Cofactor analogues for methyltransferases are disclosed. The compounds are represented by formula (I) wherein R1 is COOH or COO—; X is an organic or inorganic anion carrying one or more negative charges; Y and Y′ are H, or an alkyl; R2 is NH2, NHBoc, or H; and Z is S or Se. R comprises a carbon-carbon double bond, carbon-oxygen double bond, carbon-sulfur double bond, carbon-nitrogen double bond, a carbon-carbon triple bond, carbon-nitrogen triple bond, an aromatic carbocyclic or heterocyclic system in β-position to the sulfonium center, unsaturated c-c bond, or c-heteroatom bond where the heteroatom is O, N, S.