazioni chimico strutturali disponibili online su database accreditati e scientificamente validi (Protein Data Bank, Drug Bank, PubChem e altri), ma soprattutto dalla volontà di stimolare la partecipazione di Voi discenti e rendere quindi godibile e interattiva la nostra attuale esperienza di didattica online, causa Covid-19.
Durante l' anno accademico 2020/2021, con lo scopo di favorire lo sviluppo delle competenze nella comprensione delle strutture e dei meccanismi molecolari del funzionamento dei farmaci, abbiamo portato a sostegno degli argomenti previsti dal corso, i tanti spunti e riferimenti da Voi proposti e discussi assieme a lezione.
Saranno proprio quest'ultimi, dunque, a disegnare questo blog e a colorare la nostra tavolozza di sfumature nuove e diverse.. il laboratorio del chimico d'altronde, non è poi così distante da quello dell'artista!
Buon lavoro e buon divertimento!!
Prof. Stefano Alcaro
"Food for thought"
by our students
(total number of entries: 100)
MurA ( UDP-N-acetylglucosamine Enolpyruvyl Transferase) mechanism (JBC)
Methicillin (Pubchem)
Staphylococcus epidermidis TcaR in complex with methicillin- 3KP4
Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin – 4KQO
Crystal Structure of BlaC-E166A covalently bound with Mecillinam- 3NC8
Beta-lactam antibiotics action video (Khanacademy)
Cefmetazole (Pubchem)
Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cefmetazole- 4KOS
Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI1 complex -5YPI
Scientific reference work describing the mechanism
of hydrolysis of imipenem (Pubmed)Clavulanic acid (Pubchem)
Crystal structure of TLA-1 extended spectrum
Beta-lactamase in complex with Clavulanic Acid- 6NVUSultamicillin (Pubchem)
Ampicillin (Pubchem)
Sulbactam (Pubchem)
Crystal structure of fosfomycin resistance protein
from Klebsiella pneumoniae with bound Fosfomycin
– 5V3DStructure of the ternary complex of bacitracin, zinc,and geranyl-pyrophosphate - 4K7T
Valinomycin (ChEBI)
The structure of a valinomycin-hexaaquamagnesium trifluoromethanesulfonate compound (ACTA CRYST C)
Tet repressor class D complexed with cobalt and tetracycline – 2VKE
Structure of the Thermus Thermophilus 30S ribosomal subunit in complex with Tetracycline – 1HNW
Tetracycline (Pubchem)
Acinetobacter baumannii ribosome-Tigecycline complex - 30S subunit head – 6YTF
Streptomycin (Pubchem)
Spectinomycin (Pubchem)
Azithromycin (Pubchem)
Structure of the Thermus thermophilus 70S ribosome complexed with azithromycin -4V7Y
Fusidic acid (Drugbank)
Protein crystal structure of macrolide glycosyltransferases OleD complexed with UDP and Erythromycin A - 2IYF
Sulfanilamide (Drugbank)
Crystal structure of a ternary complex of E. Coli Dihydropteroate synthase - 1AJ0
Crystal Structure of Dihydropteroate Synthase from Thermus thermophilus HB8 in Complex with 4-aminobenzoate- 2DZA
Crystal structure of Dihydrofolate reductase from Mycobacterium tuberculosis in an open conformation in complex with trimethoprim - 4KM2
Human Dihydrofolate Reductase complexed with NADPH and Trimethoprim - 2W3A
Solution Structure of the DNA Duplex ACGCGU-NA with a 2' Amido-Linked Nalidixic Acid Residue at the 3' Terminal Nucleotide - 2BQ2
The structure of E. coli nitroreductase bound with the antibiotic nitrofurazone - 1YKI
Nitrofurazone (Pubchem)
Linezolid (Pubchem)
The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with Linezolid - 4WFA
Structure of Mycobacterium tuberculosis enoyl-ACP reductase with bound INH-NADP. – 2PR2
Pyrazinamide (Pubchem)
Structure of heat shock-related 70kDA protein 2 with small-molecule ligand pyrazine-2-carboxamide (AT513) in an alternate binding site - 5FPD
Pyrazine-2-carboxylic acid (Pubchem)
Structural basis for targeting the ribosomal protein S1 of Mycobacterium tuberculosis by pyrazinamide- 4NNI
Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 3nt RNA in complex with Rifampin - 5UHC
Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin - 2A69
Ethambutol (Pubchem)
Cryo-EM structure of Mycobacterium tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol - 7BVF
4-Aminosalicylic acid (Pubchem)
Amodiaquine (Pubchem)
Crystal Structure of Phosphoethanolamine Methyltransferase from Plasmodium falciparum in Complex with Amodiaquine - 4FGZ
Primaquine (Pubchem)
Oxidized quinone reductase 2 in complex with primaquine - 4FGJ
crystal structure of a pentamidine-oligonucleotide complex: implications for dna-binding properties - 1D64
8 topic
Antiviral drugs
Credit: Fusion Medical Animation
Influenza A virus N6 neuraminidase complex with DANA (Duck/England/56)- 6HFY
Crystal structure of influenza A virus neuraminidase N5 complexed with Zanamivir - 3SAN
The crystal structure of neuraminidase in complex with oseltamivir from A/Shanghai/2/2013 (H7N9) influenza virus - 5L15
Influenza A M2 transmembrane domain bound to amantadine- 6BKK
Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)- 6FS8
Rilpivirine (Drugbank)
Crystal structure of HIV-1 reverse transcriptase (RT) in complex with Rilpivirine (TMC278, Edurant), a non-nucleoside rt-inhibiting drug - 4G1Q
Wild Type HIV-1 Protease with Antiviral Drug Saquinavir 3OXC
Remdesivir (Drugbank)
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) - 7BV2
NMR study of DNA (5'-d(*gp*ap*ap*gp*cp*tp*tp*c)-3') self-complementary duplex complexed with Actinomycin d, minimized average structure – 1DSC
NMR Structure of HO2-Co(III) Bleomycin A(2) Bound to d(GGAAGCTTCC)(2) - 1MXK
Candida albicans Hsp90 nucleotide binding domain in complex with AUY922 - 6CJS
Crystal structure of the yeast 20S proteasome in complex with Bortezomib - 2F16
Human Abl kinase domain in complex with Imatinib (STI571, Glivec) - 2HYY
Crystal Structure of VEGFR2 (Juxtamembrane and Kinase Domains) in Complex with SORAFENIB (BAY 43-9006) - 4ASD
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with belinostat - 5EEN
Olaparib (Pubchem)
Crystal structure of the catalytic domain of human PARP1 in complex with olaparib - 7AAD
Contacts us & credits
alcaro@unicz.it - isabella.romeo@unicz.it
giulia.panzarella@studenti.unicz.it
Stefano Alcaro, Prof. of General Medicinal Chemistry and Medicinal and Toxicological Chemistry I
c/o Magna Graecia University of Catanzaro, Viale Europa 88100 Catanzaro, Italy
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