a.k.a. CRE (Carbapenem-Resistant Enterobacteriaceae)

Dr. B notes (090613)
Wet Lab stuff:
Nitrocefin is in. (2 vials of 5mg each)
- standard curve of varying amount of enzyme
- determine Km & kinetics

Graphpad prism login info (remote desktop using Windows - not sure if it will work from a Mac or Linux)
-- find remote desktop in Windows start menu from your computer and enter this info.
vdsstationpc.dyndns.org
username: vdsstationPC\vdsclass
passwerd: same as to get into laptops in lab

Alternatively, this is the computer outside of Dr. B’s office that you can go sit at.


Virtual Stuff




CDC page on CRE's: http://www.cdc.gov/hai/organisms/cre/

Link to Madeline's Mini-Research Write Up page: Beta Lactam resistant bacteria

PDB 'Featured System' page: http://sbkb.org/kb/featured_molecule_latest.html



VS4 Protocol (original)

LabVirtualScreen4_NDM-1_metalloBetaLactamase_VDS_Spring13.docx


VS4 Redo Protocol (version 3)

See: GDocs/Protocols/VirtualScreening/...

re-run the docking with the modifications made (if you didn't originally have a metal or a ligand - restart with a PDB structure that has a metal and a ligand in the active site)
post results in table below alongside your original VS4 results

VS4 Redo Again Protocol

same as above, but this time Delete the CONECT records to the Zincs (or any metals) in your PDB file after it has gone through Molprobity


INSTRUCTIONS:

  1. Choose which structure you will dock against. Fill in your name next to that entry. Only 5 researchers per target.
  2. Once you have completed docking, enter your results in Table 2. below.

Table 1. Associated PDB entries of crystal structures for NDM-1 beta-metallo lactamase
PDB ID:
Description
Researcher 1
Researcher 2
Researcher 3
Researcher 4
Researcher 5
4HKY
New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem
Alice C.
Qasim A.
Marianna U.
Miguel T.
Brandy C.
4HL1
Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin
Aaron H.
Grant T.
Jensen G.
Grayson N.
Spencer C.
4HL2
New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin (Metals were shown in PyMol, but not in GOLD)
Julia C.
Karuna A.
Jacqueline E.
Gabe H.

4GYQ
Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae-





4GYU
Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae-





4H0D
New Delhi Metallo-beta-Lactamase-1 Complexed with Mn from Klebsiella pneumoniae





4EYB
Crystal structure of NDM-1 bound to hydrolyzed oxacillin
Caroline C.
D'Ondria P.
Kevin E.
Shannon R.
William I.
4EXS
Crystal structure of NDM-1 bound to L-captopril
Gautam W.
Khady D.
William E.
Nicole W.
Brendan C.
4EXY
Crystal structure of NDM-1 bound to ethylene glycol
Emily J.
Nancy I.
Alyssa K.
Vicky G.
Hyun-Young L.
4EY2
Crystal structure of NDM-1 bound to hydrolyzed methicillin
Tony G.
Karinna L.
Melissa H.
Dax F.G.
Ramiro R.
4EYF
Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin
Imran Zafar
Feng G.
Grace T.
Daniel D.
Nicolet F.
4EYL
Crystal structure of NDM-1 bound to hydrolyzed meropenem
Priya P.
Jiaqi Z.
Stella M.
Selena I.
Renee F.
3PG4
The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)





3SPU
apo NDM-1 Crystal Structure-





3SRX
New Delhi Metallo-beta-Lactamase-1 Complexed with Cd-





3SBL
Crystal Structure of New Delhi Metal-beta-lactamase-1 from Klebsiella pneumoniae
Jesus
DE La O
James T.
Alakh R
Jessica N.
Katherine V.
3SFP
Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae




3ZR9
STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE 1 (NDM-1)-





3S0Z
Crystal structure of New Delhi Metallo-beta-lactamase (NDM-1)-





3Q6X
Crystal structure of NDM-1 in complex with hydrolyzed ampicillin
Shivani B.
Serena Z.
Shawn O
So-Youn P
Anita V.
3RKJ
Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pnueumoniae (no metal in active site- could not re-run VS4)
Keely W.
Aditi S.
Kavya K.
Min S.
Ariel C.
3RKK
Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae-
[[#|Seo]] Kelly K.





Table 2. Gold docking scores of various ligands against NDM-1 beta-metallo lactamase crystal sctructures (nonhis)
#
RESEARCHER NAME
PDB ID
'POSITIVE' CTRL1
Faropenem
-drug
Penicillin
-drug
Clavulanic Acid
-inhibitor
Aspririn
-random
Original Ligand
'
(REDO redo)
POSITIVE' CTRL1
(REDO redo)
Faropenem
-drug
(REDO redo)
Penicillin
-drug
(REDO redo)
Clavulanic Acid
-inhibitor
(REDO redo)
Aspririn
-random
(REDO redo)
Original Ligand
1
Gautam W.
4EXS
79.39
57.05
70.08
52.21
50.05
48.55






2
Khady D.
4EXS
64.47
73.75
83.51
72.77
68.75
69.83






3
Nicole W.
4EXS
64.83
72.19
84.14
70.06
68.48
69.07






4
Jesus De
3SBL
49.51
45.79
42.19
44.91
40.97
43.99






5
Tony G.
4EY2
74.86
77.57
70.23
65.34
68.7
80.27
79.27
81.04
74.00
70.93
65.83
84.15
6
Shivani B.
3Q6X
80.35
80.70
76.71
67.52
69.72
83.38






7
Serena Z.
3Q6X
80.50
81.35
76.42
67.86
69.90
84.17






8
Shawn O.
3Q6X
80.44
81.57
77.31
67.78
72.22
83.26






9
William E.
4EXS
64.56
58.59
70.18
53.04
50.03
49.58






10
Imran Zafar
4EYF
76.66
77.18
72.53
64.4
67.15
81.4






11
Caroline C.
4EYB
74.96
78.48
70.76
64.27
67.00
92.86






12
Alice C.
4HKY
86.22
74.46
76.00
66.42
67.47
77.17






13
Keely W.
3RKJ
60.2
42.1
49.6
36.2
34.9
10.7






14
Grace T.
4EYF
75.67
76.81
72.89
64.67
67.19
83.91






15
Kavya K.
3RKJ
62.44
41.00
50.69
37.24
35.31
11.45
(no metal in active site- could not re-run VS4)
NA
NA
NA
NA
NA
16
Aaron Hong
4HL1
53.95
81.18
62.39
73.67
75.92
83.60






17
D'Ondria P.
4EYB
77.48
88.22
80.07
70.88
70.65
84.19






18
Nicolet F.
4EYF
73.29
80.40
76.36
65.64
69.17
81.00
71.96
84.50
79.23
70.53
80.28
83.34
19
Grayson N.
4HL1
61.99
83.43
77.54
75.55
75.66
83.95






20
Emily J.
4EXY
79.94
74.34
70.79
74.22
73.29
38.68






21
Katherine V.
3SBL
45.23
43.29
41.76
44.03
41.26
44.41
48.70
42.78
42.78
45.21
41.33
44.95
22
Marianna U.
4HKY












23
Jessica N.
3SBL
44.69
46.04
42.63
44.92
41.33
44.37






24
Karinna L.
4EY2
77.44
78.61
69.95
65.41
68.54
78.45






25
Grant T.
4DHL1
87.93
81.35
79.90
75.43
75.63
87.95






26
Kevin E.
4EYB
75.66
77.78
71.10
64.73
67.30
89.56
80.93
80.38
76.66
69.89
69.62
87.91
27
Alyssa K.
4EXY
74.16
74.96
70.23
74.46
73.41
38.78
81.32
77.09
73.95
73.74
73.76
41.37
28
Aditi S.
3RKJ
67.72
57.63
61.38
55.15
48.43
23.76






29
Qasim A.
4HKY
49.43
75.32
73.16
65.18
67.27
69.1






30
Julia C.
4HL2
79.93
80.14
79.46
69.94
66.06
82.59






31
Feng G.
4EYF
74.74
79.93
76.12
65.54
69.33
83.12






32
Min S.
3RKJ
65.13
55.55
52.15
51.48
43.23
25.23






33
Melissa H.
4EY2
74.67
79.04
70.34
65.31
65.98
78.62
78.73
84.20
77.53
70.16
71.03
84.68
34
Shannon R.
4EYB
76.96
76.40
75.45
64.53
67.12
91.53






35
Anita V.
3Q6X
75.69
53.73
50.68
35.44
36.04
58.87






36
Marianna U.
4HKY
74.5
74.34
70.53
60.82
62.7
69.61






37
Miguel T.
4HKY
85.28
62.88
59.27
50.21
50.64
59.21






38
Seo Kelly K.
3RKK
8.73
26.09
29.38
21.15
21.97
11.93






39
Ramiro R.
4EY2
74.06
76.91
70.46
65.41
67.96
69.15






40
Priya P.
4EYL
73.73
82.76
82.54
72.63
73.77
91.35
81.51
85.92
84.55
74.62
74.79
97.04
41
So-Youn P.
3Q6X
80.43
81.96
77.29
67.84
69.82
82.84






42
Daniel D.
4EYF
73.27
77.73
73.06
64.84
66.86
82.29






43
Nancy I.
4EXY
78.89
75.23
70.63
73.48
74.21
38.53






44
Ariel C.
3RKJ
53.40
35.98
41.54
29.62
32.46
25.60






45
Vicky G.
4EXY
78.5
73.07
68.09
72.83
73.81
38.24
85.78
76.31
71.19
72.99
73.28
40.03
46
Spencer C.
4HL1
72.79
83.29
83.08
75.30
77.52
69.16






47
Stella M.
4EYL
75.28
83.23
83.07
73.62
73.58
105.56






48
Jiaqi Z.
4EYL
76.58
83.05
82.59
73.95
72.76
92.26






49
Hyun-Young L.
4EXY
80.07
74.45
71.16
74.41
74.09
38.87






50
Selena I.
4EYL
75.05
82.23
82.79
72.63
74.18
91.82






51
Brandy C.
4HKY
85.79
74.99
68.49
65.52
65.71
67.37






52
Renee F.
4EYL
75.26
66.35
68.88
54.87
56.67
58.53
84.34
69.26
71.12
59.02
59.95
N/A
53
James T.
3SBl
44.94
46.21
40.56
44.79
40.98
45.75






54
Karuna A.
4HL2
73.33
71.9
88.7
87.9
92.23
79.45






55
Jacqueline E.
4HL2
67.91
52.52
59.76
38.11
37.55
63.49
67.76
52.56
59.85
41.66
35.80
63.84
56
Kevin E. (redo)
4EYB
80.93
80.38
76.66
69.89
69.62
87.91






57
Katherine V. (redo)
3SBL
48.70
42.78
42.78
45.21
41.33
44.95






58
Gabe H.
4HL2
115.04
80.56
76.95
65.54
66.96
86.35
113.25
85.00
68.53
70.53
69.24
91.88
59
Brian C.
3Q6X
80.26
59.67
76.41
67.67
70.41
82.39






60
Salil D.
4EYB
77.28
78.37
70.60
66.56
67.08
80.15







Binding DB Info: (To Be Done)

http://www.bindingdb.org/bind/index.jsp
search for "Metallo-beta-lactamase"

Download Binding DB compounds using the 'Computed 3D by Vconf -m prep' option (Does not work)







REFERENCES:

An altered zinc-binding site confers resistance to a covalent inactivator of New Delhi metallo-beta-lactamase-1 (NDM-1) discovered by high-throughput screening.
Thomas PW, Spicer T, Cammarata M, Brodbelt JS, Hodder P, Fast W. Bioorg Med Chem. 2013 Mar 29. doi:pii: S0968-0896(13)00245-9. 10.1016/j.bmc.2013.03.031. [Epub ahead of print]
PMID: 23591260

Characterization of purified New Delhi metallo-β-lactamase-1.
Thomas PW, Zheng M, Wu S, Guo H, Liu D, Xu D, Fast W. Biochemistry. 2011 Nov 22;50(46):10102-13. doi: 10.1021/bi201449r. Epub 2011 Nov 1.
PMID: 22029287
Related citations Remove from clipboard
Kim, Y., Cunningham, M. A., Mire, J., Tesar, C., Sacchettini, J. & Joachimiak, A. NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J. 27, Epub ahead of print (2013).
King, D. T., Worrall, L. J., Gruninger, R. & Strynadka, N. C. J. New Delhi metallo-β- lactamase: structural insights into β-lactam recognition and inhibition. JACS 134, 11362-11365 (2012).


Metallo Beta-Lactamase GOLD docking paper (NOT New Delhi version though) - 071613 JTB
http://www.ncbi.nlm.nih.gov/pubmed/16378729