U.S. patent application number 13/966628 was filed with the patent office on 2014-10-30 for nanopore device for drug-like molecule screening or lead optimization to a targeted protein.
This patent application is currently assigned to International Business Machines Corporation. The applicant listed for this patent is International Business Machines Corporation. Invention is credited to BINQUAN LUAN, RUHONG ZHOU.
Application Number | 20140318970 13/966628 |
Document ID | / |
Family ID | 51788333 |
Filed Date | 2014-10-30 |
United States Patent
Application |
20140318970 |
Kind Code |
A1 |
LUAN; BINQUAN ; et
al. |
October 30, 2014 |
NANOPORE DEVICE FOR DRUG-LIKE MOLECULE SCREENING OR LEAD
OPTIMIZATION TO A TARGETED PROTEIN
Abstract
A nanosensor for detecting molecule characteristics includes a
membrane having an opening configured to permit a charged molecule
to pass but to block a protein molecule attached to a ligand
connecting to the charged molecule, the opening being filled with
an electrolytic solution. An electric field generator is configured
to generate an electric field relative to the opening to drive the
charged molecule through the opening. A sensor circuit is coupled
to the electric field generator to sense current changes due to
charged molecules passing into the opening. The current changes are
employed to trigger a bias field increase to cause separation
between the ligand and the protein to infer an interaction
strength.
Inventors: |
LUAN; BINQUAN; (CHAPPAQUA,
NY) ; ZHOU; RUHONG; (STORMVILLE, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
International Business Machines Corporation |
Armonk |
NY |
US |
|
|
Assignee: |
International Business Machines
Corporation
Armonk
NY
|
Family ID: |
51788333 |
Appl. No.: |
13/966628 |
Filed: |
August 14, 2013 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
13873854 |
Apr 30, 2013 |
|
|
|
13966628 |
|
|
|
|
Current U.S.
Class: |
204/601 ;
977/781; 977/924 |
Current CPC
Class: |
G01N 33/6872 20130101;
B82Y 30/00 20130101; G01N 33/48721 20130101 |
Class at
Publication: |
204/601 ;
977/781; 977/924 |
International
Class: |
G01N 27/447 20060101
G01N027/447 |
Claims
1. A nanosensor for detecting molecule characteristics, comprising:
a membrane having an opening configured to permit a charged
molecule to pass but to block a protein molecule attached to a
ligand connecting to the charged molecule, the opening being filled
with an electrolytic solution; an electric field generator
configured to generate an electric field relative to the opening to
drive the charged molecule through the opening; and a sensor
circuit coupled to the electric field generator to sense current
changes due to charged molecules passing into the opening, the
current changes being employed to trigger a bias field increase to
cause separation between the ligand and the protein molecule to
infer an interaction strength.
2. The nanosensor as recited in claim 1, wherein the opening
includes one of a nanopore and a channel.
3. The nanosensor as recited in claim 1, wherein the electric field
generator includes a battery and two electrodes disposed across
opposite ends of the opening.
4. The nanosensor as recited in claim 1, wherein the sensor circuit
measures current drops and durations to determine when to trigger
the bias field.
5. The nanosensor as recited in claim 1, wherein the ligand
includes a drug molecule.
6. The nanosensor as recited in claim 1, wherein the charged
molecule includes a closed functionalized end having charged
chemical groups.
7. The nanosensor as recited in claim 1, wherein the charged
particle includes one of a carbon nanotube, DNA and a
nano-wire.
8. The nanosensor as recited in claim 1, wherein the charged
particle is pulled through the opening using the biasing field and
ruptured at a critical voltage value, the critical voltage value
being determined to infer an interaction strength between the
ligand and the protein molecule.
9. A nanosensor for detecting molecule characteristics, comprising:
a membrane having one or more openings, each opening being
configured to permit a charged carbon nanotube to pass but to block
a protein molecule attached to a ligand connecting to the carbon
nanotube, the one or more openings being filled with an
electrolytic solution; an electric field generator configured to
generate an electric field relative to the opening to drive the
charged carbon nanotubes through the one or more openings; and a
sensor circuit coupled to the electric field generator to sense
current changes due to charged carbon nanotubes passing through the
one or more openings, the current changes being employed to trigger
an increase in the electric field to cause a force of separation
between the ligand and the protein molecule at a critical voltage
value, the critical voltage value being employed to infer an
interaction strength between the ligand and the protein
molecule.
10. The nanosensor as recited in claim 9, wherein the opening
includes one of a nanopore and a channel.
11. The nanosensor as recited in claim 9, wherein the electric
field generator includes a battery and two electrodes disposed
across opposite ends of the one or more openings.
12. The nanosensor as recited in claim 9, wherein the sensor
circuit measures current drops and durations to determine when to
trigger the increase.
13. The nanosensor as recited in claim 9, wherein the charged
carbon nanotube includes a closed functionalized end having charged
chemical groups.
14. The nanosensor as recited in claim 13, wherein the charged
chemical groups include carboxyl groups.
Description
RELATED APPLICATION INFORMATION
[0001] This application is a Continuation application of co-pending
U.S. patent application Ser. No. 13/873,854 filed on Apr. 30, 2013,
incorporated herein by reference in its entirety.
[0002] This application is related to commonly assigned U.S. patent
application Ser. No. 13/873,815 filed on Apr. 30, 2013,
incorporated herein by reference in its entirety.
BACKGROUND
[0003] 1. Technical Field
[0004] The present invention relates to sensors, and more
particularly to nanopore sensors and methods for detecting
interaction between carbon nanotubes and proteins.
[0005] 2. Description of the Related Art
[0006] Developing low-cost and high-throughput methods to screen
designed drug-like molecules facilitates drug discovery and
biomedical research in general. However, current methods of drug
screening usually involve tedious sample-preparation and costly
biological/chemical experiments.
SUMMARY
[0007] A nanosensor for detecting molecule characteristics includes
a membrane having an opening configured to permit a charged
molecule to pass but to block a protein molecule attached to a
ligand connecting to the charged molecule, the opening being filled
with an electrolytic solution. An electric field generator is
configured to generate an electric field relative to the opening to
drive the charged molecule through the opening. A sensor circuit is
coupled to the electric field generator to sense current changes
due to charged molecules passing into the opening. The current
changes are employed to trigger a bias field increase to cause
separation between the ligand and the protein to infer an
interaction strength.
[0008] A nanosensor for detecting molecule characteristics includes
a membrane having one or more openings, each opening being
configured to permit a charged carbon nanotube to pass but to block
a protein molecule attached to a ligand connecting to the carbon
nanotube, the one or more openings being filled with an
electrolytic solution. An electric field generator is configured to
generate an electric field relative to the opening to drive the
charged carbon nanotubes through the one or more openings. A sensor
circuit is coupled to the electric field generator to sense current
changes due to charged carbon nanotubes passing through the one or
more openings. The current changes are employed to trigger an
increase in the electric field to cause a force of separation
between the ligand and the protein molecule at a critical voltage
value, the critical voltage value being employed to infer an
interaction strength between the ligand and the protein
molecule.
[0009] A method for detecting molecule characteristics includes
generating an electric field across a membrane having an opening to
drive a charged molecule through the opening, the charged molecule
being connected to a ligand, the ligand being bonded to a protein
molecule, the opening being configured to permit the charged
molecule to pass but to block the protein molecule attached to the
charged particle, the opening being filled with an electrolytic
solution; sensing current changes due to the charged molecule
passing into or through the opening; biasing the electric field to
cause a separation between the ligand and the protein molecule; and
correlating a voltage at the separation to measure a characteristic
of a protein molecule to ligand interaction.
[0010] These and other features and advantages will become apparent
from the following detailed description of illustrative embodiments
thereof, which is to be read in connection with the accompanying
drawings.
BRIEF DESCRIPTION OF DRAWINGS
[0011] The disclosure will provide details in the following
description of preferred embodiments with reference to the
following figures wherein:
[0012] FIG. 1 is a schematic diagram showing a nanopore-based
device for drug screening wherein a complex is electrophoretically
driven through a nanopore that separates cis. and trans. chambers
in accordance with one embodiment;
[0013] FIG. 2 is a schematic diagram showing the nanopore-based
device of FIG. 1 with increased electric field biasing where the
complex is physically stuck in the nanopore in accordance with the
present principles;
[0014] FIG. 3 is a schematic diagram showing the nanopore-based
device of FIG. 2, after a rupture between a drug molecule and a
targeted protein occurs due to an elevated biasing electric field
in accordance with the present principles;
[0015] FIG. 4 shows time-dependent ionic-current signals when
electrically driving a complex through a nanopore in accordance
with one embodiment; and
[0016] FIG. 5 is an illustrative plot showing binding affinity
versus critical voltage for determining separation strength between
CNTs and proteins in accordance with the present principles;
[0017] FIG. 6 is a cross-sectional view of a channel based sensor
in accordance with another embodiment;
[0018] FIG. 7 is a cross-sectional view of a multiple nanopore
sensor in accordance with another embodiment;
[0019] FIG. 8 is a cross-sectional view of a multiple channel
sensor in accordance with yet another embodiment; and
[0020] FIG. 9 is a block/flow diagram showing a method for
nanosensing in accordance with illustrative embodiments.
DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS
[0021] In accordance with the present principles, a drug-screening
device is provided that employs a physical method with little to no
sample preparation. The drug-screening device can provide a
low-cost and high-throughput method for screening drugs. A nanopore
is employed as a force sensor to detect an affinity between a drug
molecule (ligand) and a targeted protein molecule (receptor). The
binding affinity of the complex can be derived from measured
electric signals. The application of this ultra-sensitive (e.g.,
for a binding energy of a few k.sub.BT (e.g., 1-10) between the
ligand and the protein) screening device could greatly accelerate
the process of developing new drugs, particularly for narrow
screening and lead optimization.
[0022] Screening is a method for scientific experimentation used in
drug discovery. Using robotics, data processing and control
software, liquid handling devices, and sensitive detectors,
screening permits a researcher to quickly conduct millions of
chemical, genetic or pharmacological tests. Through this process
one can rapidly identify active compounds, antibodies or genes
which modulate a particular biomolecular pathway. The results of
these experiments provide starting points for drug design and for
understanding the interaction or role of a particular biochemical
process in biology. Lead optimization is the process of optimizing
a drug and bringing a new drug to market once a lead compound has
been identified through a drug discovery process. By employing the
present principles, narrow screening and lead optimization are
improved by reducing the time and resources needed for these and
other drug discovery processes.
[0023] In one embodiment, a method and device are provided for
detecting an affinity of a drug molecule to a targeted protein
molecule using a nanopore (a nanometer-sized hole in a thin
membrane). The binding affinity of a complex may also be detected
using multiple nanopores, a fluidic channel or multiple fluidic
channels to screen drug molecules (ligands) to a targeted protein
molecule (receptor). A charged carbon nanotube (CNT) is employed to
determine the binding affinity; however, the CNT may be replaced
with other linear and charged molecules (such as DNA or a
nano-wire).
[0024] It is to be understood that the present invention will be
described in terms of a given illustrative architecture having a
nanopore; however, other architectures, structures, materials and
process features and steps may be varied within the scope of the
present invention.
[0025] It will also be understood that when an element such as a
layer, region, membrane, etc. is referred to as being "on" or
"over" another element, it can be directly on the other element or
intervening elements may also be present. In contrast, when an
element is referred to as being "directly on" or "directly over"
another element, there are no intervening elements present. It will
also be understood that when an element is referred to as being
"connected" or "coupled" to another element, it can be directly
connected or coupled to the other element or intervening elements
may be present. In contrast, when an element is referred to as
being "directly connected" or "directly coupled" to another
element, there are no intervening elements present.
[0026] Reference in the specification to "one embodiment" or "an
embodiment" of the present principles, as well as other variations
thereof, means that a particular feature, structure,
characteristic, and so forth described in connection with the
embodiment is included in at least one embodiment of the present
principles. Thus, the appearances of the phrase "in one embodiment"
or "in an embodiment", as well any other variations, appearing in
various places throughout the specification are not necessarily all
referring to the same embodiment.
[0027] It is to be appreciated that the use of any of the following
"/", "and/or", and "at least one of", for example, in the cases of
"A/B", "A and/or B" and "at least one of A and B", is intended to
encompass the selection of the first listed option (A) only, or the
selection of the second listed option (B) only, or the selection of
both options (A and B). As a further example, in the cases of "A,
B, and/or C" and "at least one of A, B, and C", such phrasing is
intended to encompass the selection of the first listed option (A)
only, or the selection of the second listed option (B) only, or the
selection of the third listed option (C) only, or the selection of
the first and the second listed options (A and B) only, or the
selection of the first and third listed options (A and C) only, or
the selection of the second and third listed options (B and C)
only, or the selection of all three options (A and B and C). This
may be extended, as readily apparent by one of ordinary skill in
this and related arts, for as many items listed.
[0028] Referring now to the drawings in which like numerals
represent the same or similar elements and initially to FIG. 1, a
cross-sectional view shows a sensor device 10 with a complex 12
moving through a nanopore 14. The complex 12 includes a targeted
protein molecule 15, a drug molecule 16, and a
ligand-functionalized molecule 18 such as a carbon nanotube (CNT)
or other charged molecule, e.g., DNA or portion thereof, nanowire,
etc.). For illustrative purposes molecule 18 will be references as
a CNT 18. A protein ligand is an atom, a molecule or an ion which
can bind to a specific site (the binding site) on a protein.
Alternative names used to mean a protein ligand are affinity
reagents or protein binders. Antibodies are the most widely used
protein ligands; however, other molecules such as protein
scaffolds, nucleic acids, peptides may also be used.
[0029] A first end portion 20 of the CNT 18 is functionalized with
charged chemical groups (such as a carboxyl group or amines). The
charged CNT 18 allows electrophoretic motion of the complex in a
biasing electric field 22. The biasing field 22 is generated by a
DC source such as a battery 24 or the like connected across two
electrodes 26 and 28. A second end portion 30 of the CNT has a
functionalized group that can be further chemically bonded with
various test drug-molecules 16, e.g. drug molecules to be
tested.
[0030] Two fluidic chambers 36, 38 (cis. and trans., respectively)
are separated by a membrane 32 and connected via the nanopore 14.
The membrane 32 may include, for example, SiO.sub.2 or
Si.sub.3N.sub.4 or any other suitable material. CNT 18 is
configured with test drug-molecules 16 and allowed to interact or
mix with protein molecules 15 to form a connection. The size of the
nanopore 14 (or nanochannel) should be larger than a size of the
CNT 18 and smaller than the size of the target protein 15, e.g. 3
nm in diameter.
[0031] A sensor circuit 25 is coupled to the electric field
generator 23 to sense current changes due to charged carbon
nanotubes passing into the opening, and to bias the electric field
generator 23 (control or bias the battery 26) through feedback 27
to reach and determine a critical voltage. The critical voltage, in
turn, is employed to determine a force of separation between the
drug molecule 16 and the protein molecule 15.
[0032] The biasing electric field circuit or field generating
circuit 23 is applied across the membrane 32, by inserting two
electrodes 26, 28 (such as, e.g., Ag/AgCl electrodes connected to
the battery 24, other electrode types may also be employed) into
cis. (this side) and trans. (the other side) chambers 36, 38,
respectively. The biasing voltage can range from about 100 mV to
about 1 V.
[0033] The fluid chambers 36, 38 are compartments that are
configured to store a solution containing test molecules. The
solution is electrolytic and may include a 1M solution, although
other solution concentrations may be employed. The complex 12 can
be prepared by mixing the tested protein molecules with
funtionalized CNTs (or other charged molecules) in the electrolyte
solution. Funtionalized CNTs include drug molecules or ligands to
be tested with the protein.
[0034] The sensor circuit 25 is coupled to the circuit 23 to
measure changes in current. The sensor 25 may include known devices
for accurately measuring transient currents in the circuit 23, such
as a patch clamp amplifier. After binding of the test drug-molecule
16 to the targeted protein molecule 15 in an electrolyte of the cis
chamber 36, the entire complex 12 is then electrically driven
towards and through the nanopore 14.
[0035] Referring to FIG. 2, in the biasing electric field 22, the
charged CNT 18 is electrically driven into the nanopore 14. The
nanopore 14 needs to be larger in size than the diameter of the CNT
18 and less than the size of the protein molecule 15. Therefore,
during the translocation process, the protein molecule 15 is too
large to move through the nanopore 14 and is stuck at the entrance
of the nanopore 14.
[0036] Referring to FIG. 3, when a biasing voltage at a critical
value (V.sub.cr) or higher is achieved, the CNT 18 can be further
pulled through the nanopore 14. The interaction strength (thus the
binding affinity) between a CNT-connected ligand 16 and the protein
molecule 15 can be inferred from the critical value V.sub.cr (e.g.,
the biasing voltage at separation).
[0037] Referring to FIG. 4, the translocation process can be
monitored by measuring the ionic current through the nanopore 14.
Time-dependent current signals during a translocation/rupture event
are illustratively shown in a plot of current (I) versus time (t).
At the beginning, the complex is outside the nanopore, and
I.sub.open is the open-pore current. At the time t.sub.1, the
complex enters the pore and the ionic current I.sub.block1 is
reduced. This is due to the fact that the complex partially blocks
the nanopore. If the biasing voltage is less than the critical
value, the current remains constant at I.sub.block1. At time
t.sub.2, the biasing voltage is increased to allow a larger pulling
force on the CNT. If the biasing voltage is larger than a critical
value V.sub.cr, the complex is pulled apart and the CNT is further
driven through the pore, and the pore becomes less blocked. Thus,
the ionic current through the pore increases to I.sub.block2.
[0038] Therefore, by monitoring a biasing voltage, it is possible
to determine the critical biasing voltage at which a rupture
between the CNT and the protein molecule occurs. The rupture force
can be estimated using q.sub.effV.sub.cr/d, where q.sub.eff is the
effective charge of the CNT after ionic screening in an electrolyte
and d is the thickness of a solid-state membrane.
[0039] Referring to FIG. 5, a plot of binding affinity versus
critical voltage illustrates a relation that can be determined
experimentally or theoretically. The binding affinity can be
inferred from the critical voltage at which the rupture between a
CNT and a protein molecule occurs. This provides a high-throughput
and low-cost way to determine the interaction between a CNT and a
protein molecule. Binding affinity may be employed as one
indication of an interaction between a ligand or drug molecule and
a protein.
[0040] Referring to FIG. 6, another embodiment shows a planar
channel 40 employed instead of a nanopore 14. The planar channel 40
is configured to permit the CNT-protein complex to be separated
such that the CNT 18 passes into the channel 40 and the protein
molecule 15 (not shown) does not. An electric field is applied as
before with the battery 24 and electrodes 26, 28 being employed to
provide the field and to measure the current changes due to the
CNT-protein complex as before. The planar channel 40 has a channel
constriction size being less than that of the protein molecule
15.
[0041] Referring to FIG. 7, in another embodiment, multiple
nanopores 114 may be employed through a same membrane 142. The
nanopores 114 function as parallel paths to process CNT-protein
complexes more rapidly. A battery 126 and electrodes 122, 124 are
dispersed or distributed to create the electric field.
[0042] Referring to FIG. 8, in another embodiment, instead of
multiple nanopores 114, multiple channels 140 may be employed.
[0043] Referring to FIG. 9, a method for detecting molecule
characteristics is illustratively shown. It should be noted that,
in some alternative implementations, the functions noted in the
blocks may occur out of the order noted in the figures. For
example, two blocks shown in succession may, in fact, be executed
substantially concurrently, or the blocks may sometimes be executed
in the reverse order, depending upon the functionality involved. It
will also be noted that each block of the block diagrams and/or
flowchart illustration, and combinations of blocks in the block
diagrams and/or flowchart illustration, can be implemented by
special purpose hardware-based systems (e.g., circuitry, memory,
etc.) that perform the specified functions or acts, or combinations
of special purpose hardware and computer instructions.
[0044] In block 202, an electric field is generated across a
membrane having an opening to drive a charged molecule, e.g., a
carbon nanotube, through the opening. The charged molecule may
include a closed functionalized end having charged chemical groups
therein. The charged molecule (carbon nanotube) is connected to a
ligand, and the ligand is bonded to a protein molecule.
[0045] The opening may include one or more nanopores or one or more
channels. The opening is configured to permit the charged carbon
nanotube to pass but to block the protein molecule attached to the
carbon nanotube. The opening is filled with an electrolytic
solution. In block 204, current changes due to the charged carbon
nanotube passing into or through the opening are sensed. The
sensing may include measuring current drops and durations to
determine a blockage in the opening. Sensing current changes are
employed to trigger increasing a biasing value to determine a
critical voltage value at which separating occurs between the
carbon nanotube and the molecule to infer interaction strength (or
affinity).
[0046] In block 206, the electric field is biased to cause a
separation between the ligand and the protein molecule. In block
208, a voltage at the separation is determined and used to
correlate to a characteristic of the protein molecule to ligand
interaction. The characteristic may include an affinity between the
ligand and the protein molecule. This information may be employed
in drug screening applications, or lead optimizations.
[0047] Having described preferred embodiments for a nanopore device
and method for drug-like molecule screening or lead optimization to
a targeted protein (which are intended to be illustrative and not
limiting), it is noted that modifications and variations can be
made by persons skilled in the art in light of the above teachings.
It is therefore to be understood that changes may be made in the
particular embodiments disclosed which are within the scope of the
invention as outlined by the appended claims. Having thus described
aspects of the invention, with the details and particularity
required by the patent laws, what is claimed and desired protected
by Letters Patent is set forth in the appended claims.
* * * * *