High throughput solid phase chemical synthesis utilizing thin cylindrical reaction vessels useable for biological assay

• US 5,798,035 A
• Filed: 10/03/1996
• Issued: 08/25/1998
• Est. Priority Date: 10/03/1996
• Status: Expired due to Term

• Current Assignee: Pharmacopeia, Inc.
• Original Assignee: Pharmacopeia, Inc.
• Inventors: Grubbs, Robert H., Kirk, Gregory L.
• Primary Examiner(s): Bell, Bruce F.
• Application Number:
  US08/726,058
• Time in Patent Office: 691 Days
• Field of Search: 422/55, 422/56, 422/57, 422/58, 422/59, 422/63, 422/82, 422/119, 422/129, 422/138, 422/188, 422/196, 422/197, 422/232, 422/233, 422/234, 422/236, 206/568, 206/569, 206/305, 206/459.5, 436/44, 436/52, 436/55, 436/47, 436/48, 436/49, 436/165, 436/169, 436/523, 436/527, 436/528, 436/518, 436/531, 436/535, 205/335
• US Class Current: 506/4
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00306 Reactor vessels in a multiple arrangement
• CPC Class Codes: B01J 2219/00308 interchangeably mounted in racks or blocks
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00355 peristaltic
• CPC Class Codes: B01J 2219/00389 Feeding through valves
• CPC Class Codes: B01J 2219/00418 using pressure
• CPC Class Codes: B01J 2219/00463 Directed sorting
• CPC Class Codes: B01J 2219/00495 Means for heating or cooling the reaction vessels
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00592 Split-and-pool, mix-and-divide processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 : the surface being inorganic
• CPC Class Codes: B01J 2219/00621 : by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00641 : the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 : the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2030/524 : structural properties
• CPC Class Codes: G01N 30/46 : using more than one column G01N30/44 takes precedence
• CPC Class Codes: G01N 30/466 : with separation columns in parallel
• CPC Class Codes: G01N 30/60 : Construction of the column
• CPC Class Codes: G01N 30/6043 : in parallel
• CPC Class Codes: Y10T 436/113332 : with conveyance of sample along a test line in a container or rack
• CPC Class Codes: Y10T 436/114165 : with step of insertion or removal from test line
• CPC Class Codes: Y10T 436/114998 : with treatment or replacement of aspirator element [e.g., cleaning, etc.]
• CPC Class Codes: Y10T 436/117497 : with a continuously flowing sample or carrier stream
• CPC Class Codes: Y10T 436/12 : Condition responsive control

Abstract

A high throughput chemical synthesis system utilizing cylindrical reaction vessels is disclosed. Reaction vessels are utilized which include a tubular member adapted for placement of electronically readable identifying indicia thereon. The identifying indicia are representative of reaction conditions within the tubular member and of one or more reagents utilized in a reaction within the tubular members. A method of performing chemical synthesis on solid phase reactive material within a plurality of reaction vessels using a plurality of reaction stages resulting in final products and employing identifying indicia representing the reaction stages is also disclosed. The method includes reading the identifying indicia located on the reaction vessels, reacting one or more reagents within the reaction vessels under particular reaction conditions which may be determined by reading the identifying indicia, thereby synthesizing chemical compounds within the reaction vessels. The method allows chemical synthesis to occur according to a predetermined set of reactions and also allows for combinatorial chemistry to be performed utilizing random mix and split techniques. The final synthesized products may be tested for chemical or biological activity. The chemical structures of desired end products may be obtained by reading recorded information wherein the reaction conditions and reagents of reaction steps have been recorded, preferably in conjunction with the identifying indicia.

Claims

1. A method of performing chemical synthesis on solid phase reactive material contained within a plurality of tubular reaction vessels, using one or more reaction stages, resulting in a plurality of final products and employing identifying indicia to represent specific reactions and reagents utilized during said one or more reaction stages, said method comprising:

reading said identifying indicia provided for each of a plurality of tubular reaction vessels,

reacting a reagent with said reactive material by flowing a reagent-containing solution through said tubular reaction vessels under particular reaction conditions, wherein said reacting is driven to completion within the reactive material by said flowing of reagent-containing solution through said tubular reaction vessels without agitation of said reactive material;

recording information concerning said reaction conditions and reagents, said information corresponding to said identifying indicia; and

repeating said reading and said reacting at least once using a different reagent, thereby synthesizing chemical compounds within said tubular reaction vessels.

2. The method of claim 1 wherein said identifying indicia comprise electronically readable indicia located on said tubular reaction vessels.

3. The method of claim 2 wherein said identifying indicia comprise a bar code and said reading step is performed using a bar code reader.

4. The method of claim 1 wherein said reactive material is coated on an inside wall of said tubular reaction vessel.

5. The method of claim 1 wherein said reactive material comprises a packing disposed within said tubular reaction vessels to allow reagents to flow through said tubular reaction vessels.

6. The method of claim 1 wherein said tubular reaction vessels are insertable into a reaction chamber wherein said reacting step is performed within said reaction chamber.

7. The method of claim 6 wherein said identifying indicia comprises the location of a tubular reaction vessel within said reaction chamber.

8. The method of claim 1 wherein said tubular reaction vessels are cylindrical in shape.

9. A method of performing chemical synthesis on solid phase reactive material contained within a plurality of tubular reaction vessels, using one or more reaction stages, resulting in a plurality of final products and employing identifying indicia to represent specific reactions and reagents utilized during said one or more reaction stages, said method comprising:

reading said identifying indicia provided for each of a plurality of tubular reaction vessels,

reacting a reagent with said reactive material by flowing a reagent-containing solution through said tubular reaction vessels under particular reaction conditions;

recording information concerning said reaction conditions and reagents, said information corresponding to said identifying indicia;

repeating said reading and said reacting at least once, thereby synthesizing chemical compounds within said tubular reaction vessels; and

wherein said tubular reaction vessel comprises a central rod axially oriented therein, said central rod being coated with said reactive material.

10. The method of claim 9 wherein said reactive material comprises a gel.

11. A method of performing chemical synthesis on solid phase reactive material contained within a plurality of tubular reaction vessels, using one or more reaction stages, resulting in a plurality of final products and employing identifying indicia to represent specific reactions and reagents utilized during said one or more reaction stages, said method comprising:

reading said identifying indicia provided for each of a plurality of tubular reaction vessels,

reacting a reagent with said reactive material by flowing a reagent-containing solution through said tubular reaction vessels under particular reaction conditions;

recording information concerning said reaction conditions and reagents, said information corresponding to said identifying indicia;

repeating said reading and said reacting at least once, thereby synthesizing chemical compounds within said tubular reaction vessels;

wherein said tubular reaction vessels are insertable into a reaction chamber, and wherein said reacting is performed within said reaction chamber; and

removing said tubular reaction vessels from said reaction chamber and sorting said tubular reaction vessels by reading said identifying indicia thereon.

12. The method of claim 11 further comprising sorting said tubular reaction vessels into two or more groups, said groups subsequently being inserted into separate reaction chambers.

13. The method of claim 11 wherein said sorting comprises sorting said tubular reaction vessels into at least a first and second group, and further comprising reacting a first reagent within the tubular reaction vessels of said first group and reacting a second reagent within the tubular reaction vessels of said second group.

14. The method of claim 13 further comprising testing the synthesized chemical compounds for a particular chemical or biological activity and identifying one or more of said compounds based upon said identifying indicia and the recorded information corresponding thereto.

15. The method of claim 14 further comprising transferring a portion of each of said chemical compounds from said tubular reaction vessels into one of a plurality of assay wells.

16. The method of claim 13 further comprising exposing said tubular reaction vessels to a controlled intensity light source.

17. The method of claim 11 wherein said identifying indicia comprises the location of a tubular reaction vessel within said reaction chamber.

18. A method of performing chemical synthesis on solid phase reactive material contained within a plurality of tubular reaction vessels, using one or more reaction stages, resulting in a plurality of final products and employing identifying indicia to represent specific reactions and reagents utilized during said one or more reaction stages, said method comprising:

reading said identifying indicia provided for each of a plurality of tubular reaction vessels;

reacting a reagent with said reactive material by flowing a reagent-containing solution through said tubular reaction vessels under particular reaction conditions;

recording information concerning said reaction conditions and reagents, said information corresponding to said identifying indicia;

repeating said reading and said reacting at least once, thereby synthesizing chemical compounds within said tubular reaction vessels; and

removing said tubular reaction vessels from said reaction chamber and randomly sorting said tubular reaction vessels into at least a first and second group.

19. The method of claim 18 further comprising reacting a first reagent within the tubular reaction vessels of said first group and reacting a second reagent within the tubular reaction vessels of said second group.

20. The method of claim 19 further comprising testing the synthesized chemical compounds for a particular chemical or biological activity and identifying one or more of said compounds based upon said identifying indicia and the recorded information corresponding thereto.

21. The method of claim 20 further comprising transferring a portion of each of said chemical compounds from said tubular reaction vessels into one of a plurality of assay wells.

22. The method of claim 19 further comprising exposing said tubular reaction vessels to a controlled intensity light source.

23. A chemical synthesis reaction vessel for performing combinatorial chemistry within a solid phase reactive material, said reaction vessel comprising:

a tubular member, said tubular member allowing reagent-containing solution to flow therethrough and having electronically readable identifying indicia thereon, said identifying indicia representing reaction conditions which have occurred or which will occur within said tubular member and representing reagents reacted or to be reacted within said tubular member; and

wherein said solid phase reactive material is disposed within said tubular member such that axial flow of reagent-containing solution through said tubular member causes the reagent-containing solution to be in communication with all of said reactive material and allows reactions to be driven to completion within the reactive material without agitation of the reactive material.

24. The reaction vessel of claim 23 wherein said identifying indicia comprise a bar code.

25. The reaction vessel of claim 24 wherein said bar code is located at a first end of the tubular member.

26. The reaction vessel of claim 23 wherein said tubular member is coated with said reactive material on an inside surface thereof.

27. The reaction vessel of claim 26 wherein said coating of reactive material on the inside surface of said tubular member is 25-100 microns thick.

28. The reaction vessel of claim 23 wherein said tubular member comprises a photo-transparent material.

29. The reaction vessel of claim 23 wherein said reactive material comprises a packing disposed within said tubular member and said reactive vessel further comprises at least one frit located within at least one end of the tubular member, said frit allowing fluid reagents to flow therethrough while retaining said packing therewithin.

30. The reaction vessel of claim 23 wherein said tubular member comprises an elongate uniformly cylindrical vessel which can be aligned and sorted in a rolling motion.

31. The apparatus of claim 30 further comprising means for controlling flow rate through said plurality of tubular reaction vessels when disposed within said one or more reaction chambers.

33. The reaction vessel of claim 26 or 32 wherein said reactive material comprises a gel.

32. A chemical synthesis reaction vessel for performing combinatorial chemistry comprising:

a tubular member, said tubular member allowing reagent-containing solution to flow therethrough and having electronically readable identifying indicia thereon, said identifying indicia representing reaction conditions which have occurred or which will occur within said tubular member and representing reagents reacted or to be reacted within said tubular member;

a solid phase reactive material disposed within said tubular member to allow for axial flow of reagent-containing solution through said tubular member in communication with said reactive material; and

an elongate rod coaxially oriented within said tubular member, said elongate rod being coated with said reactive material.

34. An apparatus for performing chemical synthesis by performing a series of reactions on solid phase reactive material comprising:

a plurality of tubular reaction vessels having electronically readable identifying indicia disposed thereon, said tubular reaction vessels containing a solid phase reactive material therein and allowing reagent-containing solution to flow therethrough, wherein said solid phase reactive material is disposed within each tubular reaction vessel such that flow of reagent-containing solution therethrough causes the reagent-containing solution to be in communication with all of said reactive material and allows reactions to be driven to completion within the reactive material without agitation of the solid phase reactive material; and

one or more reaction chambers for receiving said tubular reaction vessels therein, each of said reaction chambers having an inlet disposed to allow said reagent-containing solution to flow into said reaction chamber and axially through said tubular reaction vessels disposed therein.

35. The apparatus of claim 34 further comprising one or more guide arrays insertable into said one or more reaction chambers, each guide array receiving said tubular reaction vessels therein.

36. The apparatus of claim 34 further comprising a temperature-controlled enclosure surrounding said one or more reaction chambers.

37. The apparatus of claim 34 wherein each of said tubular reaction vessels is identically sized to allow substantially even flow of reagent-containing solution therethrough.

38. The apparatus of claim 34 wherein each of said tubular reaction vessels comprises an elongate uniformly cylindrical vessel which can be aligned and sorted in a rolling motion.

39. An apparatus for performing chemical synthesis by performing a series of reactions on solid phase reactive material comprising:

a plurality of tubular reaction vessels having electronically readable identifying indicia disposed thereon, said tubular reaction vessels containing a solid phase reactive material therein and allowing reagent-containing solution to flow therethrough;

one or more reaction chambers for receiving said tubular reaction vessels therein, each of said reaction chambers having an inlet disposed to allow said reagent-containing solution to flow into said reaction chamber and axially through said tubular reaction vessels disposed therein;

one or more guide arrays insertable into said one or more reaction chambers, each guide array receiving said tubular reaction vessels therein; and

wherein said inlet is located within a first reaction chamber cover.

40. The apparatus of claim 39 further comprising a guide cap, said guide cap comprising a plurality of apertures therein and being located between said inlet and one of said guide arrays, wherein said apertures are aligned with said tubular reaction vessels to allow said reagent to flow from said inlet into, and axially through, said tubular reaction vessels.

41. The apparatus of claim 40 further comprising a second guide cap, said second guide cap having a plurality of apertures therein and being located between one of said guide arrays and an outlet of each of said reaction chambers, wherein said apertures are aligned with said tubular reaction vessels to allow fluid reagents to flow from said tubular reaction vessels to said outlet.

42. The apparatus of claim 41 wherein said outlet is located within a second reaction chamber cover, said first and second reaction chamber covers being located at opposite ends of a reaction chamber.

43. An apparatus for performing chemical synthesis by performing a series of reactions on solid phase reactive material comprising:

a plurality of tubular reaction vessels having electronically readable identifying indicia disposed thereon, said tubular reaction vessels containing a solid phase reactive material therein and allowing reagent-containing solution to flow therethrough;

one or more reaction chambers for receiving said tubular reaction vessels therein, each of said reaction chambers having an inlet disposed to allow said reagent-containing solution to flow into said reaction chamber and axially through said tubular reaction vessels disposed therein; and

wherein said one or more reaction chambers are in fluid flow relationship to an array valve, said array valve being in fluid flow relationship with a plurality of reservoirs wherein said array valve distributes reagents from said reservoirs to the one or more reaction chambers.

44. The apparatus of claim 43 further comprising one or more pumps placed in fluid flow relationship between said array valve and said one or more reaction chambers.

45. The apparatus of claim 43 further comprising extrusion means, said extrusion means being insertable into said reaction chambers and guide array to remove said tubular reaction vessels therefrom.

46. The apparatus of claim 45 further comprising sorting means configured to receive tubular reaction vessels extruded from said reaction chambers.

47. The apparatus of claim 46 wherein said sorting means comprises a reader for reading said identifying indicia on said tubular reaction vessels.

48. The apparatus of claim 47 wherein said sorting means further comprises means for moving extruded tubular reaction vessels from a hopper.

49. The apparatus of claim 48 further comprising means for receiving said extruded tubular reaction vessels therein from said sorting means and for delivering said extruded reaction vessels to said reaction chamber.

50. The apparatus of claim 48 further comprising transport and fluid delivery means configured to receive reaction vessels therein and to align said reaction vessels with a plurality of wells in an assay plate.

51. The apparatus of claim 50 wherein said transport and fluid delivery means comprise a robotic pipettor.

52. The apparatus of claim 45 wherein said means for moving extruded reaction vessels comprises a ramp or a belt.

53. The apparatus of claim 52 wherein said means for moving extruded reaction vessels further comprises a vessel director disposed to move said tubular reaction vessels from said ramp or belt into a vessel loading device.

54. The apparatus of claim 53 wherein said vessel loading device receives a reaction chamber and guide array therein, said vessel loading device being moveable along a first and second axis.

55. A method of chemically synthesizing compounds for direct delivery to a biological assay comprising:

performing a series of reaction steps on a solid phase reactive material contained within a plurality of tubular reaction vessels having identifying indicia thereon, one or more of said reaction steps being performed using reactive agents and under conditions which may be determined by electronically reading said identifying indicia;

sorting said tubular reaction vessels into an array based upon the identifying indicia; and

transferring synthesized biological compounds from within said array of vessels into an assay plate.

56. The method of claim 55 further comprising:

randomly sorting said tubular reaction vessels after one of said reaction steps into at least a first group and second group of reaction vessels;

reacting a first reagent within the reaction vessels of said first group; and

reacting a second reagent within the reaction vessels of said second group.

57. The method of claim 56 wherein said tubular reaction vessels are sorted into more than one array and said compounds are deposited into more than one assay plate.

58. The method of claim 55 wherein said identifying indicia comprise a bar code.

59. The method of claim 55 wherein said reactive material is coated on the inside of said tubular reaction vessels.

60. The method of claim 55 wherein said solid phase reactive material comprises a packing retained within said reaction vessels by frits disposed within the ends of said reaction vessels.

61. The method of claim 55 wherein said reaction steps are performed in one or more reaction chambers configured to receive one or more of said tubular reaction vessels therein, wherein each tubular reaction vessel within a particular reaction chamber is exposed to the same chemical reagent or reaction conditions during a particular reaction step.

62. The method of claim 61 further comprising loading an elution solvent into said tubular reaction vessels.

63. The method of claim 62 wherein said tubular reaction vessels are exposed to ultraviolet radiation to release said compounds from the tubular reaction vessels.

64. The method of claim 63 wherein said compounds are deposited into said assay plate by dipping an end of a tubular reaction vessel into the surface of said assay plate.

65. A method of performing chemical synthesis on solid phase reactive material within a plurality of reaction vessels, said method comprising:

separating tubular reaction vessels into a plurality of groups and inserting each group into a different reaction chamber, said tubular reaction vessels allowing reagent-containing solution to flow therethrough and having said reactive material therein;

reacting a reagent with said reactive material within one or more of said groups of tubular reaction vessels by flowing said reagent through said reaction chambers;

recording data, said data being representative of reaction conditions and reagents within a tubular reaction vessel during said reacting step and being recorded in conjunction with information about the location of the reaction vessel in a particular chamber; and

repeating said separating, reacting and recording steps at least once.

66. The method of claim 65 further comprising

testing final products synthesized within said tubular reaction vessels;

and

identifying one or more reaction vessels having a desired final product synthesized therein.

67. The method of claim 66 further comprising evaluating said data for the one or more reaction vessels having said desired final product synthesized therein to determine the process by which said product was synthesized, so as to thereby identify said product.

68. The method of claim 66 wherein said reactive material comprises a gel.

69. A method of identifying synthesized compounds having a desired biological or chemical activity, said compounds having been synthesized during multiple reaction stages on solid phase reactive material contained within reaction vessels, said method comprising:

transferring synthesized compounds from said reaction vessels to a testing medium, said reaction vessels being tubular in shape and comprising electronically readable identifying indicia thereon representing reaction conditions which have occurred within said tubular reaction vessels;

testing for a desired biological or chemical activity the synthesized compounds transferred from said reaction vessels to said testing medium; and

electronically reading the identifying indicia on the reaction vessel wherein was synthesized a compound having said desired biological or chemical activity.

70. The method of claim 69 further comprising reading recorded information wherein specific identifying indicia correspond with specific reaction histories.

71. The method of claim 70 wherein said recorded information is used to determine the structure of said compound.

72. The method of claim 71 wherein said transferring synthesized compounds from tubular reaction vessels to a testing medium comprises depositing said compounds into an assay.

73. The method of claim 72 further comprising loading an elution solvent into said reaction vessels.

74. The method of claim 73 further comprising exposing said reaction vessels to ultraviolet radiation to release said compound from said reaction vessels.

75. The method of claim 74 wherein said compounds are deposited into said assay by dipping an end of a reaction vessel into said assay.

76. The method of claim 75 wherein said identifying indicia comprise a bar code and said reading step is performed using a bar code reader.

77. The method of claim 71 or 72 wherein said reactive material comprises a gel.

78. The method of claim 77 wherein said tubular reaction vessels are configured for insertion into a reaction chamber and wherein said reacting is performed within one or more reaction chambers.