MPEP 2144.09
Close Structural Similarity Between Chemical Compounds (Homologs, Analogues, Isomers)

This is the Ninth Edition of the MPEP, Revision 08.2017, Last Revised in January 2018

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2144.09    Close Structural Similarity Between Chemical Compounds (Homologs, Analogues, Isomers) [R-08.2017]

[Editor Note: This MPEP section is applicable to applications subject to the first inventor to file (FITF) provisions of the AIA except that the relevant date is the "effective filing date" of the claimed invention instead of the "time the invention was made," which is only applicable to applications subject to pre-AIA 35 U.S.C. 102. See 35 U.S.C. 100 (note) and MPEP § 2150 et seq.]

I.    REJECTION BASED ON CLOSE STRUCTURAL SIMILARITY IS FOUNDED ON THE EXPECTATION THAT COMPOUNDS SIMILAR IN STRUCTURE WILL HAVE SIMILAR PROPERTIES

A prima facie case of obviousness may be made when chemical compounds have very close structural similarities and similar utilities. "An obviousness rejection based on similarity in chemical structure and function entails the motivation of one skilled in the art to make a claimed compound, in the expectation that compounds similar in structure will have similar properties." In re Payne, 606 F.2d 303, 313, 203 USPQ 245, 254 (CCPA 1979). See In re Papesch, 315 F.2d 381, 137 USPQ 43 (CCPA 1963) (discussed in more detail below) and In re Dillon, 919 F.2d 688, 16 USPQ2d 1897 (Fed. Cir. 1990) (discussed below and in MPEP § 2144) for an extensive review of the case law pertaining to obviousness based on close structural similarity of chemical compounds. See also MPEP § 2144.08, subsection II.A.4.(c).

II.    HOMOLOGY AND ISOMERISM ARE FACTS WHICH MUST BE CONSIDERED WITH ALL OTHER RELEVANT FACTS IN DETERMINING OBVIOUSNESS

Compounds which are position isomers (compounds having the same radicals in physically different positions on the same nucleus) or homologs (compounds differing regularly by the successive addition of the same chemical group, e.g., by -CH2- groups) are generally of sufficiently close structural similarity that there is a presumed expectation that such compounds possess similar properties. In re Wilder, 563 F.2d 457, 195 USPQ 426 (CCPA 1977). See also In re May, 574 F.2d 1082, 197 USPQ 601 (CCPA 1978) (stereoisomers prima facie obvious).

Isomers having the same empirical formula but different structures are not necessarily considered equivalent by chemists skilled in the art and therefore are not necessarily suggestive of each other. Ex parte Mowry, 91 USPQ 219 (Bd. App. 1950) (claimed cyclohexylstyrene not prima facie obvious over prior art isohexylstyrene). Similarly, homologs which are far removed from adjacent homologs may not be expected to have similar properties. In re Mills, 281 F.2d 218, 126 USPQ 513 (CCPA 1960) (prior art disclosure of C8 to C12 alkyl sulfates was not sufficient to render prima facie obvious claimed C1 alkyl sulfate).

Homology and isomerism involve close structural similarity which must be considered with all other relevant facts in determining the issue of obviousness. In re Mills, 281 F.2d 218, 126 USPQ 513 (CCPA 1960); In re Wiechert, 370 F.2d 927, 152 USPQ 247 (CCPA 1967). Homology should not be automatically equated with prima facie obviousness because the claimed invention and the prior art must each be viewed "as a whole." In re Langer, 465 F.2d 896, 175 USPQ 169 (CCPA 1972) (Claims to a polymerization process using a sterically hindered amine were held unobvious over a similar prior art process because the prior art disclosed a large number of unhindered amines and only one sterically hindered amine (which differed from a claimed amine by 3 carbon atoms), and therefore the reference as a whole did not apprise the ordinary artisan of the significance of hindered amines as a class.).

III.    PRESENCE OF A TRUE HOMOLOGOUS OR ISOMERIC RELATIONSHIP IS NOT CONTROLLING

Prior art structures do not have to be true homologs or isomers to render structurally similar compounds prima facie obvious. In re Payne, 606 F.2d 303, 203 USPQ 245 (CCPA 1979) (Claimed and prior art compounds were both directed to heterocyclic carbamoyloximino compounds having pesticidal activity. The only structural difference between the claimed and prior art compounds was that the ring structures of the claimed compounds had two carbon atoms between two sulfur atoms whereas the prior art ring structures had either one or three carbon atoms between two sulfur atoms. The court held that although the prior art compounds were not true homologs or isomers of the claimed compounds, the similarity between the chemical structures and properties is sufficiently close that one of ordinary skill in the art would have been motivated to make the claimed compounds in searching for new pesticides.).

See also In re Mayne, 104 F.3d 1339, 41 USPQ2d 1451 (Fed. Cir. 1997) (claimed protein was held to be obvious in light of structural similarities to the prior art, including known structural similarity of Ile and Lev); In re Merck & Co., Inc., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986) (claimed and prior art compounds used in a method of treating depression would have been expected to have similar activity because the structural difference between the compounds involved a known bioisosteric replacement) (see MPEP § 2144.08, subsection II.A.4(c) for a more detailed discussion of the facts in the Mayne and Merck cases); In re Dillon, 919 F.2d 688, 16 USPQ2d 1897 (Fed. Cir. 1990) (The tri-orthoester fuel compositions of the prior art and the claimed tetra-orthoester fuel compositions would have been expected to have similar properties based on close structural and chemical similarity between the orthoesters and the fact that both the prior art and applicant used the orthoesters as fuel additives.) (See MPEP § 2144 for a more detailed discussion of the facts in the Dillon case.).

Compare In re Grabiak, 769 F.2d 729, 226 USPQ 871 (Fed. Cir. 1985) (substitution of a thioester group for an ester group in an herbicidal safener compound was not suggested by the prior art); In re Bell, 991 F.2d 781, 26 USPQ2d 1529 (Fed. Cir. 1993) (The established relationship between a nucleic acid and the protein it encodes in the genetic code does not render a gene prima facie obvious over its corresponding protein in the same way that closely related structures in chemistry may create a prima facie case because there are a vast number of nucleotide sequences that might encode for a specific protein as a result of degeneracy in the genetic code (i.e., the fact that most amino acids are specified by more than one nucleotide sequence or codon).); In re Deuel, 51 F.3d 1552, 1558-59, 34 USPQ2d 1210, 1215 (Fed. Cir. 1995) ("A prior art disclosure of the amino acid sequence of a protein does not necessarily render particular DNA molecules encoding the protein obvious because the redundancy of the genetic code permits one to hypothesize an enormous number of DNA sequences coding for the protein." The existence of a general method of gene cloning in the prior art is not sufficient, without more, to render obvious a particular cDNA molecule.).

IV.    PRESENCE OR ABSENCE OF PRIOR ART SUGGESTION OF METHOD OF MAKING A CLAIMED COMPOUND MAY BE RELEVANT IN DETERMINING PRIMA FACIE OBVIOUSNESS

"[T]he presence—or absence—of a suitably operative, obvious process for making a composition of matter may have an ultimate bearing on whether that composition is obvious—or nonobvious—under 35 U.S.C. 103." In re Maloney, 411 F.2d 1321, 1323, 162 USPQ 98, 100 (CCPA 1969).

"[I]f the prior art of record fails to disclose or render obvious a method for making a claimed compound, at the time the invention was made, it may not be legally concluded that the compound itself is in the possession of the public. In this context, we say that the absence of a known or obvious process for making the claimed compounds overcomes a presumption that the compounds are obvious, based on the close relationships between their structures and those of prior art compounds." In re Hoeksema, 399 F.2d 269, 274-75, 158 USPQ 597, 601 (CCPA 1968).

See In re Payne, 606 F.2d 303, 203 USPQ 245 (CCPA 1979) for a general discussion of circumstances under which the prior art suggests methods for making novel compounds which are of close structural similarity to compounds known in the prior art. It may be proper to apply "methodology in rejecting product claims under 35 U.S.C. 103, depending on the particular facts of the case, the manner and context in which methodology applies, and the overall logic of the rejection." Ex parte Goldgaber, 41 USPQ2d 1172, 1176 (Bd. Pat. App. & Inter. 1996).

V.    PRESUMPTION OF OBVIOUSNESS BASED ON STRUCTURAL SIMILARITY IS OVERCOME WHERE THERE IS NO REASONABLE EXPECTATION OF SIMILAR PROPERTIES

The presumption of obviousness based on a reference disclosing structurally similar compounds may be overcome where there is evidence showing there is no reasonable expectation of similar properties in structurally similar compounds. In re May, 574 F.2d 1082, 197 USPQ 601 (CCPA 1978) (appellant produced sufficient evidence to establish a substantial degree of unpredictability in the pertinent art area, and thereby rebutted the presumption that structurally similar compounds have similar properties); In re Schechter, 205 F.2d 185, 98 USPQ 144 (CCPA 1953). See also Ex parte Blattner, 2 USPQ2d 2047 (Bd. Pat. App. & Inter. 1987) (Claims directed to compounds containing a 7-membered ring were rejected as prima facie obvious over a reference which taught 5- and 6-membered ring homologs of the claimed compounds. The Board reversed the rejection because the prior art taught that the compounds containing a 5-membered ring possessed the opposite utility of the compounds containing the 6-membered ring, undermining the examiner’s asserted prima facie case arising from an expectation of similar results in the claimed compounds which contain a 7-membered ring.).

VI.    IF PRIOR ART COMPOUNDS HAVE NO UTILITY, OR UTILITY ONLY AS INTERMEDIATES, CLAIMED STRUCTURALLY SIMILAR COMPOUNDS MAY NOT BE PRIMA FACIE OBVIOUS OVER THE PRIOR ART

If the prior art does not teach any specific or significant utility for the disclosed compounds, then the prior art is unlikely to render structurally similar claims prima facie obvious in the absence of any reason for one of ordinary skill in the art to make the reference compounds or any structurally related compounds. In re Stemniski, 444 F.2d 581, 170 USPQ 343 (CCPA 1971).

See alsoIn re Albrecht, 514 F.2d 1389, 1396, 185 USPQ 585, 590 (CCPA 1975) (prior art reference studied the local anesthetic activity of various compounds, and taught that compounds structurally similar to those claimed were irritating to human skin and therefore "cannot be regarded as useful anesthetics." 514 F.2d at 1393, 185 USPQ at 587).

Similarly, if the prior art merely discloses compounds as intermediates in the production of a final product, one of ordinary skill in the art would not ordinarily stop the reference synthesis and investigate the intermediate compounds with an expectation of arriving at claimed compounds which have different uses. In re Lalu, 747 F.2d 703, 223 USPQ 1257 (Fed. Cir. 1984).

VII.    PRIMA FACIE CASE REBUTTABLE BY EVIDENCE OF SUPERIOR OR UNEXPECTED RESULTS

A prima facie case of obviousness based on structural similarity is rebuttable by proof that the claimed compounds possess unexpectedly advantageous or superior properties. In re Papesch, 315 F.2d 381, 137 USPQ 43 (CCPA 1963) (affidavit evidence which showed that claimed triethylated compounds possessed anti-inflammatory activity whereas prior art trimethylated compounds did not was sufficient to overcome obviousness rejection based on the homologous relationship between the prior art and claimed compounds); In re Wiechert, 370 F.2d 927, 152 USPQ 247 (CCPA 1967) (a 7-fold improvement of activity over the prior art held sufficient to rebut prima facie obviousness based on close structural similarity).

However, a claimed compound may be obvious because it was suggested by, or structurally similar to, a prior art compound even though a particular benefit of the claimed compound asserted by patentee is not expressly disclosed in the prior art. It is the differences in fact in their respective properties which are determinative of nonobviousness. If the prior art compound does in fact possess a particular benefit, even though the benefit is not recognized in the prior art, applicant’s recognition of the benefit is not in itself sufficient to distinguish the claimed compound from the prior art. In re Dillon, 919 F.2d 688, 16 USPQ2d 1897 (Fed. Cir. 1990).

See MPEP § 716.02 - § 716.02(g) for a discussion of evidence alleging unexpectedly advantageous or superior results.